[PyMOL] Mix pml script and PDB file

Hello, Is there a way to get one file with pymol commands (pml script) and with the structure (PDB file) ? I can get this with Rasmol and the ras script file. Can I get the same kind of file with PyMOL ? Thanks -- Sébastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aigui

Re: [PyMOL] Segmentation fault when selection is too large

Sebastien, Break it up over multiple selection statements which reuse the prior selection. For example, select mysel, resi 123+124+125 select mysel, mysel or resi 234+345+346 etc. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC

[PyMOL] Coloring Labels

Hi all! Is there a way to change the color of your labels withing PyMOL? I know you can make labels in Illustrator and add them later, but I was wondering if there was a way to change the color within PyMOL. Thanks! Laura Grell __

Re: [PyMOL] Coloring Labels

Hi Laura, set label_color, color Cheers, Tsjerk On 7/18/05, Laura Grell wrote: > Hi all! > > Is there a way to change the color of your labels withing PyMOL? I know you > can make labels in Illustrator and add them later, but I was wondering if > there was a way to change the color within Py

Re: [PyMOL] Mix pml script and PDB file

On Mon, 18 Jul 2005, Sebastien Moretti wrote: Hello, Is there a way to get one file with pymol commands (pml script) and with the structure (PDB file) ? I can get this with Rasmol and the ras script file. Can I get the same kind of file with PyMOL ? You can use the read_pdbstr command, li

RE: [PyMOL] Mix pml script and PDB file

Sebastien, Yes, you can do with with a "p1m" file, which is like a "pml" file, but data can be included as well. Also note that p1m files are intended for web publishing, so embedded Python is disallowed. In p1m files, there is an "embed" command that enables this for PDB, MOL, MOL2, SDF, and

Re: [PyMOL] Coloring Labels

Thanks for the help!! Laura >From: Tsjerk Wassenaar >Reply-To: Tsjerk Wassenaar >To: Laura Grell >CC: pymol-users@lists.sourceforge.net>Subject: Re: [PyMOL] Coloring Labels>Date: Mon, 18 Jul 2005 15:24:54 +0100>>Hi Laura,>>set lab

RE: [PyMOL] Mix pml script and PDB file

Hi, web publishing? Sounds like a nice feature... are there any documentations about that? regards Yusuf Quoting Warren DeLano : Sebastien, Yes, you can do with with a "p1m" file, which is like a "pml" file, but data can be included as well. Also note that p1m files are intended for web p

[PyMOL] spaces in atom names

In PyMol, I am selecting a subset of atoms from a pdb file, then saving the results to a pdb file. I'm having trouble with spaces in ligand atom names. For example, notice that the carbon listed below has a space as the 4th character in the name, but after loading into pymol and then saving,

RE: [PyMOL] spaces in atom names

Dan, Please include the full PDB file in your example -- in my hands, AC5 is handled just fine so long as AC is also the element symbol... I can't change PyMOL the way you ask without breaking other use cases -- sorry about that. However, recent version do tolerate internal spaces in a limited c