Re: [PyMOL] help with batch mode

As a point of minor clarification: The "quiet" option (if present) is set to zero by default for parsed PyMOL commands, but is not set for Python API calls. In other words, zoom is nearly equal to cmd.zoom(quiet=0) even though the Python definition for "zoom" has quiet=1 as a default argument

Re: [PyMOL] Pymol capabilities

Jack, Although not everyone sees PyMOL in such a narrow light, my view is that the software is best viewed as a molecular graphics platform open for integration with computational tools (e.g. semi-empirical QM/MM) via manual data import, via automated PyMOL command scripts, or via the Python prog

Re: [PyMOL] help with batch mode

Mike, As for NMR ensembles, so long as all of the structures loaded as multiple states in a single object (the default behavior for NMR ensembles in multi-model PDB format): print cmd.intra_fit(selection, state) will fit all of the other states to the indicated states and return the RMS values a

Re: [PyMOL] pymol nstall problems

David, Because of changed made to registry entries and protected filesystems, local Administrator rights are normally required in order to install PyMOL under Windows. Did the IT department recently take those away perhaps? If not, then maybe the tips posted on PyMOLWiki can help: http://www

Re: [PyMOL] partially transparent structure

Janet, Unforutnately not. At present, cartoon_transparency must be uniform over the entire cartoon representation. You can split the cartoon into multiple objects to obtain differential transparency, but as you correctly point out, that will cause a break or gap in the cartoon. Cheers, Warren

[PyMOL] Pymol capabilities

Hello, I am learning a little about molecular dynamics simulations. Currently using Amber and CP2k. Hoping to integrate CP2K into a distributed computing project using serialized computations. A friend of mine recently said Pymol is a fancy piece of software. Before I get invested in learning abou

Re: [PyMOL] help with batch mode

Hey Michael, with some commands, you can use the (somewhat poorly documented) option 'quiet=0' to get results sent to standard output, like so: load ./final/final.001.pdb load ./final/final.002.pdb fit (final.002///13-30/c,ca,n), (final.001///13-30/c,ca,n), quiet=0 Andreas Michael Summers

[PyMOL] pymol nstall problems

Hi, I've been unable to install Pymol recently on an XP Pro-SP2 system. I'll start setup.exe, and ntvdm.exe starts running but nothing progresses from there (no error messages and installshield doesn't start). I'm not sure if it's a software conflict with something else running, but it's likely (a

Re: [PyMOL] partially transparent structure

set transparency=0.5 #for optimal view ray 1024, 768 there are more transparency options. Type "set transparency" when in console and press TAB two times to see the full list of available commands SDA On Wed, 2008-02-13 at 09:38 -0800, pymol-users-requ...@lists.sourceforge.net wrote: > Message

[PyMOL] partially transparent structure

I would like to display a protein structure in the following way: The first domain of the structure in red cartoons The second domain of the structure in gray TRANSPARENT cartoons I tried splitting the structure into two objects but because the transition from the first domain to the second one i

[PyMOL] help with batch mode

Colleagues, Does anyone have a good method for generating alignment statistics in batch mode using pymol? I think I'd like to do something like: pymol -c sup.py > data.txt where sup.py is something like: load ./final/final.001.pdb load ./final/final.002.pdb fit (final.002///13-30/

[PyMOL] color on color

I have two subunits surface-painted with the color ramp from Protskin http://www.mcgnmr.ca/ProtSkin/intro/index.html I would like to color one of the subunits so that it can be distinguished, but without hiding the color ramp. Suggestions? Dave -- David N. Garboczi, PhD Phone: 301-496-4773 I