[PyMOL] Secondary structure elements

Hello, Is there a way to incorporate dssp into pymol for secondary structure annotation? Thank you. SDA

[PyMOL] Dihedrals: Not a bug, though might cause misunderstanding

Hello, I have just noticed that the dihedral angle obtained by Ctrl-Click (in Edit mode) on Ca-C bond in protein backbone is not actually the psi dihedral (N-Ca-C-N) but rather the angle between N-Ca-C-O (shown in white on the attached picture)! "dihedral" command shows the right value for psi

Re: [PyMOL] Viewing gromacs in pymol

Warren and Martin, thank you for the tips and the code, but how do I load gro and xtc files in the first place? Thanks

[PyMOL] Viewing gromacs in pymol

Hello, does pymol supports gromacs coordinate and trajectory files (gro, xtc, tpr, trr etc.)? Thanks

[PyMOL] API for CEalign

Hello, I have found a pymol wiki article about CEalign (http://www.pymolwiki.org/index.php/Cealign) - structure alignment procedure that is claimed to be better than align and super since it primarily aligns structures, not sequences. I did not find any API for CEalign. Does anybody now how could I

Re: [PyMOL] Script for iterated `align`ment

Hello, with your help I was able to write the following script to automatically load 21 structure and align 20 of them to the remaining one. * import os import re from os.path import join, getsize cmd.delete(all) p = re.compile('[A-Za-z\.]*pdb') w

[PyMOL] Script for iterated `align`ment

Hello, I have 21 pdb files in my folder. I wrote a small script to load them all at once to the Pymol ** import os import re from os.path import join, getsize p = re.compile('[A-Za-z\.]*pdb') w = re.compile('nowater') for root, dirs, files in os.walk('.

Re: [PyMOL] Sequence alignment editing

Hello, I have two structures of related organisms. I want to align them in 3D with pymol and be able to view their sequences aligned as well (corresponding to structure alignment). Right now when using Display->Sequence mode sequences are displayed simply 'as is' even after 3D 'align' command. Coul

Re: [PyMOL] problem with startup with pymol

Hi, you are lucky you know - some people dont get pymol started at all and you get this automated :) OK. I think you somehow got pymol in your console startup script or in your shell start sctipt. 1/ Console start script. Open console, goto settings->Configue Konsole (I wonder why is it K) -> sess

[PyMOL] Problems with ray and high resolution

Hello, I am trying to render an image with ray_trace_mode=1(cartoon textures). When I set ray 1024, 768 I get what I want but when I run ray 6000, 4500 I get the picture as if ray_trace_mode=0 (realistic view) had been set. Do you know any solutions? Thanks! I appreciate your help! SDA

Re: [PyMOL] Trouble with pymol tk GUI

Thanks, that was the solution. I have edited the Modules/Setup.dist file in Python2.5.2 source distribution, then edited tk/tcl versions and dirs and finaly cp Setup.dist Setup then reconfigured and installed python. Now everything works Thanks again. SDA

[PyMOL] Trouble with pymol tk GUI

Hello, I am installing pymol on opensuse 11 RC1 (kernel 2.6.25.4-8). Installation with default python 2.5.2 did not succeed - some strange problems occurred at the begging. I think python default installation might be corrupt. So I`ve compiled python 2.5.1 from source with default options and insta

[PyMOL] Yet again windows installation

Hello. I am practicing with latest pymol src on windows. 1. I have installed the latest python and ran >python setup.py build It crashed compying about lack of Visual Studio 2003 and thus C compiler. 2. I have installed cygwin, mingw and compiled glut to mingw folder. When I run >python setup.py

[PyMOL] Selecting single type amino acids within X angstrom from each other

Hello, I what to select all histidines that lie within 6 angstroms from each other. If I use > select x, resname his within 6 of resname his it selects all possible his, obviously. I tried to create a new state and select his of different states but got the same result for the same reason. Do you

Re: [PyMOL] partially transparent structure

set transparency=0.5 #for optimal view ray 1024, 768 there are more transparency options. Type "set transparency" when in console and press TAB two times to see the full list of available commands SDA On Wed, 2008-02-13 at 09:38 -0800, pymol-users-requ...@lists.sourceforge.net wrote: > Message

[PyMOL] merging many frames to one

Hello, I have a .pdb1 file with biological unit. It consists of two frames representing two chains (one per frame) together forming biologicaly significant molecule. I could apply crystallographic symmetry, instead I want to make use of file that I already have. What is the command to merge this t

[PyMOL] Fit sequence to structure with pymol

Hello everybody. Does anybody know how to perform sequence to structure fit with pymol? For example this feature in swiss-pdb-viewer is called "Fit" or "Magic fit". So, 1/ Is there a command to fit sequence to pdb& 2/ If yes, could I specify the region to fit on? Thanks!