Re: [PyMOL] Writing a script yo pymol

Hi Yotam, > I'm sorry but this is too complected. Currently, I can't afford the time > to learn another scripting languish. Consider gnuplot script files, > which are simply a list of gnuplot commands. PyMOL understands two languages. The "PyMOL language" is indeed similar to gnuplot commands

Re: [PyMOL] print hydrogen bonds involved residues

> You have to make .pml file and put the python commands inside pymol > blocks. it's "python" blocks, see: http://pymolwiki.org/index.php/Python > ... do I need to put those code in another .py file? That's also possible, yes. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology S

Re: [PyMOL] compare crystal packing of two different Space Groups

Hi Shukun, why and how did the matrix_copy command fail? If you swap step (2) and (3) everything should be fine. Try this: fetch 2xwu 2x19, async=0 as ribbon symexp mates, 2x19, 2x19, 6.0, segi=1 align /2x19//B, /2xwu//B matrix_copy 2x19, mates* By the way, the segi=1 argument of the symexp com

Re: [PyMOL] Writing a script yo pymol

Great, thank you. On Mon, Sep 12, 2011 at 10:05 AM, Thomas Holder < spel...@users.sourceforge.net> wrote: > Hi Yotam, > > > I'm sorry but this is too complected. Currently, I can't afford the time >> to learn another scripting languish. Consider gnuplot script files, which >> are simply a list

[PyMOL] Using Volumes

Greetings, One chance encounter at ACS couple weeks ago turned into a multi-day discussion about using the new volume visualization for presenting field data. Leroy Laverman from UCSB now has some example movies showing how the electrostatic field extends beyond the molecular surface and how the v

[PyMOL] Saving Issue

Dear List When I try to save an object as a PDB (after editing it slightly with the PyMOL edit mode, i.e. adjusting a dihedral angle), the "Save Molecule" dialog asks to save "all", "global" or "objects current" state. When saving with the last two, I get no coordinates in the generated file onl

Re: [PyMOL] Writing a script yo pymol

If you are more comfortable with PyMOL commands, use a .pml file (somewhat like the gnuplot script you mentioned). If you prefer Python, use a .py file, and import the necessary modules (pymol, cmd from pymol, etc.). You can find working Python scripts that call pymol in many places. To color

Re: [PyMOL] Saving Issue

Hi Martin, > When I try to save an object as a PDB (after editing it slightly with > the PyMOL edit mode, i.e. adjusting a dihedral angle), > the "Save Molecule" dialog asks to save "all", "global" or "objects > current" state. When saving with the last two, I get no coordinates in > the generated