Re: [PyMOL] problem with .pml file

ml file. Or you can specify the full path from the current directory to the .pml file after the @. You can find out PyMOL's current working directory with the "pwd" command (pressinf to toggle between the graphics view and the text output to see the result). Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] Distance and scripts

nction as a new PyMOL command. This command can take any arguments you define for the function. Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] Transparency in cartoons

u provides an overview of all available parameters. There are also predefined transparency settings available in the "Display" menu. Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] TR : alter_state for y coordinates?

be the problem is that the "b" is being interpreted as the B factor of the atom, while "a" and "c" have no special meaning. Try "x0", "y0" and "z0" as the names for the variables for your displacement. -- Lieven Buts Laboratorium voor Ultrastructuur Vrije Universiteit Brussel

Re: [PyMOL] Pymol sans display

th "pymol -cp", and it will respond to commands from standard input, which can be your terminal. Hope this helps, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] alpha carbon trace

ibbon_trace" for the ribbon representation. In this case, separate chains do not appear to get connected. -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] Ca-only and surfaces

igure out how to do it. Can someone please instruct me? For the ribbon representation: set ribbon_trace_atoms,1 I don't know about the surface representation, though. -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] comments ?

On Monday 01 August 2005 11:08, Sebastien Moretti wrote: > Hello, > I try to add comment lines in my pml scripts but I don't know how to do. > I tried #, /*, //,

Re: [PyMOL] (no subject)

print "Something's wrong!" else: cmd.save(obj+".pdb",obj) #-- Hope this helps, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] list residues in a selection

md.get_pdbstr("near") (after "import cmd" if required) you get a list of lines in PDB ATOM format for all the atoms in the selection. In principle, you can extract any information you want from these lines. Hope this helps, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel

Re: [PyMOL] run script

On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > from pymol import cmd > file=open("file.nam") > for i in file.readlines(): > cmd.load(i) You may have to strip the trailing newline ("\n") from each file name by using "cmd.load(i.strip())"

Re: [PyMOL] run script

On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > from pymol import cmd > file=open("file.nam") > for i in file.readlines(): > cmd.load(i) You may have to strip the trailing newline ("\n") from each file name by using "cmd.load(i.strip())"

Re: [PyMOL] pymol crashes with new [7167] nvidia driver

es the crashing problem, at least as a temporary solution. -- Lieven Buts Vrije Universiteit Brussel

Re: [PyMOL] pymol crashes with new [7167] nvidia driver

;hide everything,all" to the script, you can stop the default view quickly enough. I am running PyMOL 0.97 on Gentoo Linux, on a dual Pentium 4 box, with the 1.0.7167 NVidia drivers (Gentoo package version number). -- Lieven Buts Vrije Universiteit Brussel

Re: [PyMOL] effect of number of pixels on ray image quality

o any practical limitations using the PyMOL raytracer, which produces images of the requested size independent of the screen or window size, even if the image becomes so large it cannot be displayed in the PyMOL window (using "ray sizex,sizey" and "png filename"). Hope this hel

Re: [PyMOL] Coloring chemical elements with colors of your choice

uld work for all element types. The set_color command is really intended to define new colors. Best wishes to all for the new year, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] rotation origin

f.close() The first line opens a file for writing (overwriting the existing file, if any). The second line generates PDB ATOM records for all the atoms in the selection "(object)". The thrird line appends an "END" record, and the fourth line closes the file, ensuring

Re: [PyMOL] ribbon view of c-alpha only coordinates

't > connect them with lines. Try "set ribbon_trace,1". -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] transformation matrix

racts the transformation matrices from the Dali report file. If someone has a way to use this matrix in PyMol, we'd be set: #!/usr/bin/env python # Script to extract 3x4 transformation matrices from Dali report files # Lieven Buts, 22-Oct-2004 import re,sys dali = open(sys.argv[1]

Re: [PyMOL] PyMOL tutorial (moved and slightly updated)

ven know whether you spell it with an s or a c :-) ), but a good source of information seems to be at http://creativecommons.org/ . -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] unit cell

zoom out and/or change the clipping planes to show all of the unit cell. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] Cavity display?

S, recommended by Lari and got a surface picture of my > cavities within literally a few minutes, as Lari already wrote. The rTools (http://www.rubor.de/bioinf/pymol_rubor.html) also contain a fucntion to interface PASS with PyMOL. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations

DFLAGS were empty before I started. If they are not, you may have to use export LDFLAGS="${LDFLAGS} -L/usr/local/lib/i686-pc-linux" instead. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

[PyMOL] Tip: removing dummy atoms in NMR PDB files

atoms can be quickly selected with a command like select dummies,(name QA,QB,QD,QD1,QD2,QE,QE2,QG, \ QG1,QG2,QH1,QH2,QQD,QQG,QR,QZ) The atoms can then be deleted using the "remove atoms" command on the "dummies" selection in the PyMOL menu. -- Lieven Buts Department of Ult

Re: [PyMOL] Basic hardware questions

racing, but it would only be beneficial on systems with very recent graphics boards. [1] http://graphics.stanford.edu/projects/brookgpu/index.html [2] http://www.gpgpu.org/ I'm sure there are much more details to consider, but I hope this is a start. -- Lieven Buts Department of Ultrastr

Re: [PyMOL] Question about surface calculation

luded for surface generation. You can also create separate objects to generate exactly the surfaces you want. Cheers, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] restoring default surface coloring

bject") (note the parentheses and quotes) to color the object by atom type and set the carbon atoms to green. There's "cbag" for "color by atom type, carbons green", "cbaw" for white carbons, "cbay" for yellow carbons and so on. Alternatively,

Re: [PyMOL] Select Atom & Change View

more specific ("zoom (protein and chain A and resi 25 and name CA)" for example). There are many abbreviations for long selections. Type "help selections" for more information. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] H-bonds

re complete criteria. The rTools for PyMOL (available at <http://www.rubor.de/bioinf/pymol_rubor.html> ) provide an interface to the HBExplore program at <http://www.imb-jena.de/www_bioc/hbx/hbx.html>. See the rTools documentation for more details. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] make cartoon from carbon atom trace?

o not appear to get connected. Best wishes to all for 2004, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] Selecting a lot of residues

into a single-line PyMol command select group,(protein and chain A and resi 5,10,50,51,52,100) which can be copied/pasted into PyMol, or read from the file with "@list.pml". -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] Selecting a lot of residues

n and resi 50) or \ (protein and resi 51) or \ (protein and resi 52) or \ (protein and resi 100) ) Note the additional parentheses around the complete expression. This can be executed in PyMol by typing "@list.pml" and should select the indicated residues in the molecule "protein". Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel

Re: [PyMOL] you know what would be cool?

(PDB 103L). At residue 139, cosom becomes slightly larger than 1 (1.0008 or so) and acos(cosom) fails. Also, omega and sinom become zero in this case, so the divisions by sinom fail. I added some checks to normalize this situation and stop the code from crashing, but we should look into wh

Re: [PyMOL] color choices

that you can use color whatever, ... -- Lieven Buts Department of Ultrastructure

[PyMOL] Alter command and cartoon representation

nge. When I try "util.ss protein", the cartoon changes immediately. What am I missing? -- Lieven Buts Department of Ultrastructure

Re: [PyMOL] Getting started with movies for moving through a presentation

;(arg and n;cb)","(arg and n;ca)") cmd.torsion("2") cmd.unpick() cmd.set("suspend_updates",0,quiet=1) cmd.refresh() cmd.feedback('ena','sel','res') else: cmd.delete("arg") -- Lieven Buts Department of Ultrastructure Brussels Free University

[PyMOL] Re: using PyMol in PowerPoint

int. Could you provide some more details on this procedure. So far I have only managed to include an icon/object in PowerPoint that starts PyMol in an extra window (with a specified script). -- Lieven Buts Vrije Universiteit Brussel

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

, cyan, salmon, purple, pink, white (hydrogen) and slate). -- Lieven Buts Brussels Free University

Re: [PyMOL] molecular sculpting

l there, as it allows for a more "physical" or "intuitive" way of manipulating the model than moving individual atoms or turning torsion angles. -- Lieven Buts Brussels Free University

Re: [PyMOL] molecular sculpting

x27;t know about the script or the wizard (yet), but I did try the sculpting demo in the Demo menu. You can then just drag atoms by left-clicking them while holding down the control key. The dragged atom moves, everything it is connected to is dragged along, and the structure tries to minimize its

Re: [PyMOL] Babel and File Format Conversion

abel project at <http://openbabel.sourceforge.net/>. -- Lieven Buts Brussels Free University

[PyMOL] Creating separate objects from a starting structure

show sticks,three This works very well. Maybe a wizard could be created to automatically split a structure into separate objects for the different chains? -- Lieven Buts Vrije Universiteit Brussel