Re: [PyMOL] APBS plugin not working on both Ubuntu & Windows 7

Hello Brenton, I used the pdd2pqr provided by Ubuntu repositories (version 1.8) and installed it directly(with Synaptic) from there. The path on my Xubuntu system is: /usr/share/pdb2pqr/pdb2pqr.py I also tried setting something up on Windows but gave up eventually. Good luck and all the best, M

Re: [PyMOL] APBS plugin not working on both Ubuntu & Windows 7

There is an "INSTALL" file that provides instructions. The first step, calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in If you want to manually do it, it just changes the first line in the file to point to your python installation. But, since there's a whole bunch of other things ./co

Re: [PyMOL] Cartoon putty in pymol

Hi, Wenfu The putty representation uses the values on the b-factor column of the pdf file and your file has the same value for each atom (0.0), hence the error. If you want to have residues with different width you need different b-factor values for different residues. If, on the other hand you ar

[PyMOL] pymol crash when ray

Hi pymol users, I am just using pymol to open one super big molecular model (20 megadaltons). My pymol1.7 is on linux system and the computer has 32 CPU with 62GB memory storage. When I try to use command ray to make a high quality image, the pymol crash with error message like this: Pymol ran

Re: [PyMOL] pymol crash when ray

Hi Wenfu, Did you get the same error if you do the raytraicing from a script? Probably you could try with this approximation to render your molecule. Cheers, Osvaldo. On Tue, Apr 14, 2015 at 5:12 PM, wrote: Hi pymol users, > > I am just usi

Re: [PyMOL] pymol crash when ray

one more thing… Delete all objects that you are not using for this particular rendering (save it as a separate file). I have found this speeds up rendering times. > On Apr 14, 2015, at 7:49 PM, H. Adam Steinberg > wrote: > > For an instantaneous rendering of any PyMOL scene that won't crash

[PyMOL] Protein classification

Dear all, I have a set of 200 methyltransferase protein structures. For protein - ligand interactions study, I would like to classify the proteins in to different groups. I have tried to classify the proteins based on sequence but it is not satisfactory in view point of structures. Based on the