Re: [PyMOL] Graphics Workstation

Buz Barstow wrote: Dear All, I'm considering purchasing a new graphics workstation for molecular graphics and macromolecular refinement. I'm considering buying a machine with 2 quad core xeon processors, and a nVidia Quadro FX graphics card with 1.5 Gb of memory. Can the current generation of s

Re: [PyMOL] drawing axes

Thanks very much! Now, on to rotate. David Michael Lerner wrote: On Wed, Jun 11, 2008 at 11:48 AM, David Goldenberg mailto:goldenb...@biology.utah.edu>> wrote: Now, could someone point me in the right direction (so to speak) regarding translations of a molecule relative to the gr

Re: [PyMOL] launch pymol from inside an IDLE ( python-ide)

Hey Thanks a tonne Alan After your tip , I got fink IDLE to load pymol without any problem . I also got my home gentoo linux python 2.5 and idle to load pymol the same way. Now I have full code completion to write up my pymol scripts if I idle correctly. On an academic note, Just wondering why the

Re: [PyMOL] drawing axes

On Wed, Jun 11, 2008 at 11:48 AM, David Goldenberg < goldenb...@biology.utah.edu> wrote: > > Now, could someone point me in the right direction (so to speak) > regarding translations of a molecule relative to the graphics reference > frame? > By default, the translate command works in relation to

Re: [PyMOL] drawing axes

Thanks very much to Tsjerk and Carsten! I now understand how to load python scripts and can go back to using MacPyMol. This does seem to be a place where the GUI could be clarified. In MacPyMol, the run . . . command in the File menu is apparently just used for pymol scripts, while the comman

[PyMOL] Graphics Workstation

Dear All, I'm considering purchasing a new graphics workstation for molecular graphics and macromolecular refinement. I'm considering buying a machine with 2 quad core xeon processors, and a nVidia Quadro FX graphics card with 1.5 Gb of memory. Can the current generation of software, and

Re: [PyMOL] Pymol scripts are very slow doing dihedral calculations

Hi, Wouldn't it be better to use a program written especially for this purpose, like dang/dangle from the richardson group, or dssp (, or others I don't know of)? Of course, you may have a specific reason for using pymol, so this is just a suggestion! gilleain torrance On Wed, Jun 11, 2008 at 2

[PyMOL] Pymol scripts are very slow doing dihedral calculations

Dear PyMol Users, We're using Pymol to automatically extract all the backbone dihedrals from a protein. I've noticed that it's very slow doing those calculations. Normally in Fortran it will take some seconds, while in pymol it takes five minutes or even more. The command we issue is : $> /opt

Re: [PyMOL] drawing axes

Just to add onto what Tsjerk had to say about running python snippets in a .pml script. You can also encapsulate the python code in blocks like this: python python end This works with all newer version of pymol (>1.0) and enhances readability of the code quite a bit. HTH Carsten >

Re: [PyMOL] drawing axes

Hi David, Regarding the first part of your question, the way to load a python (not a PyMol) script is: run axes.py .. and not @axes.py. The latter is used for loading PyMol scripts (.pml). You _can_ use python code in a .pml script, but then you better, or in some cases have to, start with a sla