Rosetta Academic Training Webinar
The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series.
What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST
Where: Your office!
Click here for more details and registration
(For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en)
Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version.
Hope to see you there,
Nir London.
Rosetta Design Group | http://rosettadesigngroup.com/
Normally when Chimera saves a session it includes the PDB data as part of the session file.
Is there a way to prevent that and have the individual pdb models saved as PDB files?
Thanks, Matt
On Mar 31, 2009, at 3:03 PM, Matthew Dougherty wrote:
Normally when Chimera saves a session it includes the PDB data as part of the session file.
Is there a way to prevent that and have the individual pdb models saved as PDB files?
The short answer is no.
Chimera originally preserved molecular data as embedded PDB files in it's session files (embedded as strings). Over time it became clear that this was problematic because a) PDBs are pretty verbose and slow to parse, and b) some molecular data is just problematic to store in PDB format. In particular, the 5-digit limit for atom serial numbers in CONECT records is a deal breaker. So two and a half years ago (1.2304 release) the embedded-PDB-file approach was abandoned and the data was simply stored as Python lists and dictionaries. This resulted in smaller session files with faster restore times and less memory use. We anticipate using Python's pickle mechanism to further reduce restore times and memory use (during the .pyc compile) in the next release. So the only part of the PDB file preserved more or less intact is the header lines (as a dictionary of lists of strings). So the long answer is also no!
Sorry.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I was writing some python code involving PDB data.
looking at pre-existing code involving PDB:
m = om.open(pdb_path, 'PDB')[0] rlist = m.residues
for r in rlist:
lc = 'monomer residue %d' % (r.id.position) if r.isHelix: lc += ' HELIX' elif r.isSheet: lc += ' SHEET'
I was trying to track down the data structure for r/rlist, to see if there are any other parameters I could use besides isHelix, isSheet, and id.position. where would that be located in the Chimera package?
thanks, Matt
I have a chimera session file that is being passed around. Different users are using savepos with no common nomenclature for the view_name.
How can I get a list of all view_names?
thanks, Matt
I am trying to incorporate a new pdb structure into an existing session file that has a number of savepos view_names.
The new pdb file that is pretty much the same as the old pdb file, just a few side chains moved. So in reset default, they are pretty much sync'd up.
when I try some of the other view_names, the new pdb structure does not match. Its as though the same transformations used in the old PDB structure are not being applied to the new PDB structure.
How can I sync the new PDB structure to the various view_names?
thanks, Matt
"reset list" will show the view names in the Reply Log.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote:
I have a chimera session file that is being passed around. Different users are using savepos with no common nomenclature for the view_name.
How can I get a list of all view_names?
thanks, Matt _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Matt, The command "reset list" will list the names of saved positions in the status line and Reply Log. Best, Elaine
On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote:
I have a chimera session file that is being passed around. Different users are using savepos with no common nomenclature for the view_name.
How can I get a list of all view_names?
thanks, Matt
thanks,
how would I get the same list in python?
On Apr 2, 2009, at 4:01 PM, Elaine Meng wrote:
Hi Matt, The command "reset list" will list the names of saved positions in the status line and Reply Log. Best, Elaine
On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote:
I have a chimera session file that is being passed around. Different users are using savepos with no common nomenclature for the view_name.
How can I get a list of all view_names?
thanks, Matt
Hi Matt, If the new structure is sufficiently well matched to the old one when they are in the default (untransformed) positions, then after you reset to the various positions, you can bring the new one in by applying the same transform as is used for the older similar structure.
For example, if your older similar structure is model 3 and the newer one is model 10, and you have just reset to a position that leaves the new model stranded, try the command
matrixcopy 3 10
to bring 10 into the proper position. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
How "reset" dealt with new models not in the original saved position was improved (after release 1.3) so that the new models will maintain their transformation relative to the lowest-numbered model that was included in the position. I guess your older similar model is not the lowest-numbered. Or, if it is, you could try using a recent daily build. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 2, 2009, at 1:52 PM, Matthew Dougherty wrote:
I am trying to incorporate a new pdb structure into an existing session file that has a number of savepos view_names.
The new pdb file that is pretty much the same as the old pdb file, just a few side chains moved. So in reset default, they are pretty much sync'd up.
when I try some of the other view_names, the new pdb structure does not match. Its as though the same transformations used in the old PDB structure are not being applied to the new PDB structure.
How can I sync the new PDB structure to the various view_names?
thanks, Matt
import Midas Midas.positions.keys()
FYI, most command-line commands are implemented in the Midas module, usually in a function of the same name as the command. So the implementation of "reset" is in "def reset" in Midas/__init__.py. The implementation for commands that do the same things as tools (e.g. findhbonds, volume) are usually found in that tool's module though.
--Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 2, 2009, at 2:06 PM, Matthew Dougherty wrote:
thanks,
how would I get the same list in python?
On Apr 2, 2009, at 4:01 PM, Elaine Meng wrote:
Hi Matt, The command "reset list" will list the names of saved positions in the status line and Reply Log. Best, Elaine
On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote:
I have a chimera session file that is being passed around. Different users are using savepos with no common nomenclature for the view_name.
How can I get a list of all view_names?
thanks, Matt
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Matt, You can find out about the (C++) attributes/methods of a class by using help() in the IDLE interpreter, e.g.:
help(chimera.Residue)
There is also declaration of the Python-visible attributes of Atom/ Residue/etc. in the source distribution in libs/_chimera/pyinterface. The more convenient way nowadays to get pyinterface is by browsing our SVN repository, i.e. from:
/trunk/libs/_chimera/pyinterface – Chimera
The other thing you might want to know that seems germane to your specific query is that the PDB headers are stored in the pdbHeaders dictionary in Molecule (key: header type [e.g. REMARK], value: list of strings).
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 2, 2009, at 1:23 PM, Matthew Dougherty wrote:
I was writing some python code involving PDB data.
looking at pre-existing code involving PDB:
m = om.open(pdb_path, 'PDB')[0] rlist = m.residues
for r in rlist:
lc = 'monomer residue %d' % (r.id.position) if r.isHelix: lc += ' HELIX' elif r.isSheet: lc += ' SHEET'
I was trying to track down the data structure for r/rlist, to see if there are any other parameters I could use besides isHelix, isSheet, and id.position. where would that be located in the Chimera package?
thanks, Matt _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
One of the people in my lab has a series of images that they want to turn into MPEG's
Because they are familiar with Chimera, I would like to solve their problem using Chimera rather than train them on FCP.
Is there a way to do this either with chimera commands or developing a short python script?
thanks, Matt
Hi Matt,
Chimera uses ffmpeg to encode a series of images into a movie. ffmpeg is included with Chimera in the "bin" directory. If you record a movie in Chimera using the "movie" command or "Movie Recorder" dialog, the command used to encode the movie is reported in the reply log (Favorites menu). Here's an example:
/Users/goddard/chimera/chimera-twain-AGL/install/Chimera.app/Contents/Resources/bin/ffmpeg -r 25 -i /var/folders/+g/+gO21g+SFqCxNgLVgIvElk+++TM/-Tmp-/chimovie_YZ1R-%05d.ppm -y -f mov -b 2000 -bufsize 200 /Users/goddard/chimera_movie.mov
The "-r" option gives playback frame rate in frames per second. The -i gives the input image files. The "%05d" in that specification represents the 5 digit image number in the file name (e.g. image-%05d.jpg represents image-00000.jpg, image-00001.jpg, image-00002.jpg, ...) The "-f" is the output format (mov = quicktime). The "-b" gives bit rate it kilobits/second which determines quality versus file size.
You can invoke ffmpeg directly from a terminal window on Mac or Linux without starting Chimera. For more options search for ffmpeg on the web.
Tom
Matthew Dougherty wrote:
One of the people in my lab has a series of images that they want to turn into MPEG's
Because they are familiar with Chimera, I would like to solve their problem using Chimera rather than train them on FCP.
Is there a way to do this either with chimera commands or developing a short python script?
thanks, Matt _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (6)
-
Elaine Meng -
Eric Pettersen -
Matthew Dougherty -
Matthew Dougherty -
Nir London -
Thomas Goddard