September 2014 - Chimera-users - RBVI Mailing Lists

use Chimplug
by Pande, Ajay K 19 Sep '14

19 Sep '14

How would one use Chimplug plug-in in Chimera? I would like to generate CRD/PSF files for the ligand for use in CHARM. Thanks Ajay

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open amber trajectory error
by Renato Freitas 19 Sep '14

19 Sep '14

I am trying to open a zipped amber trajectory with chimera but I am getting the following error: ################################# Traceback (most recent call last): File "/home/disk0/rfreitas/softwares/chimera/share/chimera/triggerSet.py", line 83, in invoke self._funcData, triggerData) File "/home/disk0/rfreitas/softwares/chimera/share/DBPuppet/__init__.py", line 329, in portOnTop self.remove_webinfo(self.listen_port) File "/home/disk0/rfreitas/softwares/chimera/share/DBPuppet/__init__.py", line 369, in remove_webinfo with lock: File "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", line 120, in __enter__ self.acquire() File "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", line 32, in acquire self._createFile() File "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", line 86, in _createFile os.write(self.fd, "%d\n" % os.getpid()) OSError: [Errno 28] No space left on device Error processing trigger "Focus In": OSError: [Errno 28] No space left on device File "/home/disk0/rfreitas/softwares/chimera/lib/python2.7/site-packages/filelock.py", line 86, in _createFile os.write(self.fd, "%d\n" % os.getpid()) See reply log for Python traceback. ################################################ if I unzip the file, I can open it without problems. Since I have many files to look and they are very big (> 300 MB zipped) I don't want to unzip every file whenever I have to look at the trajectory. Any help will be appreciated. thanks, Renato

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reading .sd files
by Fabian Glaser 16 Sep '14

16 Sep '14

Hi, I have tried to read .sd files with docking ligands, without success. Is there a way to ready results of docking in .sd format in Chimera? Thanks a lot, Fabian _______________________________ Fabian Glaser, PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL fglaser(a)technion.ac.il Tel: +972 4 8293701 Fax: +972 4 8225153

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use of software to model structure
by Elsa Marquez 15 Sep '14

15 Sep '14

Hi there! I'd like to create a model of a protein that hasn't been crystallized yet, there are a few other highly homologous proteins that have been crystallized and are at PDB, so I was wondering if CHIMERA, or if you know about other software, can be used to model the unknown protein structure based on the known structure of homologous proteins. Thank you, I really appreciate your help! Elsa Marquez

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Trajectory B-factors
by George Tzotzos 15 Sep '14

15 Sep '14

Hi everybody, Is there a way to calculate the B-factors of the backbone atoms of protein residues in a MD trajectory? I checked earlier correspondence and saw that it can be done in Chimera with pdb structures. Many thanks in advance for any suggestions Regards George

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Feature request: parallel MatchMaker?
by Jonathan Sheehan 11 Sep '14

11 Sep '14

Hi- I'm a huge fan of Chimera, and I frequently need to superimpose a dozen or more comparative models onto a template protein using MatchMaker. At present, one cannot even rotate the view until all matches have completed, which can take a few minutes on a single core. Based on old messages[1], it sounds like you might be "interested in allowing use of multiple cores for specific compute intensive tasks," and this seems to me like a good candidate. This use case involves many matches, which I think are completely independent of one another. Also, these models have identical length and sequence, so the runtimes should be fairly close to one another (although that wouldn't necessarily be true in the general case). I'm sure that adding multi-threading to a tool is not trivial, but it seems as though this feature might have a high "bang for the buck" on today's multicore machines. Thanks for considering it, -Jonathan 1. E.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005901.html -- Jonathan Sheehan, Ph.D. Computational Structural Biology Vanderbilt Univ. Ctr. for Struct. Biol. 5137 MRB3, 465 21st Avenue S. Nashville, TN 37232-8755 615-936-2516

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Origin issue of mrc file from chimera to pymol
by Kai Zhang 11 Sep '14

11 Sep '14

Dear Chimera users, I found the pdb files fitted to mrc maps in Chimera do not always fit the same map opened by Pymol. It seems that the origins are calculated differently between Chimera and Pymol. I can easily handle an entire map of mrc file. But if the map has been cut, it's very difficult to find out what really needs to be modified to fit both chimera and pymol. Does anyone know an easy way to deal with this issue? Best wishes Kai

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Analysis of the multiple alignments + structures
by James Starlight 06 Sep '14

06 Sep '14

Dear Chimera Users! I'd like to perform analysis of the set of the sequences (presented in the FASTA multiple-alignment file) together with the some (not all) X-ray structures available for several of the sequences presented in its database to detect conservative motifs (from sequence) and make conclusions about its functional importance (based on the analysis of the Xray data) to make conclusions between conservation of sequence and it's functional relevance. Could you provide me with the some useful Chimera plugging as well as for some tutorials Kind regards, James

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Models views
by James Starlight 03 Sep '14

03 Sep '14

Dear Chimera users! I'd like to find possible option in Chimera for splitting 2 alligned models into 2 adjacent (e.g on left and right parts of the screen) object view (like what in Pymol 'Grid objects' is actually do). I didn't find this in the tutorials and will be very thankful if someone suggest me with this together with the list of some other commands usefull for the analysis of the aligned structures. Kind regards, Gleb

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Measuring dihedral angles using chimera
by Aswani Kumar Kancherla 02 Sep '14

02 Sep '14

Hello Chimera Users, I have recently installed chimera version 1.9 in Linux OpenSuSe 11.4 and am trying to get acquainted with its features. I am trying to measure dihedral angles (specifically the angle chiSS defined by Cb-Sg-Sg'-Cb' about disulfide bonds) for a list of pdb files containing NMR structure ensembles. I was trying to do this using a script (kindly given by a friend and pasted below) to which I can pass the coordinates of the four atoms and get the measured values for the "reply log" information. I need to put the files in a directory called pdb_files, open chimera and call the script and retrieve information from the "reply log". However, there is a problem: Since the coordinates of (Cb,Sg, etc ) will be different for each of the ensemble (since each ensemble is structure of a different molecule), I need to pass the coordinates dynamically for each pdbid. I have found from Chimera User group archives that reply log can be saved using a function. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html So that should solve one issue. I can save the reply log and parse it later. What is the best way to measure specific dihedral angles from multiple pdb files ? Is it possible to invoke chimera in tty mode and make it execute functions? In that case, I could probably write a shell script to invoke chimera once for each pdb and ask it to execute python script having appropriate atom coordinates. I apologize for slightly long an e-mail. Any hints or directions to enable me figure out how to get this done efficiently in chimera will be of great help to me. with regards, Aswani *script:* *================================================================* *import os* *import Matrix* *from chimera import openModels, selection, runCommand* *#angle #0:resno@CB :resno@SG :resno@SG :resno@CB 34.6289* *# Directory containing PDB files* *directory = 'pdb_files'* *# Get paths to all files in the specfied directory * *paths = [os.path.join(directory,f) for f in os.listdir(directory) if f.endswith('.pdb')]* *for pdbfilename in paths:* * filename = pdbfilename.split("/")[1]* * openModels.open(pdbfilename, baseId = 0) # Open as model #2* * runCommand('angle #0:863@CB :980@SG :1130@SG :1235@CB') # calculate torsion angle* * runCommand('close #0') # close molecule and map* *=================================================================* -- K.Aswani Kumar Graduate Student Molecular Biophysics Unit Indian Institute of Science Bangalore-560012 Karnataka, India.

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Chimera-users September 2014