June 2014 - Chimera-users - RBVI Mailing Lists

Saving Sessions with surface data
by Arjun Dayal 03 Jun '14

03 Jun '14

Hi, I imported several .STL files into Chimera that I generated using TrakEM2. These import as individual surface objects in Chimera. I am then able to color the objects differently and generate some publication-quality screenshots. However, I am unable to save and restore the Chimera session. Upon trying to restore the session, I am presented with a blank screen. The program does not report any errors and even says "Done opening SESSION.py". It seems that the program never loaded the surface files. How does Chimera know where the surface files are located? I saw no mention of their location inside the session PY file. How can I save my session so that next time I open Chimera, all of my surfaces load with the colors, transparency, etc. that I assigned them in Chimera? -- Arjun Dayal Pritzker School of Medicine | Class of 2016 University of Chicago

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rotamers, contacts, H-bonds
by Elaine Meng 03 Jun '14

03 Jun '14

Hello Maryam, This sounds like a chimera-users question (chimera-dev is more about programming), so I CC'd that address. You can use Distance measurements, Find Contacts/Clashes and/or FindHBond to look at the interactions of the residue. See menu under Tools.. Structure Analysis, and instructions: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> For looking at rotamers of amino acids, both same type as native (no mutation) or different type (mutation) you could use the Rotamers tool (in menu under Tools… Structure Editing). The rotamers list also connects to finding contacts and Hbonds through its Columns menu, see "evaluation" in the Rotamers manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot…> For examples of measuring distances, identifying contacts and H-bonds, and using Rotamers, I recommend you try the "Structure Analysis and Comparison" tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 28, 2014, at 2:05 AM, "maryam.khoshnejat" <maryam.khoshnejat(a)modares.ac.ir> wrote: > hello > could you help me? > i should model specific mutant residue of protein . i have PDB file and rotamer of mutant residue > how can i find coordination of mutant residue based on backbone and CB coordination of native residue , rotamer and atom bonding distance > i need a code for finding coordination of mutant residue > regards

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Fetch biological unit?
by Hurt, Darrell (NIH/NIAID) [E] 02 Jun '14

02 Jun '14

Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Chimera-users June 2014