RE: [PyMOL] alternative method for loading coordinates

Tina, If you're willing to switch into Python, there is an undocumented "read_pdbstr" function which can take a PDB file as a string variable. See modules/pymol/importing.py for the code. Temporary files are unnecessary. However, I'm not sure that I completely understand your que

[PyMOL] Re: PyMOL-users digest, Vol 1 #408 - 11 msgs

Hi List! I'm glad to see others enjoying MDK 9.1. But pymol rpm for RH is a friend of MDK, I suggest you use pymol-0_90-bin-linux-libc6-i386.tgz It works terrifically for me. Dear Warren, realy great job! If possible, a proper pymol rpm for MDK 9.1 would be very welcome, since I believe there's

[PyMOL] alternative method for loading coordinates

Hello, Is there an alternative loading PDB coordinates, other than "load "? Let's say after threading against a large database of protein templates, I need one PyMOL script generated for each of the templates. I could as well generate one PDB file for each to load, but it would be difficult to man

RE: [PyMOL] pymol problems with Mandrake 9.1

Thanks for this Warren, but now I get a fresh set of error messages (still no menus) with no obvious explanation along the lines of missing package xxx. Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.2/threading.py", line 408, in __bootstrap self.run(

RE: [PyMOL] pymol problems with Mandrake 9.1

Dan, Opinions may vary, but I see RPMs are pretty heavily tied to the distribution. The kind of errors you're seeing are to be expected when trying to install cross-distribution. RPM doesn't look at the file system (AFAIK), it looks in the RPM database for the names of (Redhat-

RE: [PyMOL] incorporation of unusual amino acids

Uwe, > We plan a research project where we want to stepwise incorporate D-amino > acids into a peptide. To determine the exchanges it would be very useful > if > PyMol could assist. > If I might dream I would like to have D-amino acids (and maybe other un- > usual amino acids) available in the mut

RE: [PyMOL] individual surfaces?

Dirk, The trick for displaying "contact" surfaces in PyMOL is to create separate objects for each surface: create res431, resi 431 create res440, resi 440 show surface, res431 or res440 For CPK, you don't need to do this show spheres, resi 431+440 Cheers, Warren -- mailto:war...@del

[PyMOL] pymol problems with Mandrake 9.1

Hi everyone Having previously used RedHat I've just put Mandrake 9.1 on my latest machine (ease of installation, disk partitioning). To my surprise (naively perhaps) the standard RH-derived RPMs on the pymol site lead to chains of missing dependencies that I don't reach the bottom of. Eventually

[PyMOL] incorporation of unusual amino acids

We plan a research project where we want to stepwise incorporate D-amino acids into a peptide. To determine the exchanges it would be very useful if PyMol could assist. If I might dream I would like to have D-amino acids (and maybe other un- usual amino acids) available in the mutation-tool; som

Re: [PyMOL] individual surfaces?

Am Dienstag, 9. September 2003 09:14 schrieb Dirk Kostrewa: > Dear PyMol users, > > I'm currently trying to display individual surfaces around different > selections of a molecule to show how they contact each other. The trick is to define the selections as individual objects: create obj1, (resi

Re: [PyMOL] individual surfaces?

Hi Dirk, The best way to go there is to create two objects. One of one part of the protein and one of the other, and show the surfaces of each of them. Good luck, Tsjerk Dirk Kostrewa wrote: Dear PyMol users, I'm currently trying to display individual surfaces around different selections

[PyMOL] individual surfaces?

Dear PyMol users, I'm currently trying to display individual surfaces around different selections of a molecule to show how they contact each other. However, either I get only the last surface displayed or a joined surface using the command examples below: this one gives only the surface of re