- Chimera-users - RBVI Mailing Lists

finding salt bridges
by Elaine Meng 28 Feb '09

28 Feb '09

> Hi everybody, I just realized my previous suggestion would not include the positively charged histidines, and I have not been able to think of a selector for just those nitrogens. > 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 Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab 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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Reverse of AddH
by Francesco Pietra 27 Feb '09

27 Feb '09

Hi: Is it possible to remove all hydrogens by command, without intervening manually on the pdb file? I have to rmsd the starting (no H) pdb with the final structure after MD (with H). AddH command to the starting structure would place H not optimized, while MD has also changed the C-backbone conformation. Thanks francesco pietra

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solvent accessible area
by Bala subramanian 27 Feb '09

27 Feb '09

chimerians, I want to calculate the solvent accessible surface area for each atom and write it in the pdb file, kindly tell me how to do it. This is something i used to do with GRASP. it calculates the sasa for each atom and it can be written as a pdb file with sasa in the last column. Thanks, hve nice weekend Bala

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solvent accessible area
by Boaz Shaanan 27 Feb '09

27 Feb '09

Hi Bala, The program areaimol in the ccp4 package will do just that (i.e. generate a pdb file with the sasa value in the b-factor column). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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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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