- Chimera-users - RBVI Mailing Lists

Non-gui chimera in a shell?
by James Vincent 09 May '06

09 May '06

Hello, I've read several threads about nongui use of chimera and that some work was started. This work seemed mainly aimed at getting a web server script to run chimera and return some result back to a browser. I'm interested in running chimera in a stand alone python script. I'd like to do molecular calculations using the various tools but all on a command line, no graphics. It seems the --nogui option would get this, but the OS X version does not seem to implement that. Perhaps I'm missing something. Can anyone help? ideally I'd like to just have a plain python script that imports the chimera package but does not choke on all the graphics stuff, and then lets me use the chimera object model and other programming objects. Thanks for any assistance, Jim ---- James J. Vincent, Ph.D. National Cancer Institute National Institutes of Health Molecular Modeling and Bioinformatics Section Laboratory of Molecular Biology Building 37, Room 5120 37 Convent Drive, MSC 4264 Bethesda, MD 20892 USA 301-451-8755 jjv5(a)nih.gov

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manual
by Oscar Moran 08 May '06

08 May '06

does exists a printable version of the manual? (pdf, ps or even simple ascii) oscar Oscar Moran, PhSc Istituto di Biofisica Consiglio Nazionale delle Ricerche Via DeMarini, 6 I-16149 Genova, Italy Tel. +39-0106475-558 / 522 Fax +39-0106475-500

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transparency at the command line
by Miguel Ortiz-Lombardia 07 May '06

07 May '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi chimerics, I'm not very familiar (yet) to python scripting in chimera, so I am trying to prepare a movie using just line commands in a file. I would like to gradually increase the transparency of a model's surface that has been colored in "rainbow by residue" style. My question is then: is there a way to control the overall transparency of a surface from the command line? I could resort to colordef commands at every step, but this would make things very hard with the rainbow coloring... Thanks a lot! Miguel ( trying to learn more python in the meantime ;) ) - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFEXaezF6oOrDvhbQIRAnUNAJ9UJOF3RWv7ohXj+pcmQeD6rU4VBwCfb7PK PDzmG1mMWWL6iW9o+a+ooXk= =Flu6 -----END PGP SIGNATURE-----

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B-factors
by Narender Singh Maan 05 May '06

05 May '06

Dear Chimera users, i am looking for a way to write down the average B-factors for each residue from a pdb file (which shows atomic bfactors). I tried using chimera attributes which can color the protein and shows a histogram for bfactors, but i am not able to get those average values in reply log or some other written file. Please let me know if i can get any help in this. thanxs ns

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Chimera under KDE (update)
by Mingfeng Yang 05 May '06

05 May '06

Please disregard my previous message. I just tried to kill the KDE system process one by one and found out that skim (an input program) is the one should be blamed. Mingfeng

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Can't input anything under KDE
by Mingfeng Yang 05 May '06

05 May '06

I am using Chimera build 2199 under KDE 3.5.2, and I can't input anything into the command line (and other input dialogs) of chimera. The linux distribution is Kubuntu Dapper Drake. If I get into the KDE environment with failsafe mode, everything is fine. And I remember chimera works fine under KDE 3.5.2 under gentoo. I guess some service(s) of KDE must have confliction with chimera, but I couldn't figure out which one. :( Best, Mingfeng

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absolute scale?
by Cathy Lawson 02 May '06

02 May '06

Hi, Is there a way to set an "absolute scale" for viewing in chimera? I'm trying to make pictures in multiple Chimera sessions with different molecules and would like for the results to be all on the same scale. I naively thought I could do this with the "camera" scale but then I noticed that for two different sessions where this value was set to 1.0, the actual scales are quite different. Chimera help revealed that the camera scale is relative to the original size when the model was first opened. Any suggestions would be appreciated! thanks, Cathy Lawson *********************************************************************** Catherine L. Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology Rutgers University 610 Taylor Road, Piscataway, NJ 08854 cathy.lawson(a)rutgers.edu tel 732 445 8074 fax 732 445 5312 http://rutchem.rutgers.edu/~lawson http://roma.rutgers.edu/~lsbb *********************************************************************

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Broken labels!
by Changhoon Kim 02 May '06

02 May '06

Hello? I am using Chimera on Windows XP. It's "beta version 1 build 2199 2006/01/24". When I tried to display residue labels, many of the labels were unrecognizable. I've attached the picture showing the broken labels. Sometimes the distance labels are also unrecognizable. I hope it would be fixed soon. Regards Changhoon Kim

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libGL.so
by Isaac Amela Abellan 02 May '06

02 May '06

Hello, I'm using Linux and when I had tried to execute chimera this message appeared: "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1. Please read installation instructions." I said it several times to my system administrator and he solved it using your instructions (see below): "If Chimera terminates with the error OpenGL misconfiguration detected, that means that you have two different versions of libGL.so installed -- one in /usr/lib (installed by your graphics card drivers) and one in /usr/X11R6/lib (possibly installed by Mesa, which if so would mean no hardware graphics acceleration if this version were used). Reinstalling your graphics card drivers should remove the /usr/X11R6/lib version. Alternatively, you could rename or remove the /usr/X11R6/lib version yourself. With the latter approach you might want to verify that all OpenGL applications that you use continue to work before permanently removing the library. On startup, you may see the warning Xlib: extension "Xfre86-DRI" missing on display "0.0". That means that there was no graphics driver found for your card that uses the DRI, direct rendering interface, technology for fast 3D graphics. The solution is to either ignore the warning or to upgrade your hardware and software (see Mesa/OpenGL issues below)." The problem is that when I reboot my computer the problem still appears and we should do the same procedure explained above. We can't configure the system conservating the libraries of my card drivers (/usr/lib) without removing the Mesa ones (/usr/X11R6/lib). How can we solve the problem? We will be waiting for your response. -- ------------------------------------------------ Isaac Amela Abellan PhD Student Laboratory of Bioinformatics Institute of Biotechnology and Biomedicine (IBB) Autonomous University of Barcelona (UAB) 08193 Bellaterra, Barcelona. Spain. Phone: 34-93-5812807 e-mail: iamela(a)bioinf.uab.es ------------------------------------------------

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Stereo angle value
by Prof. Fabrizio Briganti 02 May '06

02 May '06

Hi, I have not been able to find any reference to the value for the angle difference between Right and Left views in Stereo Images made with Chimera. Can you help me find it? Is there any way to change such angle value? Thanks Fabrizio

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