[PyMOL] New PyMOL plugin for analysis of biomolecular channels

Dear PyMOL user, we would like to inform you that there's a new PyMOL plugin available. The plugin incorporates a functionality of the new tool MOLE 2.0 for detection and analysis of channels, pores and cavities in biomacromolecules. Further information with appropriate links to the publication

[PyMOL] ALPHA cgo causes COLOR to be ignored

Dear PyMOL users, I'm wondering about coloring CGO objects in PyMOL. In the recent version 1.7. If ALPHA is specified for a cgo object, all the colors are neglected. In version 1.6 and previous everything works just fine. Is this a bug, an intension or am I missing a point somewhere? Let's take

[PyMOL] ramp_new command always produce symetrical ramp

Dear PyMOL users, I was wondering if it is possible to produce a ramp which is not symmetrical. Ie. By command ramp_new e_pot_color, e_pot_map, [-10, 0, 10], [red, white, blue] I can specify the range of colors red-white-blue in the range -10 0 10. In case my range would be [-10, 5, 1

Re: [PyMOL] ligand superimpose (multiple structures) and RMSD value

HI Abdul, Not sure if this is the solution you would like to, but there are several tools which are tailored specifically for this purpose (i.e. superimposition of small molecules). One of them is SiteBinder (http://webchem.ncbr.muni.cz/Platform/App/SiteBinder), it allows you to do variety

Re: [PyMOL] ligand superimpose (multiple structures) and RMSD value

- webchem.ncbr.muni.cz/Platform/MotiveQuery/Index If you would have further questions, just let me know. Lukas From: Folmer Fredslund [mailto:folm...@gmail.com] Sent: Monday, February 9, 2015 4:21 PM To: Lukáš Pravda Subject: Re: [PyMOL] ligand superimpose (multiple structures) and

Re: [PyMOL] Removing chloride ions from CIF files

Hi Brenton, Have you specified that cl is element? remove element cl should work. At least it worked for me for a different cif structure from PDB Hope it helps Lukas -Original Message- From: Brenton Horne [mailto:brentonho...@ymail.com] Sent: Tuesday, March 17, 2015 8:49 PM To: pymo

Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

Hi Brenton, fetch 4v7y, type=cif is the command you are looking for All the best Lukas Pravda --- CEITEC - Central European Institute of Technology Masaryk University Brno, Czech Republic --- From: Brenton Horne [mailto:brentonho...@ymail.com] Sent: Thursday, March 19, 20

Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

Which version of PyMOL do you have? Mine is 1.7.4 and it is working just fine. So in case you have and older version(< 1.3 I guess) it might not work properly. Lukas From: Brenton Horne [mailto:brentonho...@ymail.com] Sent: Friday, March 20, 2015 12:02 AM To: Lukáš Pravda Subject:

Re: [PyMOL] show the long helix filament

Hi Yeping, What is the PDB id you are working with? Perhaps you have to download the biological assembly rather than asymmetric unit. I’d suggest you to go to the PDBe entry (pdbe.org/PDBID) and from the quick links select download ‘Assembly composition XML’. Take a look which assembly id ha

[PyMOL] Grammar for PyMOL selection algebra

Dear PyMOL users, I am trying to add support for pymol-like selection algebra into one of your software tools. Therefore, I was wondering, if there is any formal description of the language available in for example as context-free grammar. I was trying to find something in the source code rath