- Chimera-users - RBVI Mailing Lists

Add hydrogens to get -NH2 group
by Daniel Svozil 02 Dec '05

02 Dec '05

Hi all, if I use addH tool on the C-N, I would expect to get C-NH2, but I get C-NH3 instead. How should I proceed to get C-NH2 correctly? Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

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Sequence alignment
by David G. Morgan 01 Dec '05

01 Dec '05

Hi, I'm learning to use the sequence alignment tools in chimera. I know that I can highlight sequences in the alignment window and select residues in the structure, but is it possible to do the opposite? In other words, I'd like to box or otherwise select some residue(s) in the structure and have that region highlighted or otherwise marked in the aligned sequence window. David Gene Morgan Advanced Microscopy & Proteomics Molecular & Cellular Biology University of California at Davis 530 752 2693 (lab) 530 752 3085 (FAX)

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Feature Request: Expose rotation to python
by Charlie Moad 29 Nov '05

29 Nov '05

The repr of an xform shows the opengl rotation matrix. I want to get this efficiently in python, but I don't believe it is exposed. Could a getter please be added returning a 4x4 tuple, so a Numeric array can be trivial/efficiently made from it? If there is a current approach please let me know. Thanks, Charlie

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estimaded standard deviation (sigma levels) for electron densities in volume viewer
by Pattanayek, Sabuj 28 Nov '05

28 Nov '05

Hi, Is it possible to specify the estimated standard deviation (sigma level) for electron densities in the volume viewer? Currently, I have to eyeball the distribution of the volume data and place the bar accordingly. Thanks, Sabuj Pattanayek

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Question about connectivity
by Frederick Gimble 22 Nov '05

22 Nov '05

I have just begun using Chimera on my Mac, and find that it will be able to produce the graphics that I need for publication and display purposes. I recently opened a pdb file of a protein that we study bound to DNA and used the depiction, nucleotides tool to render the DNA backbone as ribbons with the bases shown as slabs. I noticed a discontinuity in one of the DNA strands, which may be caused by the severe distortion of the DNA. I think that this also happened with a previous program that I used called SPOCK that I used to draw the DNA strands as worms. In that case I could repair the break by changing the settings for the connectivity distances. How would I repair the break in Chimera? Thanks for your help. Sincerely, Fred Gimble Frederick S. Gimble, Ph. D. Associate Professor Department of Biochemistry BCHM 315 175 S. University St. Purdue University West Lafayette, IN 47906 Telephone: (765) 494-1653 Fax: (765) 494-7897 Email: fgimble(a)purdue.edu

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Chimera failed abnormally
by Johan Börjesson 22 Nov '05

22 Nov '05

Hi I have downloaded the chimera-1.2184-win32.exe version of Chimera and installed it on my laptop running on an Celeron M 370 processor. The operation system is Windows XP. The problem is that I get an error message when I try to run the program. Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message. Hope that you can tell what the problem is and what I can do about it. Best regards Johan Börjesson Dept. of Biochemistry Lund University, Sweden

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Move atoms (selections) in Chimera
by Daniel Svozil 21 Nov '05

21 Nov '05

Hi, is there any possibility, how to move atoms (selections) in Chimera? If, e,g,, I want to make C-H bond a bit longer? move command seems to work only with model. Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

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Selecting Protein portions
by Reiner Villavicencio 20 Nov '05

20 Nov '05

Dear all, I have read a couple of literature which uses the Chimera program. Before performing a docking run, most of them selects only the relevant residues within a certain region (for example in a 20 angstrom core). May I ask how is this done in Chimera? I mean do the "unrelevant" portions get deleted? Thank you and good day - RV "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

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creating cubes and other 3D shapes
by Stephen A. Smith 19 Nov '05

19 Nov '05

Hi I want to create a cube (box; 1Å^3, 2Å^3, etc.) at specific grid points and color them as needed. Is this possible in Chimera? It is easy to do with spheres by specifying an atom at the desired location and then defining its VDW radius. I would like to create cubes and rectangles of various sizes, related to regions of my protein, to denote specific atomic / residue features. Any help would be greatly appreciated. Thanks Steve __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

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Reference Manual
by Reiner Villavicencio 17 Nov '05

17 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? I realized that under the documentation section of the website, that only online references are present. Having an offline user guide would be more convenient because there is no need to go online everytime a problem is encountered. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Sciences and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

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