September 2009 - Chimera-users - RBVI Mailing Lists

hydrogen bond representation
by Bala subramanian 04 Sep '09

04 Sep '09

Friends, Is there any way to represent hydrogen bonds as dotted lines instead of a solid line in Chimera. Sometimes hbond analysis in chimera shows same atom to be involved in two hydrogen bonds, why is it so ? Thanks, Bala

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2D projections
by Ana Luiza 03 Sep '09

03 Sep '09

Hi, Is it possible to build 2D projections from a 3D surface in Chimera? Thanks, Ana Luiza.

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wglMakeCurrent failed
by Stefano Marzi 03 Sep '09

03 Sep '09

Hi, With the new production releases, from 1.2540 to the very last one 1.4_b28596, for windows, I am keeping getting the wglMakeCurrent failure. This happens when I try to make a movie. I have searched in the Chimera-user mailing list archive but I have found only a thread by Greg Couch saying that this bug has been fixed already one year ago, September 2008. Could anyone please help me with that? Thank you, Best Stefano Marzi

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Rendering with nogui
by Kevin Wu 02 Sep '09

02 Sep '09

Hi, It seems like it's not possible to render figures or models in Chimera when using the nogui option. Is there anyway around this? I'd like to use Chimera in a program to render models to display. Regards, Kevin

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chimera latest build
by Bala subramanian 01 Sep '09

01 Sep '09

Friends, 1) I downloaded the chimera's today's build and tried to change the nucleic acid representation using..Depiction in Tools. I get the following error. Kindly write me what is going wrong ? TclError: unknown option -width TclError: unknown option -width File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ See reply log for Python traceback. Thanks, Bala

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substitute single residue
by Andrew P. Hinck 01 Sep '09

01 Sep '09

Dear all, I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions. Andy Hinck Andrew P. Hinck, Ph.D. Professor, Department of Biochemistry, MC 7760 University of Texas Health Science Center at San Antonio San Antonio, TX 78229-3900 office: 210-567-8780 mobile: 210-725-4438 fax: 210-567-8778 email: hinck(a)uthscsa.edu websites: http://hincklab.uthscsa.edu http://nmr.uthscsa.edu

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Chimera works on Snow Leopard
by Thomas Goddard 31 Aug '09

31 Aug '09

Hi John, I tested Chimera 1.3 and 1.4 daily builds on Mac OS 10.6 (Snow Leopard). All the tests worked fine. I ran our test suite using the Aqua Mac Chimera 1.4 snapshot and it all passed. I tested Chimera 1.3 production releases Mac Aqua and Mac X11 by hand opening a few data sets (molecules and volume data) and doing some coloring and encountered no problems. Tom -------- Original Message -------- Subject: Re: Snow Leopard ? From: Elaine Meng To: John Gerlt Date: 8/27/09 9:12 AM > Hi John, > I don't know for certain, so I'm turning over the question to the rest > of the staff (cc'd on this message). To whomever answers: could > include response on chimera-users list if you think others will have the > same question... thanks! > Best, > Elaine > > > On Aug 27, 2009, at 9:08 AM, John Gerlt wrote: > >> Elaine, >> >> Apple is issuing OS 10.6 tomorrow. For reasons I don't understand, I >> like to be current. But, as I recall from the past, when I tried to >> be current and install a new OS (10.5?), Chimera would not work. Do >> you know if Chimera will work with 10.6? >> >> Thanks. >> >> John

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Centro-symmetric space groups
by Michael Day 31 Aug '09

31 Aug '09

How do you get Chimera to recognize centrosymmetric space groups. If I include the space group on the CRYST1 card of the PDB file all is well for non-centrosymmetric groups but when a center of symmetry enters the picture all bets are off. I'm using Tool->Higher-Order Structure->Unit cell For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion. Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Chimera-users September 2009