Re: [PyMOL] states for distance objects
Thanks Warren,
However, in my case, I don't want to cycle through distances between the same
two atoms but each distance object contains references to different atom pairs.
To be more specific, I have a set of ten different protein-ligand interaction
types, represented by distance measurements of sets of atom pairs each, through
which I would like to go through with the movie controls. As each interaction
type contains different subsets of protein-ligand distance measurements I can't
use your suggestion. Any other trick I could use?
Sorry for being not clearer in the first place.
Cheers, Bernd
-Original Message-
From: Warren DeLano [mailto:war...@delsci.com]
Sent: Friday, August 14, 2009 18:58
To: Kuhn, Bernd {PRCB~Basel}; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] states for distance objects
Hello Bernd,
The trick is to create the distance objects using atoms already present in the
states you wish the distances to occupy. For example:
# load NMR structure
fetch 1nmr, async=1
# measure N to C distance in each frame
distance demo, 1/N, 85/C
# play
set movie_fps, 1
mplay
Cheers,
Warren
From: Kuhn, Bernd [mailto:bernd.k...@roche.com]
Sent: Friday, August 14, 2009 5:04 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] states for distance objects
I have a set of objects generated by distance commands through which I would
like to cycle, for example with the movie controls. Using create to generate
individual states of a single object does not work as the distance objects do
not contain atoms. Is there a solution to this problem?
Many thanks, Bernd
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Re: [PyMOL] Summary of Extracting Amino Acid Sequence from PDB File
Buz Barstow b...@mac.com wrote:
Thanks to everyone who replied to my query about extracting an amino
acid sequence from a PDB file!
Here is a summary of responses of my query;
1. Use SwissPDBViewer
...
6. Use PDBSET (part of CCP4)
t_coffee comes with s perl script unpack_extract_from_pdb. For
instance, in the following it extracts all of the sequences from the
entire PDB dataset:
nice -15 find /u4/pdb -name '*.pdb' \
-exec ./extract_from_pdb -chain ALL \
-infile '{}' -mode fasta -seq_field ATOM \; all_pdb_seq.aa
Note, this takes a long time! It would probably be significantly faster
if a persistent perl was used, instead of restarting the perl script
from scratch for each file.
Regards,
David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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Re: [PyMOL] coordinate transformation
Vivek, Create a copy of the original chain, modify the chain, and fit the copy to the original. For example # PyMOL 1.2 .pml input fab AAA, orig create copy, orig set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180 unpick fit origCA, copyCA Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Mon 8/17/2009 1:44 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] coordinate transformation Hello, I am trying to modify dihedral angles of a polymer chain. Once I perform all the required steps, I am able to orient the chain and align the chain along the same axis as the original chain. But unfortunately, pymol moves the chain to a different position. Basically, it changes the coordinates in a way that the center of the chain is at the origin. I want the chain to lie along the original chain with backbones coinciding with each other (almost). Is that possible in pymol ? -- Thank you and Regards, Vivek Ranjan -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
