[PyMOL] Orient a specific residue relative to a a CGO surface

Hi, I'm new to pymol scripting and would appreciated some help on a simple problem. I have created a pseudo surface using cgo spheres. I would like to load in a pdb file and place the 8th residue such that the center of the helix is in 0,0,0 and the ca is along the x-axis. Then I would like to

[PyMOL] side chain helper

Dear all, I'm currently using PyMol v1.2b2 and think I may have found a little glitch. While preparing a figure with waters and stick representations on a cartoon backbone with the sidechain helper switched on the sphere representation of the waters disappear leaving only nonbonded crosses. If

[PyMOL] not getting pymol gui

Hai all, Few days back, i wrote a mail regarding the problem of not getting pymol gui while starting pymol. The folllowing are the errors it throws when i give pymol in command line. freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' This may hurt performance.

Re: [PyMOL] drawing a spring/arrow with pymol

Dear pymol users Is it possible to draw distance between two coordinates. i want to measure distance between *Center of mass of two atoms* {13.668 -9.582 5.011} and atom 20224 {13.668 -9.582 5.011} i tried like this: dist spring, {13.668 -9.582 5.011},{13.668 -9.582 5.011}, label=0 but it did

Re: [PyMOL] side chain helper

Paul, Thank you for that bug report! The command: extract waters, solvent solves the problem by pulling solvent atoms out into a separate object (named waters). Cheers, Warren From: Paul Mcewan [mailto:paul.mce...@nottingham.ac.uk]

Re: [PyMOL] not getting pymol gui

Bala, Based on that error, it appears that Chimera's Tk installation is intefering with PyMOL's ability to get at its own Tk installation. Are any PYTHON, TCL, or TK environment variables defined in your path? If so, then they may need to be cleared out in order to run PyMOL. Cheers, Warren

[PyMOL] Missing external GUI and search for the APBS plug-in for PyMOL

Hi, I was trying to find out how to locate and use the APBS plug-in for MacPyMOL and when I mailed to the APBS-users list I was advised to rename MacPyMOL.app to PyMOLX11Hybrid.app which would make the APBS plug-in work in PyMOL. I tried following this suggestion and being a complete novice

Re: [PyMOL] Missing external GUI and search for the APBS plug-in for PyMOL

I've seen this before when something went wrong with launching X11. Have you tried launching X11 first, verifying that it works, and then launching PyMOLX11Hybrid while X11 is already running? On Fri, Mar 13, 2009 at 1:15 PM, Atreyi Chatterjee chatterj...@mail.nih.gov wrote: Hi, I was trying

Re: [PyMOL] Arrows

Hi Falgun, As I mentioned, you need to load the script on the command line: pymol arrows.py or when already running Pymol you load the script with: run arrows.py The @ is for loading pymol scripts, which are different from python scripts. Please read more about the pymol syntax. Also, it

[PyMOL] Saving figures for publication

Hi, I need to make figures in tiff format with at least 600 dpi resolution as required by the journal. The default resolution in Pymol figures is 72. Is there a simple way to increase the resolution (and save it in tiff format)? Alternatively, I can 'convert' from png to tiff afterwards --

Re: [PyMOL] Saving figures for publication

DPI is a function of print size and image pixel dimensions. Pymol or any other program that displays graphics does not have a dpi. The 72 dpi you are referring to is a typical (for some systems) display resolution in pixels per inch. If your journal figure is going to be 3 x 3 inches, for

Re: [PyMOL] Saving figures for publication

Dear Abhinav 2009/3/13 Abhinav Kumar abhin...@slac.stanford.edu: Hi, I need to make figures in tiff format with at least 600 dpi resolution as required by the journal. The default resolution in Pymol figures is 72. Is there a simple way to increase the resolution (and save it in tiff