Re: [PyMOL] PyMOL-users Digest, Vol 5, Issue 22

Is there any 32 bit version of pymol? I am unable to install it in XP - Original Message

Re: [PyMOL] Support for gromacs trajectories and cube files

Hi Martin, > ...got the svn code compiled with -D VMD... Great! > CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded > as "ProtOut". > PyMOL>load /home/martin/workspace/testdata/topol.tpr > CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded > as "topol.tpr". > PyMOL>load /

Re: [PyMOL] Support for gromacs trajectories and cube files

...got the svn code compiled with -D VMD... If i load a PDB, then load a topology and then try to load a trajectory via "load" loading the trajectory fails, complaining like this: CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded as "ProtOut". PyMOL>load /home/martin/workspace/testdat

Re: [PyMOL] Measure side chain shift

Hello: Not exactly sure what you are asking here but if you want to calculate the distance moved you could use the distance command: distance atomx, atomy to tell you how far atoms in the residues has moved. you can also calculate dihedrals (ie/ X values) using the dihedral command dihedral name_

Re: [PyMOL] problems using "within" in selections

Anne, Okay, the problem has been identified and fixed in the open-source code. It was an all-or-nothing failure to expand geometry in situations where the sole target atoms are one or both last two atoms in the source object (a rare scenario). Cheers, DeLano Scientific LLC Email Support Service

[PyMOL] Measure side chain shift

Hi, I am a new user of Pymol. I am currently working on mutant protein structures and I would like to compare the side chain shift between the mutant and wild-type structures. May I know how could I measure the side chain shift? Thanks a lot! Phoebe

Re: [PyMOL] problems using "within" in selections

Anne, There is definitely a problem with PyMOL here: that ZnA object is not behaving correctly with respect to any of the distance-based selection operators, and so for it is not yet clear why. However, create nearZnA, 1q74 within 6 of (ligands and chain A) does work. Cheers, DeLano Scienti

[PyMOL] problems using "within" in selections

I was trying to study the ligands in a structure, and then zoomed in on a Zn ion in molecule A: create ligands, 1q74 and het and not resn HOH (Selector: found 28 atoms.) create ZnA, ligands and chain A (Selector: found 1 atoms.) create nearZnA, 1q74 within 6 of ZnA (Selector: found 0 atoms

[PyMOL] Quadro4 + newest nvidia drivers => broken stereo

Hi All A quick fix to the problem with the newest nVIDIA linux drivers and broken stereo is to install the nvidia-glx-legacy package if it is available for your distribution. In Ubuntu this contains the 7184 driver which was the last to support TNT, TNT2, TNT Ultra, GeForce, and GeForce2 ch