[PyMOL] compare crystal packing of two different Space Groups

Dear Pymol users, I want to compare the crystal packing and contacts of two different space groups of the same protein using pymol. Here's what I did: (1)loaded two structures; (2) aligned two structures; (3) generated symmetry-related objects of two structures. However, the symmetry-related molec

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

I've never found a clean way to do this - what I do is to save a PDB file with the original model and the relevant symmetry mates, which I then use for the alignments. There may be a way to do is with object groups, however. (FYI, you'll probably also need to rename the chain IDs for the symmetry

Re: [PyMOL] Show Sticks - Turns Molecule Blue

This should get you on the way on compiling from svn. http://www.pymolwiki.org/index.php/Linux_Install#Mint11_Linux_.28Ubuntu.29_-_Tested_for_PyMOL_1.4.1 Best Troels 2011/9/9 Sean Law > Hi PyMOLers, > > I have tried installing both PyMOL 1.3 and PyMOL 1.4.1 on OpenSuse (old > Pentium 4) and

Re: [PyMOL] print hydrogen bonds involved residues

You have to make .pml file and put the python commands inside pymol blocks. Try look here for an example. http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752

[PyMOL] Writing a script yo pymol

Hi. How hard it is to write a (python?) script that will rotate the figure and color some atoms? Nothing fancy... I searched a little bit but couldn't find a quick and dirty tutorial for script writing. Thanks -- My other email account has a "professional" signature. ---

Re: [PyMOL] Writing a script yo pymol

Well, not hard. I made a script that can rotate a molecule around a line. And I made a large tutorial to take one through the available functions of this script. It is a pymol command file, ".pml". Check out: http://www.pymolwiki.org/index.php/Rotkit Troels Emtekær Linnet Karl-Liebknecht-Straße

Re: [PyMOL] Show Sticks - Turns Molecule Blue

Assuming you're using a recent version of openSUSE (11.3, 11.4, or Factory), feel free to grab the svn compiled version from http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol -David 2011/9/11 Troels Emtekær Linnet : > This should get you on the way on compili

Re: [PyMOL] Writing a script yo pymol

Thanks. 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. Sure you can do some sophisticated stuff but you don't have to. All my files will be simple atom list i