初步整理的一些较常用的命令，时间有限，未能注释。后续会进一步注释。 http://pymolwiki.org/index.php/Main_Page Pymol log_open log-file-name.pml Pymol log_close Creat a file to record the commands Pymol load 2vlo.pdb Pymol load 2vlo.pdb, test Pymol show representation Pymol hide representation Representation: cartoon, ribbon, dots,spheres, surface, mesh Pymol label all, chains Pymol hide ribbon, chain f+g+h+i+j Or Pymol select test, chain f+g+h+i+j Pymol hide ribbon, test Pymol select selection-name,selection-expression Pymol color color-name Pymol color color-name, selection-expression Pymol color red, ss h Pymol color yellow, ss s Pymol color green, ss l+ selection-expression selector + identifier symbol: chemical-symbol-list, e. Pymol select polar, symbol o+n name: atom-name-list, n. Pymol select carbons, name ca+cb+cg+cd resn: residue-name-list, r. Pymol select aas, resn asp+glu+asn+gln resi: residue-identifier-list, l. Pymol select mults10, resi 1+10+100 residue-identifier-range Pymol select nterm, resi 1-10 alt: alternate-conformation-identifier-list,alt Pymol select altconf, alt a+b chain: chain-identifier-list, c. Pymol select firstch, chain a segi: segment-identifier-lis, s. Pymol select ligand, segi lig flag: flag-nummer, f. Pymol select f1, flag 0 numeric_type: type-nummer, nt. Pymol select type1, nt. 5 text_type: type-string, tt. Pymol select subset, tt. HA+HC id: external-index-number, id Pymol select idno, id 23 index: internal-index-number, idx. Pymol select intid, index 23 ss: secondary-structure-type, ss Pymol select allstrs, ssh+s+l+ Pymol select chain a and resi 100 andca Pymol select a/100/ca /objectname/segiidentifier/chainidentifier/resiidentifier/nameidentifier /objectname/segiidentifier/chainidentifier/resiidentifier /objectname/segiidentifier/chainidentifier /objectname/segiidentifier resiidentifier/nameidentifier chainidentifier/resiidentifier/nameidentifier segiidentifier/chainidentifier/resiidentifier/nameidentifier objectname/segiidentifier/chainidentifier/resiidentifier/nameidentifier Cartoon: Pymol cartoon type, (selection) automatic, loop, tube, oval, rectangle,arrow, dumbbell, skip Pymol set cartoon_flat_sheets, 1 Pymol set cartoon_flat_sheets, 0 Pymol set cartoon_smooth_loops, 1 Pymol set cartoon_smooth_loops, 0 Pymol set cartoon_oval_width, 0.2 Pymol set cartoon_oval_length, 1.5 Pymol set cartoon_rect_width, 0.5 Pymol set cartoon_rect_length, 1.5 Pymol set cartoon_loop_radius, 0.2 Pymol set cartoon_fancy_helices, 1 Pymol set cartoon_fancy_sheets, 1 Pymol set cartoon_dumbbell_width, 0.1 Pymol set cartoon_dumbbell_length, 2 Pymol set cartoon_dumbbell, 0.2 Pymol set cartoon_transparency, 0.5 Pymol set cartoon_refine, 20 Pymol set cartoon_color, green fft HKLIN protein.mtz XYZIN protein.pdbMAPOUT 2fofc.ccp4 LABIN F1=FWT PHI=PHWT GRID SAMPLE 5 END Pymol load glucosyltransferase.pdb, pro Pymol load 2fofc.ccp4 Wizard -- Density Pymol remove resn HOH Pymol select upg, chain b Pymol as cartoon, pro Pymol as stick, upg Pymol orient, upg Pymol isomesh upg-d, 2fofc, 2.0, upg, carve=1.5 Pymol set stick_radius, 0.2 Pymol set mesh_radius, 0.01 Pymol isomesh name, map, level ]]] load pdb file:pdb1lza # Load in a PDB file (lysozyme) util.cbaw #Set normal CPK colours and render as sticks so we cansee the coordinates through the mesh show sticks, pdb1lza setnormalize_ccp4_maps, 1 # Load in the electrondensity map (CCP4 format) load 1lza.ccp4 #This was obtained fromthe Uppsala Electron Density serverhttp://fsrv1.bmc.uu.se/eds/ #First we make sure that map normalisation is turned on- this means that we can contour at sigma levels (ratherthan absolute values) isomesh mesh,1lza.ccp4, 2.0 # Contour the map at 2.0 sigma across the wholecell color green, mesh select res,////87 # Select one residue -ASP 87 isosurface surf,1lza, 1, res, carve=2 # Createan isosurface at 1.0 sigma, just in the vicinity ofthis residue #(onlyin a region with 2 angstrom of the selected residue) set transparency,0.5 #Make the isosurface semitransparent move z, -20 #Zoom out a bit so we can see it better Movie: Load the file 1L0T_sidechains mset 1 x120 #Reserve space for 120 frames setray_trace_frames, 0 # Make sure thatray-tracing is turned off for movie generation-otherwise, this would take a LONG time util.mroll(1,120,1) #Use a built in utility function to generate a full 360-degree rotation roundthe y-axis, over 120 frames mplay #Play the movie
Pymol 的Windows Autodock Vina 插件发布！ 作者-Goetz Parsiegla “We useAutodock Vinawith theAutodock Vina plugin for PyMOL written by Daniel Seeligerto perform docking of various lipids and inhibitors to crystal structures of Lipases. Docking results are compared with experimental biochemical in vitro activity measurements of the enzymes using automatic titration techniques in our Laboratory (Results will be published soon). We use Autodock Vina instead of Autodock because of its faster search algorithm and the parallel execution of the code on multi core processors (for a comparison seeOlegs Trotts page at Scripps). ThePyMOLplugin permits to easily setup and execute an Autodock Vina run, and display the results in the Pymol graphical windows for their interpretation. We adapted the original code of the plugin, which was developed to be used in a Linux environment to function flawlessly under Windows XP,Vistaor Windows 7 (32 and 64 bits).” Autodock Vina Pymol Windows插件下载地址 ： http://eipl.cnrs-mrs.fr/bioinformatic.php Autodock Vina Pymol Linux插件下载地址 ： http://wwwuser.gwdg.de/~dseelig/adplugin 欢迎对分子模拟和药物设计有兴趣的朋友加入 Autodock QQ群：68093966
上午听叶博讲课，主要是讲PyMOL软件的使用，以前也用过该软件看一些蛋白的结构，却只是当作一个viewer来用。正好趁此机会恶补一下。 http://pymol.sourceforge.net/ Pymol=python+molecule,据说python是一个比较牛的计算机语言，由作者喜欢的一个马戏团的名字而来，所以用这种语言来编辑处理分子构相，就是PyMOL了。据实验室作结构的人说，真正搞结构的是不会用PyMOL的，呵呵，反正我的要求也很低，能够了解一点相关的功能就很知足了。 基本命令（也可使用鼠标操作，但个人认为太繁琐，不如命令来得简单） pwd# show current directory dir# list file in the current directory cd directory #change directory load xxx#注意要打上扩展名，例如1LMK.pdb，否则会error creat name, (selection) #name=object to creat, selection=atom to include in the new object, 非常实用的功能 Manipulating object: show representation, (selection) hide representation, (selection) #the available representations are: (前面是个人比较常用的) lines, spheres, ribbon, cartoon, sticks, surface, /// mesh, dots, labels, extent Turn an object on and off:(这个直接用鼠标就ok了) enable/disable, object-name #turn on/off all representation Basic atom selections: name atom names缩写 n. 例子：show cartoon, (n. 1LDK/) resnresidue typesr. resiresidue numberi. chainchain ID c. elemelement symbole. Selection algebra: 就是怎么选择 交集是and、，例如 1LDK and chain A and i. 1-103 并集是or/|，补集是not/! Change your point of view: zoom, (selection)#fit the selection to screen orient, (selection)#align molecular axis center, (selection) # size not changed turn axis, angle #rotate camera move axis, distance#translate camera Align (个人认为最重要的功能)： align (source), (target) #the source object will be moved and rotated to fit the target object 例如： align (prot1 and chain A), (prot2 and chain B) 在align的过程中会产生一个root mean square deviation (RMSD),这个值可在一定程度上衡量alignment的效果。 Set control (可以通过这个命令来调整所有参数的值，可惜没有什么详细的介绍) 例如 set sphere_scale, 0.5, (n. Fe) #decrease Fe atom size to 0.5 set bg_rgb, #set background as white set ribbon_sampling, 1 Measurement (又一个十分重要的功能，可以真正挖掘结构的意义) dist #测量两个原子之间的距离，ctrl+右键选择第一个原子，ctrl+中键选择第二个原子，然后测量dist。 angel # 测三个原子之间的夹角，ctrl＋中键选择第三个原子，然后测量angle dihedral #测量四个原子之间的二面角 还有制作Movie的一些技巧，不过对于我来说暂时还没什么用。
pymol官方PDF手册 基本命令 （也可使用鼠标操作，但不如命令来得简单） pwd # show current directory dir # list file in the current directory cd directory #change directory load xxx # 注意要打上扩展名，例如 1LMK.pdb ，否则会 errorc reat name, (selection) #name=object to creat, selection=atom to include in the new object, 非常实用的功能 Manipulating object: show representation, (selection) hide representation, (selection) #the available representations are: ( 前面是个人比较常用的 )lines, spheres, ribbon, cartoon, sticks, surface, /// mesh, dots, labels, extent 例如： stick mol1 resi 100 # mol1 为显示在 pymol 右边的分子名称 Turn an object on and off:( 这个直接用鼠标就 ok 了 ) enable/disable, object-name #turn on/off all representation Basic atom selections: name atom names 缩写 n. 例子： show cartoon, (n. 1LDK/) resnresidue types r. resiresidue number i. chainchain ID c. elemelement symbol e. Selection algebra: 就是怎么选择 交集是 and 、 ，例如 1LDK and chain A and i. 1-103 并集是 or/| ，补集是 not/! Change your point of view: zoom, (selection) #fit the selection to screen orient, (selection) #align molecular axisc enter, (selection) # size not changed turn axis, angle #rotate camera move axis, distance #translate camera Align ( 个人认为最重要的功能 ) ： align (source), (target) #the source object will be moved and rotated to fit the target object 例如： align (prot1 and chain A), (prot2 and chain B) 按整条链叠合 align mol1 resi N1, mol2 resi N2 按某一个残基叠合 align mol1 resi N1-N2 name n+ca+c+o ， mol2 resi N3-N4 name n+ca+c+o 按某段残基的主链进行叠合 在 align 的过程中会产生一个 root mean square deviation (RMSD), 这个值可在一定程度上衡量 alignment 的效果。 Set control ( 可以通过这个命令来调整所有参数的值，可惜没有什么详细的介绍 ) 例如 set sphere_scale, 0.5, (n. Fe) #decrease Fe atom size to 0.5 set bg_rgb, #set background as white set ribbon_sampling, 1 Measurement ( 又一个十分重要的功能，可以真正挖掘结构的意义 ) dist # 测量两个原子之间的距离， ctrl+ 右键选择第一个原子， ctrl+ 中键选择第二个原子，然后测量 dist 。 angel # 测三个原子之间的夹角， ctrl ＋中键选择第三个原子，然后测量 angle dihedral # 测量四个原子之间的二面角 Launching PyMOL File for startup commands Launching PyMOL from an external program Running PyMOL in batch mode Suppressing PyMOL output Launching Python programs File for startup commands Linux: Whenever PyMol starts, a '.pymolrc' file containing commands is run. All you need to do is create ".pymolrc" and place it in your home directory. Alternatively, you can instead create ".pymolrc.py" which contains actual Python code instead of just PyMOL commands. Windows: On Windows, use 'pymolrc', 'pymolrc.py' or 'pymolrc.pym'. Warren DeLano Launching PyMOL from an external program If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program as shown in examples/devel/start_pymol.py . NOTE: This approach is not recommended, since the PyMOL launching process is subject to change without warning. The recommended approach is to just use PyMOL as your python interpreter: pymol -r script.py pymol -qcr script.py Warren DeLano Running PyMOL in batch mode To perform PyMOL commands from stdin (file, pipe) without opening an OpenGL window, try: pymol -qc Suppressing PyMOL output Just type: feedback disable,all,actions feedback disable,all,results -From Python: cmd.feedback("disable","all","actions") cmd.feedback("disable","all","results") Will suppress most of PyMOL's normal chatter. Launching Python programs Running a Python script from PyMOL, usually the command: run script.py Is enough. Of course, the file script.py needs to be in the working directory. For more detailed examples, see the commands to launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started: pymol example.py # synchronous, in PyMOL module pymol -r example.py # synchronous in __main__ module pymol -l example.py # asychronous in a new module You can also launch python programs from within PyMOL with the commands: run example.py # synchronous in pymol module run example.py,main # synchronous in __main__ module spawn example.py # asychronous in a new module spawn example.py,global # asychronous in the PyMOL module spawn example.py,main # asychronous in the __main__ module Displaying biochemical Properties Selecting secondary structures Color by atom type from a script Displaying double bonds Calculating dihedral angles Adding hydrogen bonds Color by B-factor Polar surface area Displaying solvent accessible surface Display C-Alpha trace of proteins Display Phosphate trace of nucleic acids Align proteins with CA fit Selecting secondary structures Examples: select helix, (ss h) select sheet, (ss s) select loop, (ss l+'') Color by atom type from a script The "util" module contains a number of functions that color the atoms according to type, with different colors for the C atoms. For instance, util.cbay three in a .pml script will color object "three" by atom type, with the carbon atoms in yellow ("color by atom yellow"). Other functions from ../modules/pymol/util.py are cbag, cbac, cbas, cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, white (hydrogen) and slate). Lieven Buts Displaying double bonds You can try going into lines mode and turning on the valence display: hide show lines set valence, 0.1 a higher value for valence spreads things out more. I don't know of a way to get the dotted notation. Michael George Lerner Calculating dihedral angles The get_dihedral function requires four single-atom selections to work: get_dihedral prot1///9/C, prot1///10/N, prot1///10/CA, prot1///10/C Adding hydrogen bonds Regarding H-bonds. There isn't a built-in function yet, but you can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins or provide ligands with valence information and then use h_add. Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens. EXAMPLE 1: Show hydrogen bonds between protein and docked ligands EXAMPLE 2: Show hydrogen bonds between two proteins There is also a script drawing nice hydrogen bonds from Gareth Stockwell Warren DeLano Assign color by B-factor Robert Campbell has a color_b.py python script on his PyMOL web page that you can use. it has a number of options including the selection and two types of colouring schemes (rainbow versus a blue-magenta-red gradient) and two types of binning of the colours (equal number of atoms in each colour or equal spacing of colours along the B-factor range). See http://biophysics.med.jhmi.edu/rlc/work/pymol to download. There is a script 'data2bfacor' to display arbitrary data assigned to atoms as well. Robert L. Campbell Polar surface area For a solvent accessible PSA approximation: set dot_density, 3 remove hydro remove solvent show dots set dot_solvent, on get_area elem N+O get_area elem C+S get_area all For molecular PSA approximation set dot_density, 3 remove hydro remove solvent set dot_solvent, off get_area elem N+O get_area elem C+S get_area all Showing dots isn't mandatory, but it's a good idea to confirm that you're getting the value for the atom dot surface you think you're using. Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait... Warren DeLano Display solvent accessible surface Using the surface display mode, PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1.4 angstroms, rolled over the protein atoms. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein. PyMOL can only show solvent accessible surfaces using the dot or sphere representations: for dots: show dots set dot_mode,1 set dot_density,3 for spheres: alter all,vdw=vdw+1.4 show spheres Kaushik Raha Displaying the C-Alpha trace of proteins hide show ribbon set ribbon_sampling,1 And if your model only contains CA atoms, you'll also need to issue: set ribbon_trace,1 Warren DeLano Displaying the Phosphate backbone of nucleic acids Should you ever want to show the phosphate trace of a nucleic acid molecule: def p_trace(selection="(all)"): s = str(selection) cmd.hide('lines',"("+s+")") cmd.hide('spheres',"("+s+")") cmd.hide('sticks',"("+s+")") cmd.hide('ribbon',"("+s+")") cmd.show('cartoon',"("+s+")") cmd.set('cartoon_sampling',1,"("+s+")") cmd.set('cartoon_tube_radius',0.5,"("+s+")") cmd.extend('p_trace',p_trace) and then: p_trace (selection) Luca Jovine Align proteins with CA fit If the proteins have significant homology, then you can use the align command: align prot1////ca,prot2 which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the next version will definitely have it. Coloring molecules Coloring secondary structures Color by atom type from a script CMYK-safe Colors Color by B-factor Creating a Color bar Coloring insides and outsides of helices differently Coloring all objects differently List the color of atoms Coloring secondary structures Examples: color red, ss h color yellow, ss s color green, ss l+'' When "the colour bleeds from the ends of helices and sheets into loops," try setting cartoon_discrete_colors to 'on' (or 1). set cartoon_discrete_colors, 1 or from the the "Cartoon" menu of the external GUI find "Discrete Colors" as the last item in the menu. Robert Campbell Color by atom type from a script The "util" module contains a number of functions that color the atoms according to type, with different colors for the C atoms. For instance, util.cbay three in a .pml script will color object "three" by atom type, with the carbon atoms in yellow ("color by atom yellow"). Other functions from ../modules/pymol/util.py are cbag, cbac, cbas, cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, white (hydrogen) and slate). Lieven Buts Use CMYK-safe Colors Some RGB triplets do have equivalents in CMYK space, and as a result, a figure that looks great on a screen can come out with unpredictable colors when printed. Most applications do a good job with RGB-to-CMYK conversions for photos, but do not do such a good job with graphics that use pure primary colors. For example, reds are generally OK, but pure blues and greens do not translate very well. Here are some RGB values that are within the CMYK gamut (i.e. are "CMYK-safe"). In general, colors in PyMOL can be assigned manually: set_color green= Note that there are default atom colors such as "carbon", "nitrogen", "oxygen", "hydrogen", "sulfur", etc. which should also be redefined: set_color carbon= Here's still another URL. Although the list of colors is not extensive, you can see colors: CMYK-safe RGB colors Gil Prive, Dave Fahrney and Warren DeLano Assign color by B-factor Robert Campbell has a color_b.py python script on his PyMOL web page that you can use. it has a number of options including the selection and two types of colouring schemes (rainbow versus a blue-magenta-red gradient) and two types of binning of the colours (equal number of atoms in each colour or equal spacing of colours along the B-factor range). See http://biophysics.med.jhmi.edu/rlc/work/pymol to download. There are other scripts there as well. Robert L. Campbell Creating a Color bar To show a vertical/horizontal color bar indiacting the b-factor variation, use the script pseudobar.pml on the structure pseudobar.pdb , or do the following: 1. Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Be sure that CA's are separated by a contant value, say 5 Angstroem. 2. Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 , define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks). Bartholomeus Kuettner Coloring insides and outsides of helices differently Q: does anyone know how to color the inside of helices a different color than the outsides? A: set cartoon_highlight_color, red Warren L. DeLano Coloring all objects differently Q: Is there a simple way to colour each object currently loaded, with a different colour? A: There is a script color_obj.py that does the job. The script is also available at http://www.ebi.ac.uk/~gareth/misc USAGE color_obj(rainbow=0) This function colours each object currently in the PyMOL heirarchy with a different colour. Colours used are either the 22 named colours used by PyMOL (in which case the 23rd object, if it exists, gets the same colour as the first), or are the colours of the rainbow Gareth Stockwell List the color of atoms To retrieve the color for a residue as identified in an expression, you can either iterate over a selection from the PyMOL command line iterate all, print color Alternatively, this can be done from a Python script . Rendering molecules Displaying in ball-and-stick mode Adjusting width of cartoons Calculating a partial surface Displaying surface inside a molecule Displaying all states of a multiple model/NMR structure Displaying dashed lines Adjusting size of selection indicators Adjusting ray traced picture size Ray tracing maps Nice PovRay settings Making stereo pairs Meaning of get_view parameters Viewing direction vectors (axes) Ray-traceable text labels CGO label orientation Displaying in ball-and-stick mode Q: I've tried several settings and commands but cannot figure out how to make a simple ball-and-stick representation of a molecule. Can it be done in Pymol? A: Yes, but it is non-obvious: hide lines show sticks show spheres set stick_radius=0.1 set sphere_scale=0.25 You can change the two numbers above to fit preferences. Warren DeLano Adjusting width of cartoon Try varying the following. For strands: cartoon_rect_length cartoon_rect_width For helices: cartoon_oval_length cartoon_oval_width or for "fancy" helices: cartoon_dumbell_length cartoon_dumbell_width cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon) In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness. Robert Campbell Calculating a partial surface There is a, until now, undocumented way to calculate a surface for only a part of an object without creating a new one: flag ignore, not A/49-63/, set delete indicate show surface If the surface was already computed, then you'll also need to issue the command: rebuild Warren DeLano Displaying surface inside a molecule As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is: set ambient=0 set direct=0.7 set reflect=0.0 set backface_cull=0 Which gives no shadows and only a few artifacts. As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray". util.ray_shadows("heavy") set two_sided_lighting=1 set backface_cull=0 Warren DeLano Displaying all states of a multiple model/NMR structure Just go to the movies menue and click 'show all states'. Jules Jacobsen Displaying dashed lines between two atoms I think the following commands will do what you want: select a, ///A/501/02 select b, ///B/229/N distance d, a, b This will give you a dashed line object d which is labelled with the distance between the two atoms 'a' and 'b' - you can get rid of the label using hide labels, d btw, if you want to ray-trace the image, I find the dashes come out a bit fat - so I tend to use set dash_gap, 0.5 set dash_radius, 0.1 before the 'ray' command. Gareth Stockwell · Adjusting size of selection indicators Adjusting size of selection indicators Try: set selection_width, 6 set selection_width, 7 Warren L. DeLano Adjusting ray trace-image size The pymol ray tracer can generate an image of any size. ray height,width Example: ray 3000,2400 png filename.png For more options, try 'help ray' Evan Stein and Ben Cornett Ray tracing maps For better quality maps with a white background. set ray_trace_fog,0 set ray_shadows,0 set antialias,1 ray 1600,1200 png img.png (it will take quite a while...) Then open img.png using an external image viewer. It should be high enough resolution to print nicely. Warren DeLano Nive PovRay settings I typically use the make_pov.py script and "run" it from pymol once to load the function, and then I do "make_pov('povray.inp')" to create the povray.inp file. Then I edit that file to insert some lines like: fog { distance 10 fog_type 2 fog_alt 10. fog_offset -160. up 0.,1.,.4 colour rgbt1.0, 1.0, 1.0, 0.1 turbulence 0.8 } In this case I'm not really doing depth-cueing but adding fog at the lower background edge (there were two planes defining the background and a surface below the molecule) rising up towards the front upper edge of the scene. "fog_type 2" means a "rising fog" along the "up" vector. fog_type 1 is a constant fog. To get pure depth cueing, you would want "up" to be along the 0., 0., 1. vector (I think!). You'll need to play around with the distance and fog_offset parameters. You wouldn't necessarily want the "turbulence" parameter in there either. Check out "Atmospheric Effects" in the povray documentation for many more details: http://www.povray.org/documentation/view/201/ Robert Campbell Making stereo pairs Try: ray angle=-3 png image1.png ray angle=3 png image2.png This is superior to using the "turn" command because it also rotates the light source. That way shadows will look right. To make even more beautiful stereo images, use a program like Illustrator or Canvas to add the stereo/depth cued labels. This is a little tricky to describe, but I'll give it my best shot. Place the two images side by side with their centers separated by 6.0 - 6.5 cm, and aligned horizontally. Now add all your labels on the LEFT figure. select all of your labels and duplicate them. Move the duplicated labels to the RIGHT side. For clarity sake let's assume we have 3 labels on the LEFT side (a,b, and c -- we will call then aL and aR for the left and right labels, respectively). Place aL near a recognizable feature of the LEFT figure that you are trying to label. Now horizontilly align aR with aL. Now using only the L/R arrow keys move the aR label until the identical portion of the actual label (let's say the lower right hand tip of the 'a') is vertically aligned with the identical portion of your model (let's say where the C alpha-C beta bond leaves the ribbon backbone) on both the LEFT and RIGHT images. Repeat these steps for each pair of labels. This is a nice method for adding stereo labels because it does not require looking at your computer screen in wall-eyed stereo for 2 hours in order to get proper placement of labels. By assuring that the labels are positioned in the LEFT and RIGHT images at positions that are identical with respect to the part of the model that is being labeled you automatically are also placing them so they are at the proper depth when the figure is finally viewed in stereo. Scott Classen and Warren DeLano Meaning of the get_view output Of the 18 numbers in the output array, 0-8 is the 3x3 rotation matrix, 9-11 is the camera location, 12-14 is the origin of rotation, 15-16 are the clipping distances, and 17 is the orthoscopic flag. Robert Campbell, Paolo Martel and Warren Viewing direction vectors Create a python script (I call it axes.py ): # axes.py from pymol.cgo import * from pymol import cmd from pymol.vfont import plain # create the axes object, draw axes with cylinders coloured red, green, #blue for X, Y and Z obj = # add labels to axes object (requires pymol version 0.8 or greater, I # believe cyl_text(obj,plain, ,'Origin',0.20,axes= , , ]) cyl_text(obj,plain, ,'X',0.20,axes= , , ]) cyl_text(obj,plain, ,'Y',0.20,axes= , , ]) cyl_text(obj,plain, ,'Z',0.20,axes= , , ]) # then we load it into PyMOL cmd.load_cgo(obj,'axes') Then you just need to do "run axes.py" from the pymol command line. You can modify the "3" in the above description of the text labels to change the size of the labels. If you are running a version of pymol older the 0.8, then you cannot add the text (that's why I included colour coding of the axes). You can also use just lines instead of cylinders if you wish: obj = would work as well to define the axes object. Ray-traceable labels You can use the cgo text (line or cylinder versions) as I mentioned in my reply about drawing the xyz axes, but be warned that the labels rotate with your molecule, so getting them oriented perpendicular to the view may be a pain (unless there is something I've missed). Warren's example from a previous reply of his ( cgotext.py ): # draw text using cgo from pymol import cmd from pymol.cgo import * from pymol.vfont import plain cgo = , , ] pos = wire_text(cgo,plain,pos,'Hello World',axes) pos = cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes) cmd.set("cgo_line_radius",0.03) cmd.load_cgo(cgo,'txt') cmd.zoom("all",2.0) Robert Campbell CGO label orientation You could use the cmd.rotate and cmd.translate to position the labels, but it is likely to be somewhat painful. If I'm not mistaken, the rotation will always be about and axis through the origin and so you may need to translate the label into the correct position. Thus if you have your label in an object called 'text', you could do, cmd.rotate(axis='x',angle=20.,object='text') and repeat this with different angles, until you get the orientation correct. Then use: cmd.translate(vector=' ',object='text') (using the appropriate vector, of course!) to position the label. Not ideal, but if it is sufficiently important, it can be done! Modeling with PyMOL Saving transformed coordinates Translate/Rotate objects Moving one segment relative to the rest Split states to objects Altering secondary structures Altering van der Waals radii Altering atom coordinates Deleting bonds Converting D- to L- amino acids Adding disulfide bonds Adding hydrogen bonds Protonating ligands Superposition of two molecules Saving with transformed coordinates Here is a simple script that saves the molecule with coordinates from the current orientation. (invoke it with 'run save_transformed.py' and type the new save_transformed.py command thereafter). Paulo Martel Translate or rotate individual objects There is a "translate" function similar to "rotate", the docs for these don't exist yet, because the implementation isn't finished. However, feel free to use them in the following forms: translate vector,object-name,state (vector needs to be something like ) translate ,pept rotate axis,angle,object-name,state (axis can be either the letter x,y,z or a 3D vector ) rotate x,90,pept rotate ,10,pept Warren DeLano Moving one segment relative to the rest This means moving two parts of one object into different directions. The easiest way to do this is to split the objects and then use the rotate command. EXAMPLE: split.pml Warren DeLano Split states to objects There is also a new command in the 0.95 series: split_states object-name which will spread a PDB "biological unit" (or any multi-state object -- including SD files) over a series of independent objects. This makes it possible to interact with such objects more naturally than with "all_states = 1". Warren DeLano Altering secondary structures: Examples: alter A/10:34/, ss='H' alter A/35:40/, ss='L' alter A/41:60/, ss='S' Altering van der Waals radii Example: alter (elem Fe),vdw=1.8 rebuild (The value for Fe is wrecked in PyMOL at the moment, so running the above line might be a good idea). Warren DeLano Altering atom coordinates Example: alter_state 1,(pdb1cse),x=x-10.0 The latter section can contain formulae involving at least the xyz coordinates, lots of constants and the (+-*/) operators. Deleting bonds Select the bond using Ctrl-right-click, then either unbond pk1,pk2 or hit Ctrl-D. Warren DeLano Converting D- to L- amino acids The inversion function was changed in version 0.95 to take advantage of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the center atom as pk1 and two stationary atoms as pk2 and pk3. Then type Ctrl-E to invert. Warren DeLano Adding disulfide bonds You can use the "bond" command to attach them: bond 24/sg,26/sg bond 56/sg,99/sg unpick (unpick will hide the bond baton which gets displayed.) Additionally, the residue names can be changed for bonded cysteines: alter cys/,name='CYX' or for specific residues alter 24+26+56+99/,name='CYX' Warren DeLano Adding hydrogen bonds Regarding H-bonds. There isn't a built-in function yet, but you can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins or provide ligands with valence information and then use h_add. Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens. EXAMPLE 1: Show hydrogen bonds between protein and docked ligands EXAMPLE 2: Show hydrogen bonds between two proteins There is also a script drawing nice hydrogen bonds from Gareth Stockwell Warren DeLano Protonating ligands If your ligands come in with valid valencies and formal charges, PyMOL's h_add command can protonate ligands. (NOTE that there is a minor technical hiccup with SD-files which are loaded by default as immutable "discrete" objects.) Suffice it to say that in order to make changes to the chemical structure, an object must be loaded with the "discrete" flag set to zero. Unfortunately, much of the molecular editing stuff remains to be documented. Here's an example sequence, but I'm not sure it will help to much...as indicated in the manual, this is immature functionality with some major gaps. Attach in particular is very limited... # show valences set valence=0.05 # load cysteine fragment fragment cys # remove hydrogens remove (hydro) # edit gamma S edit cys////sg # add hydrogen attach H,1,1 # add planer, trivalent nitrogen onto C terminus edit cys////C attach N,3,3 # edit that nitrogen edit (elem N and neighbor cys////C) # attach a tetrahedral methyl (note random position) attach C,4,4 # here's an example of adding a whole residue from the library edit cys////N editor.attach_amino_acid("pk1","ace") # now restore missing hydrogens (note that the names are off...) h_add Warren DeLano Superposition of two molecules Using pair_fit requires that you specify a set of paired atoms in each structure. Fortunately, you no longer have to specify each pair separately, so long as the ordering is the same in each selection (almost always true). pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and name P ) Another example: pair_fit prot1///11-26/CA, prot2///34-49/CA would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2. Movies with PyMOL Encoding video files Encoding video files Assuming you have created a lot of .png files and would like to encode a .mpeg, .avi or other video format, a number of solutions are known: The DiVX encoder using mplayer/mencoder ? There's binaries for Unix and Windows. It makes rather nice compression on a 800x600 (probably higher). It doesn't take too long to produce the nicer quailty movies, but much longer than simply · mencoder "mf://*.png" -mf type=png:fps=18 -ovc lavc -o output.avi · · Another good program for converting images into movies of different formats is VideoMach : http://gromada.com/VideoMach.html · · · · TMPGEnc from http://www.tmpgenc.net/ is very fast, easy to use, and produces very nice ouput (MPEG-2). Unfortunately, it does not handle images larger than 720 x 576 pixels. · · · · The latest Adobe Premiere recipe: · Microsoft's MPEG4 V2, 960x720 @ 30 fps, which PowerPoint automatically · treats as full-screen (due it's wacky metrics). · · Using this codec, a recent 24-second movie consumed only 4.5 MB of space, · but looks much better than a 640x480 Cinepak-based movie with a file size of · around ~40 MB. It definitely pays to use the latest technology · · · · A freeware jiffy to convert png files to an animation is imgcon , · which proved to be very useful: http://www.fmrib.ox.ac.uk/~yongyue/imgcondl.html · · Advanced PyMOL features Meaning of get_view parameters Altering atom coordinates Translate/Rotate objects Moving one segment relative to the rest What is in a selection How does the density wizard work What is molecular sculpting? Align proteins with CA fit Meaning of the get_view output Of the 18 numbers in the output array, 0-8 is the 3x3 rotation matrix, 9-11 is the camera location, 12-14 is the origin of rotation, 15-16 are the clipping distances, and 17 is the orthoscopic flag. Robert Campbell, Paolo Martel and Warren Altering atom coordinates Example: alter_state 1,(pdb1cse),x=x-10.0 The latter section can contain formulae involving at least the xyz coordinates, lots of constants and the (+-*/) operators. Translate or rotate individual objects There is a "translate" function similar to "rotate", the docs for these don't exist yet, because the implementation isn't finished. However, feel free to use them in the following forms: translate vector,object-name,state vector needs to be something like translate ,pept rotate axis,angle,object-name,state axis can be either the letter x,y,z or a 3D vector rotate x,90,pept rotate ,10,pept Warren DeLano Moving one segment relative to the rest This means moving two parts of one object into different directions. The easiest way to do this is to split the objects and then use the rotate command. EXAMPLE: split.pml Warren DeLano What is in a selection? Atom selections aren't directly exposed to Python, but you can have PyMOL build a Python list containing whatever information you need: Using PyMOL commands: list= or using a Python script (in PyMOL): from pymol import cmd,stored stored.list= Warren DeLano How does the Density Wizard work? The answer: · Load a map · Load a model structure · Activate the Density Wizard · Control-middle click to pick any atom in the model to get the map drawn about it. Each of the blue rows in the Wizard is a pop-up menu. You can select multiple or different maps to be displayed at different levels as you traverse the model. Warren DeLano What the heck is molecular sculpting? Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL. To actually use this feature: Load a PDB file. Configure the mouse for editing (Mouse menu) or click in the mouse/key matrix box. Select "auto-sculpting" from the Sculpting menu. Select Sculpting from the Wizard menu. Ctrl-middle-click on any atom in your protein to activate sculpting the green part will be free to move the cyan part will be a fixed cushion to provide context the grey part will be excluded. Now perform any conformational editing operation in the green region such as: ctrl-left-click-and-drag on an atom ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond. You can adjust the radius and cushion using the blue pop-up menus. Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future. Warren DeLano Align proteins with CA fit If the proteins have significant homology, then you can use the align command: align prot1////ca,prot2 which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the next version will definitely have it. Python scripting Launching Python programs Using the PyMOL commandline What is in a selection Does a selection exist Get Coordinates from python Create objects from PDB strings Measure distances from python Coloring all objects differently List the color of atoms List secondary structures Process key events from shell Alter key bindings Viewing direction vectors (axes) Ray-traceable text labels CGO label orientation 3D marks on atoms Save and load objects (pickle) Building ChemPy models Launching Python programs 1. Running a Python script from PyMOL , usually the command: run script.py Is enough. Of course, the file script.py needs to be in the working directory. You can also launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started: pymol example.py # synchronous, in PyMOL module pymol -r example.py # synchronous in __main__ module pymol -l example.py # asychronous in a new module You can also launch python programs from within PyMOL with the commands: run example.py # synchronous in pymol module run example.py,main # synchronous in __main__ module spawn example.py # asychronous in a new module spawn example.py,global # asychronous in the PyMOL module spawn example.py,main # asychronous in the __main__ module 2. Running PyMOL from a Python script requires two commands: import pymol pymol.finish_launching() Using the PyMOL commandline Are you aware that the PyMOL command line is also a Python command line? You can just use PyMOL interactively in that fashion. PyMOLprint 1+1 2 PyMOLfrom random import random PyMOLprint random() 0.739460642143 The only major difference is that the default namespace for PyMOL is "pymol" not "__main__" PyMOLprint __name__ pymol Warren DeLano What is in a selection? Atom selections aren't directly exposed to Python, but you can have PyMOL build a Python list containing whatever information you need: Using PyMOL commands: list= or using a Python script (in PyMOL): from pymol import cmd,stored stored.list= Warren DeLano Does a selection exist? The function below will return true if the selection is defined. from pymol import cmd from types import * def sele_exists(sele): sess = cmd.get_session() for i in sess : if type(i) is ListType: if sele==i : return 1 return 0 Igor Pechersky Get coordinates from Python The actual C-langauge arrays aren't exposed, but there are at least three different ways you can modify coordinates from within Python: · You can get a python object which contains the molecular information, modify the coordinates in that object, load the modified molecule into PyMOL, update the modified coordinates to the original model, and then delete the modified object. ( Example in a python script ) · Another approach is the "alter_state" function, which can perform the same transformation in a single PyMOL command statement: alter_state 1,pept,(x,y)=(-y,x) Likewise sub-selections can be transformed as well: alter_state 1,(pept and name ca),(x,y,z)=(x+5,y,z) · A third approach is to use alter_state with the global "stored" object: Example in a Python script ) Approaches 2 gives the best performance, approach 3 gives more flexibility, and approach 1 gives you a reusable and fully modifiable Python object. Warren DeLano Create objects from PDB strings I thought I'd post this example, just in case anyone else cares about this: delete all cmd.read_pdbstr("""HEADER CREATED BY CONVERTPROSPECT 27-JAN-02 2tnf \ REMARK 1 \ ATOM 1 N PRO A 9 1.895 67.213 -38.182 1.00 0.00 N \ ATOM 2 CA PRO A 9 1.703 68.680 -38.402 1.00 0.00 C \ .... ATOM 1153 C GLY A 157 6.927 59.108 -38.901 1.00 6.00 C \ ATOM 1154 O GLY A 157 6.700 59.292 -37.676 1.00 6.00 O \ TER 1155 GLY A 157 \ MASTER \ END \ ""","2tnfa") hide all show cartoon color grey .... Reece Hart Measure distances from Python Use Python (and the run command with .py files). from pymol import cmd f=open('dist.txt','w') dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha') f.write("%8.3f\n"%dst) f.close() You could measure the whole protein this way by putting a loop around the distance command: from pymol import cmd f=open('dist.txt','w') atom = cmd.get_model("mol1////ha").atom for i in range(len(atom)-1): sele1 = 'mol1///%s/HA'%atom .resi sele2 = 'mol1///%s/HA'%atom .resi dst=cmd.distance('tmp',sele1,sele2) f.write("%14s %14s %8.3f\n"%(sele1,sele2,dst)) f.close() The output "dist.txt" would then look like: mol1///4/HA mol1///5/HA 4.748 mol1///5/HA mol1///6/HA 4.828 mol1///6/HA mol1///7/HA 4.861 mol1///7/HA mol1///8/HA 4.784 mol1///8/HA mol1///9/HA 4.936 mol1///9/HA mol1///10/HA 4.833 mol1///10/HA mol1///11/HA 4.933 mol1///11/HA mol1///12/HA 4.813 Warren DeLano Coloring all objects differently Q: Is there a simple way to colour each object currently loaded, with a different colour (in the same way that you can colour each chain in a molecule differently)? This would be really useful in visualising a set of superposed structures. A: There is a script color_obj.py that does the job. The script is also available at http://www.ebi.ac.uk/~gareth/misc USAGE color_obj(rainbow=0) This function colours each object currently in the PyMOL heirarchy with a different colour. Colours used are either the 22 named colours used by PyMOL (in which case the 23rd object, if it exists, gets the same colour as the first), or are the colours of the rainbow Gareth Stockwell List the color of atoms To retrieve the color for a residue as identified in an expression, you can either iterate over a selection from the PyMOL command line iterate all, print color Alternatively, this can be done from a Python script . import pymol pymol.color_list = cmd.iterate('all', 'pymol.stored_ss.append(string.ljust(ss,1))') print string.join(pymol.stored_ss) Warren DeLano Process key events from shell The following scripts turns the view 30 deg around the y-axis, each time you press the enter key in the python shell (the original shell you started pymol from), just as an example: #use "spawn spawn_demo.py, local" to invoke this python script from within pymol wait="" i=0 while i 12 and wait!="x": cmd.turn("y", 30) print "Press enter key to continue or x + enter to terminate" wait=raw_input() i=i+1 print "Done" Markus Meier Alter key bindings It's not GUI, but you could simply bind a function key such as F1 to a command: cmd.set_key('F1',lambda :cmd.show('sticks')) Warren DeLano Viewing direction vectors Create a python script (I call it axes.py ): # axes.py from pymol.cgo import * from pymol import cmd from pymol.vfont import plain # create the axes object, draw axes with cylinders coloured red, green, #blue for X, Y and Z obj = # add labels to axes object (requires pymol version 0.8 or greater, I # believe cyl_text(obj,plain, ,'Origin',0.20,axes= , , ]) cyl_text(obj,plain, ,'X',0.20,axes= , , ]) cyl_text(obj,plain, ,'Y',0.20,axes= , , ]) cyl_text(obj,plain, ,'Z',0.20,axes= , , ]) # then we load it into PyMOL cmd.load_cgo(obj,'axes') Then you just need to do "run axes.py" from the pymol command line. You can modify the "3" in the above description of the text labels to change the size of the labels. If you are running a version of pymol older the 0.8, then you cannot add the text (that's why I included colour coding of the axes). You can also use just lines instead of cylinders if you wish: obj = would work as well to define the axes object. Ray-traceable labels You can use the cgo text (line or cylinder versions) as I mentioned in my reply about drawing the xyz axes, but be warned that the labels rotate with your molecule, so getting them oriented perpendicular to the view may be a pain (unless there is something I've missed). Warren's example from a previous reply of his ( cgotext.py ): # draw text using cgo from pymol import cmd from pymol.cgo import * from pymol.vfont import plain cgo = , , ] pos = wire_text(cgo,plain,pos,'Hello World',axes) pos = cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes) cmd.set("cgo_line_radius",0.03) cmd.load_cgo(cgo,'txt') cmd.zoom("all",2.0) Robert Campbell CGO label orientation You could use the cmd.rotate and cmd.translate to position the labels, but it is likely to be somewhat painful. If I'm not mistaken, the rotation will always be about and axis through the origin and so you may need to translate the label into the correct position. Thus if you have your label in an object called 'text', you could do, cmd.rotate(axis='x',angle=20.,object='text') and repeat this with different angles, until you get the orientation correct. Then use: cmd.translate(vector=' ',object='text') (using the appropriate vector, of course!) to position the label. Not ideal, but if it is sufficiently important, it can be done! Robert Campbell 3D marks on atoms Here's a script graph.py which can be used to put marks on the positions of every atom in a selection. There are several types of marks included now, e.g. cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix operator these can be extended a bit, to 2D counterparts for example, or to elongated or rotated shapes. I should still include some documentation but in brief the usage is as follows: graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' | 'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = , rgb2 = , mtx = , , ], name = "graph" Selection should be obvious, as is shape. Size is a relative indicator for the size, though at present I haven't fixed things such that a size 1 tetrahedron matches a size 1 dodecahedron. r is the radius of the lines. rgb1 and rgb2 are the start and end color for each line. mtx is the matrix operator, which works on the original shape centered around the origin (before translation to the point of the atom from the selection). Tserk Wassenaar Save and load objects There is a convenient format: ".pkl", that works like PDB, but is a Pickled copy of the PyMOL Model Class. The main advantage this has over .pdb is that it saves and restores extra properties such as secondary structure code, atom types, van der waals radii, formal and partial charges, etc. load myprot.pdb dss show cartoon alter 100-110/, ss='H' alter 65-67,ss='L' save myprot.pkl ... quit program, complete your PhD, take a vacation, and come back... load myprot.pkl show cartoon will work. ".pkl" has the additional advantage of being a simple molecular object useful in straight Python, outside of PyMOL. All you need to do is have a copy of PyMOL's "chempy" module available in your PYTHONPATH from chempy import io model = io.pkl.fromFile("myprot.pkl") for atom in model.atom: print atom.name Warren DeLano Building ChemPy models This is a snap. Just "run" the following Python program from within PyMOL. from chempy.models import Indexed from chempy import Bond, Atom from whrandom import random from pymol import cmd model = Indexed() # create some atoms for a in range(1,11): at = Atom() at.name = "X%02d"%a at.coord = model.atom.append(at) # now create some bonds for a in range(1,10): bd = Bond() bd.index = # zero-based indices! model.bond.append(bd) # now load and label cmd.load_model(model,"example") cmd.label("example","name")
标签: pymol
