- Chimera-users - RBVI Mailing Lists

Multiscale model of RNAP : fibrous aspect
by Damien Larivière 27 Feb '09

27 Feb '09

Dear Elaine, I used the Multiscale Model tool to create a low resolution surface of the PDB 1L9U (TAQ RNA polymerase). The attached image is what I got with a resolution 4 : a fibrous structure. So, I wonder what such a fibrous aspect means or whether it means the tool has some difficulties to create the surface with this specific protein ? Thanks for your help Damien

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How to refer to Chimera in a Newsletter
by Gary Newton 26 Feb '09

26 Feb '09

Hello... I am writing a newsletter for the SER-CAT synchrotron beamlines sector 22 at APS - the newsletter is called the "SER-CAT Spectrum" and is distributed primarily to beamline users. I have included a simple protein drawing produced by CHIMERA and indicated that the drawing was produced by CHIMERA. Should I include a trademark symbol or perhaps a copyright symbol after the name? Thanks for any advice. Best, Gary Newton University of Georgia Athens, GA

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searching chimera archieve
by Bala subramanian 26 Feb '09

26 Feb '09

Dear Elaine, Long time back, I posted a question on *searching chimera archive for a keyword*. Just for an example, i gave "salt bridge" as a key word in the following link, but it dose nt show me the queries on salt bridge in chimera archive. I dnt undertand why ?. It would helpful for chimera loves like me not to repeat same queries and also to understand all ways of analyzing salt bridge based on previous queries. I am sorry if this question is not relevant to chimera technical issues. http://www.cgl.ucsf.edu/chimera/docs/feedback.html Cheers, Bala

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how to quickly delete several markers
by Juha Huiskonen 26 Feb '09

26 Feb '09

Dear Chimera developers & users, I am visualizing template matching results of volume data in Chimera, and I have to discard hundreds of false positives matches, represented as markers. Now I select some markers and then delete the selected markers from the Volume Path Tracer menu. This is quite slow, and for me it would be really handy, if I could delete (all linked) markers just by clicking (one of them) them. Maybe "delete markers with mouse" feature could be added to Volume Path Tracer module? Or is there already a faster way to do this? Thanks a lot in advance for your suggestions! Juha -- Dr. Juha Huiskonen Max Planck Institute of Biochemistry Department of Molecular Structural Biology Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 89 8578-2632 Fax: +49 89 8578-2641 GSM: +49 176 20786875 E-mail: huiskone(a)biochem.mpg.de http://www.helsinki.fi/~huiskone/

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angles after match
by julien(GWDG) 25 Feb '09

25 Feb '09

Dear all, thank you for the very nice software. I continuously like it. I have the following problem. For different molecules, I would like to know what are the transformation that link them. I can do for example match #0 #1 matrixget - From this matrix I have the rotation information and the translation information. I would like to extract the angles. For that I need to know what convention you used. I guess those are Euler angles (?), but I need to know what is the order of rotation xyz, xzy... Finally how do you get ride of the gimbal lock problem if you use Euler angles. Thank you for your constant help. (Sorry if this question is a duplicate) many greetings julien

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slab representation of nucleic acid
by Bala subramanian 25 Feb '09

25 Feb '09

The slab representation of nucleic acid under Depiction is not working. I made the following settings *show backbone as* atoms/bonds, *show sugar as* atoms/bonds, *show base* as slab. But the representation is not displayed on the screen. What could be the reason. I myself have used it before and i am not aware why this happens now. Regards, Bala

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finding salt bridges
by Elaine Meng 24 Feb '09

24 Feb '09

On Feb 24, 2009, at 1:51 PM, Jeremy Schmit wrote: > Does Chimera have a tool for identifying salt bridges? I was able > to use the findHbond tool to count intermolecular H-bonds in the > lysozyme crystal, but I can't seem to find an analogous tool for > salt bridges. In fact, the term "salt bridge" does not yield a > single result on the Chimera site. > Thanks, > Jeremy Hi Jeremy, There isn't a tool for specifically finding salt bridges, but you can consider them as a subset of hydrogen bonds. You could select only atoms in charged functional groups and then limit H-bond detection to that selection. Example commands to first select by atom type and then find the H-bonds: sel O2- | O3- | N3+ | Ng+ findhbond selRestrict both saveFile ~/mydir/myfile If the subunits of interest are different chains in the same model (same input file), you could then postprocess the output (for example, with "grep" on unix) to count only those between the chains. If each subunit is opened as a different model, you could add "intramodel false" to the findhbond command. There are analogous options on the FindHBond graphical interface: "Only find H-bonds with both ends selected" and find just the "inter-model" bonds. findhbond command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> findhbond GUI: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… > atom types: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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copy in a file the distance on the screen
by fabriceg＠univ-reunion.fr 24 Feb '09

24 Feb '09

Dear Users, When analyzing a trajectory file, I would like to monitor a distance (or series of distances) and save it to a file for each frame (getting a time series). I can do it but the values remain on the screen only! I am sure there is a simple script for making this. Thanks for any answer. Best wishes. Fabriceg

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Sequence vs Sequence plot using minrms....
by Sergio Garay 24 Feb '09

24 Feb '09

Hi all I run minrms with defaults values on my two proteins and I was able to obtain many useful alignments. But when I load the results on chimera, it doesn´t show me the sequence vs sequence plot. Is there any particular way to do that? Or there is any special minrms command (option) to obtain this? All the other plot were right (rms vs sequece and the alignment plot). Any help will be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Match -> Align used with a pair of homodimers
by E. Merkley 24 Feb '09

24 Feb '09

Hello chimera friends: I am trying to get a structure-based sequence alignment for a pair of homologous proteins that are homodimers. If I proceed as described in the tutorial and in the 2006 BMC Bioinformatics paper, by first using Matchmaker, then using Match -> align, the Match -> Align fails to produce a reasonable alignment. The sequence identity from the Matchmaker output is 26.5%, but only 1.0 % from the Match -> Align step. If I delete the second monomer from each protein, Match -> Align works quite well. However, it seems like this alignment won't take into account any differences in the tertiary structure between the two proteins. That is, I think I want the global alignment of the whole dimer for the structural alignment, since the active sites is are at the interface. Any suggestions? I'm using version 1.2540, and my two proteins are PDB codes 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and hand-edited to be 1 model with A and B chains). Thanks yet again, Eric

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