- Chimera-users - RBVI Mailing Lists

Labeling Residues
by Stephen P. Molnar, Ph.D. 01 Dec '04

01 Dec '04

I have to admit to being completly flumoxed [sic] by this one! How do I label an individual residue: According to help the format is: wt %(1-letter code)s%(number)s Now I have an enzyme, 1QTI.pdb in which I wish to label the SER200 label. I have tried every combination of the example on the help page that I can think of without success. What is the exact format for creating that label? Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry

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netCDF trajectories?
by John R. Frank 24 Nov '04

24 Nov '04

Tom and other users, Based on this posting, I deduce that Chimera's Movie capability cannot yet display netCDF trajectories: http://www.cgl.ucsf.edu/pipermail/chimera-users/2004-June/000171.html MMTK generates netCDF trajectories. Can you recommend any already-built tools for converting them to multi-model PDBs? Or, perhaps you can direct me to the parts of Chimera where I could help add netCDF trajectory support? John -- ___________________________ John R. Frank <jrf(a)mit.edu> Physics Graduate Student mobile: 857-928-0614

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Re: [Chimera-users] Select Function
by Elaine Meng 23 Nov '04

23 Nov '04

Dear Dr. Molnar, All chains present in structures open in Chimera should be listed. If two chains have the same ID, however, they will not have separate listings in Select/Chain. Another thing that might be confusing is that residues can be assigned to chains named "het" or "water": Any HETATM residue that does not already have a chain identifier is assigned to chain HET, unless the residue is named WAT or HOH, in which case it is assigned to chain WATER. Additional possibilities are a bug or something strange with the input files. If you have some input files that demonstrate the problem (and don't mind sharing them), you could send them to me or to chimera-bugs(a)cgl.ucsf.edu along with a short explanation of how to duplicate the problem (how files were opened, what order). Best, Elaine ------------- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Select Function
by Stephen P. Molnar, Ph.D. 23 Nov '04

23 Nov '04

I want to load two files, one for the protein and the other for the ligand. This is, of course, not a problem. The question is how do I get both files to be present as choices in Select/Chain? Some times both of them are there, but at other times only the first one that I loade. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry

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Chimera / APBS
by Thomas Goddard 23 Nov '04

23 Nov '04

Hi Miguel, Eric Pettersen passed to me your question about Chimera reading APBS electrostatic potential maps. It looks easy to add -- probably only take me a couple hours if it is the OpenDX file format described in the APBS documentation. Could you provide me an small example file? I'll be on vacation this week starting this afternoon but I can probably do it early next week and send you the Python code for use in your current version of Chimera. Tom

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orientation matrix
by Miguel Ortiz Lombardía 18 Nov '04

18 Nov '04

Hi all, Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation. Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish? Thank you! Miguel -- University of York Structural Biology Lab email: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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orientation matrix
by Miguel Ortiz Lombardía 31 Oct '04

31 Oct '04

Hi all, Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation. Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish? Thank you! Miguel -- University of York Structural Biology Lab email: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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Chimera production release
by Eric Pettersen 20 Oct '04

20 Oct '04

We have now made a production release, version 1.2038, that corrects a few problems in the 1.2029 snapshot and adds a tiny number of new features. The salient new features that weren't in the 1.2029 snapshot are: Actions...Label now allows much more flexible labeling of residues Per-Model Clipping now allows a model's clip plane to be aligned with the clip plane of another model, and allows a clip plane to be flipped 180 degrees. The 1.2029 bug fixes are explicitly listed in the 1.2038 release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2038.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [Chimera-users] Specifying residue color of residues with a text file
by Elaine Meng 20 Oct '04

20 Oct '04

Hi David, You can specify residues and corresponding R,G,B values using Define Attribute, which is included in our newer releases (snapshot 1.2029 and production release 1.2038, of which I recommend the latter). Basically, this tool reads a file that specifies the residues and the associated values. The manual page for Define Attribute can be viewed at: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… including three examples near the end: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… There are two general approaches you may want to consider: (1) the direct approach that you described. Just reassign R,G,B values to the existing attribute of atom color and/or residue ribbonColor. This is most like the third example, except that you would use residue specifications by number (e.g., :12.A) instead of name, and the color specifications would be in the form of R G B (e.g., 1.0 0.2 1.0) instead of color names. (2) a less direct approach but one that provides more flexibility in how you show the data. Create your own new attribute (as in the first example). Then, you can use Render by Attribute (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html) to show these values with colors, atom radii, and/or "worm" radii. The data will show as a histogram, and the mapping to colors and radii can be controlled with markers you place on the histogram. This may be a lot to digest, so please feel free to contact us with any further questions/issues. Thanks, Elaine ------------------- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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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[Chimera-users] Specifying residue color of residues with a text file
by David Piper 20 Oct '04

20 Oct '04

Chimera, Is it possible to provide a color input file that would include a residue number and an [R,G,B] value to color each residue in a structure? Or does one simply have to select each residue seperately within the program and specify an [R,G,B] value? For example, I would like to map some experimentally measured, functional data onto a model structure by coding it into a color. Would be much easier to use a lookup table of values than click and set each one. Thanks, David

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