October 2011 - Chimera-users - RBVI Mailing Lists

delegate
by Zoe Cournia 24 Oct '11

24 Oct '11

Hello, I am trying to use the "delegate" command from the Midas program in Chimera, but the error message I get is that "delegate is not yet implemented". Is there an available "Extension Mechanism" in chimera? If not, is it possible to get the source code for Midas in order to compile it and use it with delegate? Thanks a lot for any help. Best Zoe -- ------------------------------- Dr. Zoe Cournia Investigator - Lecturer Level Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece zcournia(a)bioacademy.gr Office: +302106597195 Lab: +302106597568 Cell: +306944223123 -------------------------------

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Error: Cannot write preferences file:
by Andrew Voronkov 24 Oct '11

24 Oct '11

Dear Chimera users I have problems with preferences file and actually when I run command line for example I instantle get the message: Cannot write preferences file: C:\Documents and Settings\avoron\Application Data\.chimera\preferences Maybe that is some problem with netowrk rights or security options and setup as far as reinstallation doesn't help. Best regards, Andrew

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Upgrade your video/graphics driver. hirose
by HIROSE Junzo 24 Oct '11

24 Oct '11

Dear Sir Side View doesn’t work. I got the following command in Side View. Unable to share graphics data with main window. Upgrade your video/graphics driver. How can I resolve this problem? Dr. Junzo HIROSE ****************************************** Fukuyama Univ. JAPAN TEL 084-936-2111 Email: hirose(a)fupharm.fukuyama-u.ac.jp ****************************************

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Cavities/Pockets
by George Tzotzos 22 Oct '11

22 Oct '11

I'm wondering if there's a way to work out the relative hydrophobicity of pockets/cavities of related receptors. Fetching CASTp IDs and rendering the surfaces of the cavities gives a crude idea of hydrophobicity of a given cavity. However, I'm looking for something that goes beyond visualisation. Any ideas would be most welcome. Best regards George

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protein sequence editing at sequence level
by frederick lee 21 Oct '11

21 Oct '11

hello chimera users, i know how to add or delete an entire sequence entry, but i can't figure out how to delete a portion of a sequence entry or a set of aligned sequences. currently, i have to go to another program (e.g., jalview) to accomplish that. is there a way to do that within chimera? also when i edit a protein structure (e.g., remove chains) and save the resulting structure, the sequence information of the *original* structure is kept in the pdb file. is there a way to only save sequence info corresponding to the structure actually saved? thanks much in advance. fred (relatively new chimera user)

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sym complains group t parameters
by Joe Ping-Lin Hsiao 21 Oct '11

21 Oct '11

Hi, I found an online post about how to use the sym command to duplicate models. The post is here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-June/006433.html The commands in the post are: open 1ei3 sym #0 group t,5,280 axis 1,0,.4 coord #0 surf true I got an error of "Invalid symmetry group syntax "t,5,280"" from the sym command. The versions that I have are daily build Oct 18 on Mac, and Oct 13 on Windows. Thanks, Joe

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split segmented map
by Gabor PAPAI 21 Oct '11

21 Oct '11

Dear chimera team, I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that? Thanks in advance! Best regards, Gabor ----------------- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748

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how to run the command line chimera without actually opening the GUI
by nurul 20 Oct '11

20 Oct '11

Hello, I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.

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.prmtop/.dcd combination for movie
by Francesco Pietra 20 Oct '11

20 Oct '11

Hello: I am running parm7 amber files with namd, thus having a .prmtop file and a .dcd file. Is there any possibility of having such a melange treated by movie? thanks francesco pietra

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problem in coloring a selected region
by Manish Manish 20 Oct '11

20 Oct '11

Dear Chimera Developer, I want to select a region in protein molecule and then color. I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part. I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915 and Chimera 1.5.3 . Regards Manish

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Chimera-users October 2011