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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[PyMOL] Summary of Extracting Amino Acid Sequence from PDB File
Dear All, 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 2. Use Pymol 1.2 load $TUT/1hpv.pdb save 1hpv.fasta # or by selection save 1hpv_A.fasta, chain A 3. With Phenix, you can use the "phenix.print_sequence" tool to output the sequence in FASTA format. 4. If the PDB file is in the PDB, you can download the primary sequence from here. 5. Use MOLEMAN2 6. Use PDBSET (part of CCP4) All the best, ---Buz -- 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
Re: [PyMOL] Summary of Extracting Amino Acid Sequence from PDB File
Buz Barstow 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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[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
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
