- Chimera-users - RBVI Mailing Lists

Calculation of SASA with probe size of 0.8Å
by Amy Davenport 21 Sep '12

21 Sep '12

Hi all, I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8Å to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. Thank you, Amy Davenport Migliori UCSD

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Estimated RMSD after using Modeller feature
by Claudia Fernandes 21 Sep '12

21 Sep '12

I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function. I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)? As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it. Any help would be welcome. Regards, Cláudia Fernandes

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Modeller-Chimera interface
by James Valdes 21 Sep '12

21 Sep '12

Hello Chimera, I'm using the Modeller interface via Chimera and I was wondering if the models produced takes into account multiple templates (e.g., selecting all) from a multiple alignment produced by MAFFT (http://mafft.cbrc.jp/alignment/software/) I appreciate any insight you may provide. Cheers, James Jason Valdés, Ph.D.

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arrow heads for pipes and planks
by Evan Kantrowitz 20 Sep '12

20 Sep '12

Hi, Probably a dumb question, but I cannot figure out how to show arrow heads on pipes and planks. I found this info Show arrow on helix and Show arrow on strand (both default true) place arrowheads on the C-terminal ends of secondary structure elements to indicate N→C directionality. These are not on the pipes and planks tool. What is the format on the command line to use this commands I tried Show arrow on helix Show arrow on helix true Thanks Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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saving a rotated map
by Filip Van Petegem 20 Sep '12

20 Sep '12

Dear chimera users, I have a problem with saving a cryoEM map after rotating/translating it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 format) This seems to work fine, but when I save the reoriented map (in any of the available formats), and try to open it, it is back to the original position. Is there any way to save the reoriented map file? Best regards, Filip Van Petegem -- Filip Van Petegem, PhD Associate Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpetegem(a)gmail.com http://crg.ubc.ca/VanPetegem/

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solvation box transformed
by Visvaldas K. 20 Sep '12

20 Sep '12

Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis

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Chimera running on a remote computer over ssh >>>> use virtualgl to avoid graphics problems
by Dieter Blaas 19 Sep '12

19 Sep '12

Those who encountered lots of problems with the graphics when running chimera remotely for example you receive error messages like this one: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 might be interested in the following solution: 1) install VirtualGL (http://www.virtualgl.org/) on both PCs 2) outcomment the indicated lines in the 'chimera' startup script 3) connect to the server by using 'vglconnect' 4) start chimera on the server with 'vglrun chimera' that's it! if [ -z "$nogui" ] then case "`uname -s`" in Linux) # preload our C++ runtime to avoid # ATI graphics driver bug # LD_PRELOAD=libotf.so <<<<<<<<< # export LD_PRELOAD <<<<<<<<< if test -e "$CHIMERA/bin/python2.7" then python="$CHIMERA/bin/python2.7" else in those cases where chimera works without this trick you might still see a substancial improvement in transmission speed! Best, 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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Re: [Chimera-users] chimera utility help
by Elaine Meng 17 Sep '12

17 Sep '12

Dear Sotirios, You would use Join Models option "C-N peptide bond" as described in these instructions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> "C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond." If you do not see that option, maybe you have an older version of Chimera and should upgrade to a newer version. If you do see that option and you have followed the instructions as above but are still not able to apply, please save a session file and use menu "Help... Report a Bug" and attach the session file to the bugreport. I just tried it on two example proteins and seemed OK, but maybe there is something different about your structure. Thanks! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 17, 2012, at 9:10 AM, Sotirios Katsamakas wrote: > Dear Elaine C. Meng, > I followed your suggestion and I created a separate side chain of the 25 amino acids with specified phi and psi values for its residues. But I am still not able to Join Models, through the homonymous section. I am selecting the C terminus of the constructed side chain (#0:25@C) and the N terminus of the protein (#1:26@N) respectively, but when I go to the panel the apply button stays inactive. I am sure it must be something obvious but it eludes me. Thank you in advance and I am looking forward in hearing from you. > > Best Regards, > Sotirios Katsamakas.

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Difference between atoms' coordinates on screen and in a PDB file
by Mateusz Dobrychłop 14 Sep '12

14 Sep '12

Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz

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Denaturing a protein
by vamsee 14 Sep '12

14 Sep '12

Hi Elaine, Thanks for the answer for the previous question. I am back with one more :) Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? Thanks again Vamsee

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