October 2011 - Chimera-users - RBVI Mailing Lists

Labelling helices
by George Tzotzos 19 Oct '11

19 Oct '11

I've been looking at the documentation to find a way to number (label) protein helices. Perhaps I didn't use the right keywords so I didn't find anything helpful. What I would like to do is give ascending numbers to individual protein helices starting from the aminoacid terminus onwards. Any suggestions will be greatly appreciated. Regards George

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Display misconfiguration error
by Enrico Morelli 19 Oct '11

19 Oct '11

Dear all, after the update to the latest version of chimera, in some machines I receive the error: Display misconfiguration. Please increase the color quality (24bit color or grater), update your display (graphics) driver, ....... I've a lot of workstation with the same graphis cards (Nvidia Quadro) and the same operating system (ScientificLinux 5). I didn't do anything except upgrade chimera. The previous version works fine on all PCs, and the new one in some PCs give me the display misconfiguration. I checked the PCs where the chimera doesn't works, all has the Nvidia drivers working in 24bit mode and with graphic acceleration enabled. So, I don't know how can solve the problem. Someone can help me? Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

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bug reporting broken for the last day or so
by Eric Pettersen 18 Oct '11

18 Oct '11

Hi all, If you used "Report A Bug" (or the automatic bug-reporting dialog) in the last day or so, the bug report didn't get properly handled by our site despite the dialog itself saying that the bug report was successfully submitted. So if you need help with a problem contained in such a report you will need to resubmit it. Sorry! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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sequencial fitting
by Guimei Yu 18 Oct '11

18 Oct '11

Hi Sir or Madam, I am trying the sequential fitting in Chimera following the on-line video provided in your Homepage. But when I tried to use the "fit" command, it couldn't be recognized by the program. What's the possible reason about this? Is it because of the version? Thanks a lot! Sincerely, Guimei Yu Graduate Purdue University

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pH-dependent surface potential
by Dieter Blaas 15 Oct '11

15 Oct '11

Hi, Is there an (easy) way of displaying the surface potential at different pH values within Chimera? The Chimera-contained Coulombic Surface Colouring does not appear to take into consideration the pH-dependent protonation state (as far as I understand it assumes pH 7). Thanks a lot for hints, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories. Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Connect and align duplicated models
by Joe Ping-Lin Hsiao 14 Oct '11

14 Oct '11

Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more. Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate? Thanks, Joe

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Gasteiger charge
by Ibrahim Moustafa 13 Oct '11

13 Oct '11

Dear Chimera developers: I want to assign Gasteiger charges for a ligand, as a preparative step for docking. The ligand is GTP, extracted from a protein complex structure. I wanted to add the Gasteiger partial charge, and explicitly chose to have a total charge of ³-4² on the ligand molecule. However, the program assigned partial charges that sum to total charge of ³-2² instead of ³-4². Any idea why the program assigned the Gasteiger partial charges incorrectly, ignoring the input total charge on the ligand. Thanks in advance for your help. Regards, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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how to display specific residues and atoms in chimera
by Abir 11 Oct '11

11 Oct '11

Hello, I am new to chimera. I am trying to make an animation of an actual reaction. I have the frames saved as pdbs. I guess one can use the MD movie tool to make the animation in chimera. However, I want to show only specific residues and atoms from my active site in the movie and not the entire system (my system is a ribozyme). I played with chimera for a while, but could not figure out how to do that. It will be great if I get some help regarding this issue. Thanks a lot. Regards, Abir

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Building Togl with 8.6b2
by Clifford Yapp 07 Oct '11

07 Oct '11

I've been trying to compile Chimera's latest Togl against the most recent 8.6b2, and I'm not quite seeing how to go about it. A straight configure doesn't seem to find GL/gl.h... does it require use of the GNUmakefile in the toplevel? That file seems to need Mesa - can this version of Togl be built without it? Should I be pointing the configure to the unix dir or the macosx dir when doing the Aqua build? Also, has anyone tried running the Togl gears demo with the NSOpenGL based version of Togl? Does it work? Cheers, CY

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"Unrecognized command" in chimera
by Victoria James 07 Oct '11

07 Oct '11

Hi there, I am having a problem with the chimera command line. Whenever I try and tell it to do anything it says "unrecognised command", e.g. even the most basic "sel" I get prompted with "Unrecognized command: 'sel'" This has only started happening today.. I has a crisis with my computer yesterday and I had to restore all the files from a recent back up which may explain the problem, but I'm unsure how to fix it. I have just tried downloading the program again, but I am still getting the same problem. Is anyone able to help? Thanks in advance. Vicky

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Chimera-users October 2011