- Chimera-users - RBVI Mailing Lists

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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new Chimera snapshot release
by Eric Pettersen 19 Oct '04

19 Oct '04

Hi all, A new Chimera snapshot release (version 1.2029) is now available for download. I've summarized the major changes since the last release (1.1951) below. A list of _all_ the changes since the last release is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2029.html Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu General changes --------------- The "web fetch" part of the "File...Open" dialog has been split off into its own "Fetch by ID" dialog. The Fetch dialog now supports fetching NDB IDs. Labels are now offset in the viewing coordinate system (rather than the model coordinate system), making them much less likely to be obscured. Moved C3' off of ribbon backbone so that the sugar ring isn't distorted. New Tools --------- Nucleotides (Graphics): create various nucleotide-specific depictions, such as stylized representations of base pairings or filled sugar rings Define Attribute (Utilities, Programming): assign values to new or existing attributes of atoms, residues, or models. Particularly useful in conjunction with the Render by Attribute tool. Tool Changes ------------ AddH improved to avoid steric clashes (and appears in model panel) Match -> Align can handle circular permutations in multiple alignments [formerly only in pairwise] Movie can read PSF/DCD files from CHARMM, NAMD, and X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame) Multalign Viewer can save a subset of an alignment to a file Multiscale Models includes the zone-selection options Near and Contacts PipesAndPlanks now connects the secondary structure elements with loops Web Data preference category renamed to Web Access and includes HTTP proxy options Render by Attribute implements Radii section (atom radius scales with attribute value) and Worms section ("worm" ribbon radius scales with attribute value) Ribbon Style Editor scalings are now treated similarly to cross sections (per-residue, no startup default except in New Molecules preferences); new "residue class" tab allows specification of which atoms should guide the ribbon, this generalizing ribbons to polymers other than standard peptides and nucleic acids ViewDock includes new interface for choosing compounds by descriptor values New Commands ------------ addaa: add amino acids to the C-terminus of a peptide/protein addh: add hydrogens (command implementation of AddH) bond/~bond: create and delete bonds chirality: report the R/S configuration of a chiral center (see User's Guide for caveats) defattr: define a new attribute and/or assign attribute values (command implementation of Define Attribute) rangecolor: color over a range according to attribute values rmsd: evaluate the RMSD between specified sets of atoms (without matching) Command Changes --------------- atom specification operators added for union (|) and negation (~) [previously just intersection (&) and operators for combining attributes] hbonds has "tilde version" (~hbonds) which removes the pseudobonds showing hydrogen bonds labelopt info has "res" or "residue" keyword indicating that only residue name and number should be shown (not atom name) rainbow can color by model (previously only by residue or chain); likewise for Rainbow tool select has "up" or "down" arguments which behave like up-arrow and down-arrow to broaden and narrow a pre-existing selection

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