- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] importing sdf files from PubChem
by Elaine Meng 05 May '07

05 May '07

Hi Mark, You're welcome! I tried getting an SDF directly from PubChem, and that caused the same error you sent, again fixed by cutting and pasting the contents into another SDF file. Cutting/pasting (or otherwise getting rid of bad invisible characters) is the way to go for SDFs from PubChem, at least for now. We may take a look at those files (although I doubt there is a high demand for viewing 2D structures in Chimera!). Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 5, 2007, at 7:32 AM, Mark Andrake wrote: > Elaine, > > Thanks so much for your fast reply. > I can see from the users group that you guys do such a great job in > responding to user questions and concerns. > > After a quick gaze and trying on my laptop chimera at home - > it looks like there must be a hidden character issue. > I also had tried MS Word and saved it as a txt file > (in case there was some problem in the browser creating the file) > but maybe MS Word does not flatten out the file with just ASCI > characters. > > Next time I will try cutting and pasting through something like > WordPad first. > > In any case your test.sdf opened fine in my laptop chimera. > Thanks so much - have a great weekend! > > Mark > > Mark Andrake, Ph.D. > Research Associate > > Fox Chase Cancer Center > ICR428 > 7701 Burholme Ave. > Philadelphia, PA 19111 > 215-728-3654 > mark.andrake(a)fccc.edu > > > Elaine Meng wrote:Hi Mark, >> I've attached the test.sdf file mentioned in my previous message. >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> UCSF Computer Graphics Lab and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> >>

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selecting a unique ligand structure from multiple copy
by Jean-Didier Marechal 03 May '07

03 May '07

Hi everyone, I am working with different protein structures that have at least two copies of the ligand in their binding site. How could I select only one of them? (I'd like a selection specification that does not require the atom numbers if possible). Cheers JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

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wwPDB Announcement: Release of Remediated PDB Data
by Cathy Lawson 03 May '07

03 May '07

***wwPDB Announcement: Release of Remediated PDB Data*** The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files. The entire archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non- polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards. A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http:// www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with the current production site at ftp:// ftp.rcsb.org. Both sites share the same directory structure. Starting May 1, the remediated data will be served using gzip compression. Your input is very important to us. PDB users are encouraged to test the remediated data files between now and July 2007. The details of the final transition will be announced on the wwPDB website (http:// www.wwpdb.org) Detailed information about the wwPDB remediation project can be found at http://remediation.wwpdb.org. Comments about the files should be sent to info(a)wwpdb.org. Major announcements will be made at the wwPDB website (http:// www.wwpdb.org) as well as on the individual member websites.

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Ligand structure minimization
by Jean-Didier Marechal 02 May '07

02 May '07

Dear all, I don't know whether my problem falls in "bug" or "user request" category, pcorry if I use the wrong list. I am preparing a course where students will perform some protein-ligand dockings. I was thinking in minimizing the ligand in chimera using the "minimize structure" tool. I have installed the 1.2356 (that's what I thought but the message in the "About UCSF Chimera" pop up window says 1.2376 actually) version of chimera on ubuntu 6.10 and when I try to minimize my ligand (a HIV protease inhibitor), I am stopped at the PARMCHK run. Chimera seems to have compatibility problems with numpy. I join here the message given in the reply log file: .... Charges for residue U0E determined Total charge for #0: 1.0000 Running PARMCHK for U0E1.pdb command: /usr/local/chimera/bin/antechamber/exe/parmchk -i /tmp/tmpc6R8F8/parmchk.in.0 -f mol2 -o /tmp/tmpc6R8F8/frcmod.0 -p /usr/local/chimera/share/MMMD/parm/gaff.dat Finished PARMCHK for U0E1.pdbThis version of Chimera uses numpy for calculations. Numeric is only available in Chimera 1.2318 and earlier. Is there an easy way to move around this problem or should I install a earlier version of chimera for the moment? cheers, JD

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How does chimera invoke msms?
by aladdin 30 Apr '07

30 Apr '07

I need to know the solvent accessible surface of a protein, that means the info of solvent accessibility of residues or atoms . If I directly run "msms" with "-af" option, I can get an .area file in which stored such information. But in chimera's surface model, I cannot find what I need. How can I get the solvent accessible info in chimera? Thanks. liren --------------------------------------------

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Re: [Chimera-users] mutating amino acid side chain_deleting single atom
by Gary Laco 24 Apr '07

24 Apr '07

Hi, How can I mutate an amino acid side chain in a protein to another residue using Chimera? Also, how do I delete a single atom on an amino acid (for example a hydrogen). I looked through all the tools and did not find a way to do it. Thanks, Gary Gary S. Laco, Ph.D. Assistant Professor of Biochemistry Lake Erie College of Osteopathic Medicine-Bradenton 5000 Lakewood Ranch Blvd. Bradenton, FL 34211 Office: 941-782-5666 Fax: 941-782-5729 E-mail: <mailto:glaco@lecom.edu> glaco(a)lecom.edu

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movie and 'side view'
by jean-francois menetret 23 Apr '07

23 Apr '07

Is it possible to include the 'side view' during movie recording ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Secondary Structure Editing
by anat＠chem.ch.huji.ac.il 23 Apr '07

23 Apr '07

Hi, I would like to know if it's possible to edit (manually) the secondary structure attribute of single amino acid in the computed sequence given by Chimera (e.g. from strand to helix). Thank you for your help, Anat, the Hebrew university of Jerusalem. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Chimera-users Digest, Vol 48, Issue 17
by Puey Ounjai 21 Apr '07

21 Apr '07

Dear all; I am wondering can we manually assign secondary structure to each residues in the PDB file in chimera? Thanks Puey

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Chimera crash
by hsosa＠aecom.yu.edu 21 Apr '07

21 Apr '07

Hi, I'm having problems later with chimera. Sometimes when rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash with blue screen and reboot. It seems like a new problem as I've bee using chimera for a while and it didn't' happen before. As far as I know everything is the same in the computer. I'm running the latest snapshot release of chimera but that doesn't seem to be the problem. I deinstalled this version and installed the latest production release and got the same problem. Any ideas what the problem may be ?. Thanks Hernando System details UCSF chimera version 1.2382 (or 1.2304) OS: Windows XP service pack-2 Computer: Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.00.27.05 ForceWare version 91.36 -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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