[PyMOL] plugin dependencies

Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is

Re: [PyMOL] MTZ Files

Hi Keitaro, > Is map automatically extended around the view-center within some > radius by crystallographic symmetry operations? This feature won't be in the v1.4 release of PyMOL. It might however show up in a later update release. > Can other reflection formats be opened? > For example, .hkl

Re: [PyMOL] MTZ Files

Dear Jason, I'm really excited about it. I'll send some MTZ files. BTW, I have two questions. Is map automatically extended around the view-center within some radius by crystallographic symmetry operations? Can other reflection formats be opened? For example, .hkl file that is generated by CNS

[PyMOL] RMSD and Helices in a Protein

Hello: I have a protein with several helices and believe only one of them (the one closest to that active center) moves significantly during a simulation. Can someone suggest a way to use pymol to highlight the movement of the helices in this protein. I want to select 20 structures from a trajec

[PyMOL] MTZ Files

Greetings, We're wrapping up our work for the PyMOL v1.4 release. A new Incentive PyMOL feature will be the ability to load and calculate maps from MTZ files. These files can be tricky to read for various reasons (endian issues, machine word size variance, etc). I would like to test my MTZ read

Re: [PyMOL] Rendering Large Scene Crashes Pymol

Upgrading to 64 bit version of licensed Pymol 1.3 fixed all rendering issues. On Wed, Mar 2, 2011 at 1:33 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Ian & Tsjerk, > > > You can try to set hash_max (set hash_max,200) to put a limit on memory > > usage. Then again, an immediat

Re: [PyMOL] Different color on each side of strand

I was also thinking along that line :) But that is pretty trick for a structure like beta-barrel, since you have to actually shrink the barrel toward the center. here is another hack that might work: 1. render only the black outline of the cartoon representation of your protein: set ray_trace_

Re: [PyMOL] Different color on each side of strand

Hi Keitaro, You can try to create a copy from the piece containing the sheet, colour it differently, and change the coordinates slightly. It's a bit tricky maybe, especially if you've got quite a bit of curvature. Hope it helps, Tsjerk On Wed, Mar 9, 211 at 3:22 PM, Keitaro Yamashita wrote: >

Re: [PyMOL] pisa

Hi Kanika, First of all, please try to phrase your questions in fully written english, in stead of a phonetic-like writing with lots of abbreviations... It's sometimes kind of hard to follow. The reason for it, as well as other very useful hints are expanded on http://www.catb.org/~esr/faqs/smart-

Re: [PyMOL] Different color on each side of strand

Hi, Yes, there're definitely a few (?) exceptional cases. But maybe people don't use this feature in such case. Anyway, this feature is not included in current PyMOL, right? Then, is it hard to implement this feature (many changes in code required)? Keitaro 2011/3/8 gilleain torrance : > Hi, >

[PyMOL] Fwd: pisa

- I hope this makes my point clear 1BX7...the author determined structure is monomeric..PISA generate dimeric assembly REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK