October 2016 - Chimera-users - RBVI Mailing Lists

Assisstance to claculate RMSD value
by Shreyas Iyer 08 Oct '16

08 Oct '16

Respected Sir/Madam, I wanted to know how to calculate RMSD values between any 2 homology models of a protein with the help of USCF Chimera. Please guide me as soon as possible. Awaiting a positive reply. Yours Sincerely, Shreyas Iyer

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fit in map and multimodel pdbs
by Martin Lawrence 07 Oct '16

07 Oct '16

Dear Chimera Users, I have a pdb file for an entire virus (biological assembly) that I can read into Chimera just fine, as either a multimodel PDB with 60 different models, or as a PDB lacking model and endmdl cards, but with the atom number of the multi-model pdb preserved. The model is placed very close to the density for the virus in a tomogram. When I use the fit in map command, the single model pdb moves nicely by a couple of nm and a few degrees into the tomogram density. For the multimodel map I must first use the combine command in the model panel to combine the 60 differernt models, but that then also moves nicely into the density. However, in both cases, when I try to write out the slightly rotated/translated coordinates to a PDB file, I wind up with a semi-corrupted PDB file containing **** in many locations, especially for the last half of the file. Since the virus is pseudo T=31 with 18 chains in the viral asu, the pdb model has more than 2 million atoms and 1048 chains; the chains obviously cannot be uniquely identified with a single letter, the atom numbers exceed the the allowed format, and residues are renumbered and then also exceed the allowed format. I can fix this by hand to some extent, and could write a jiffy to put it back into the multiple model format, but feel like there is a more elegant solution to this problem already embedded in Chimera. Preferably one that will allow high throughput down the road. Any advice would be appreciated! Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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question
by Jaynes, Jesse 06 Oct '16

06 Oct '16

Hi Folks: I am interested in generating a 23 amino acid peptide with several ornithines present. Is it possible? If not can I construct it with glutamine as a replacement for ornithine and then just take the carbonyl group and replace the oxygen with 2 hydrogens. Thank You, Jesse Jaynes

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Split view feature
by Markus Heller 04 Oct '16

04 Oct '16

Hi all, Not sure split view is the proper term for what I'm looking for but here goes: I want to compare to structures of two proteins bound to their respective ligands, and I do NOT want to do this as overlay. What I want is a split screen or split view in the Chimera main window, where one structure is displayed on the left, and the other on the right. Movements (rotation, translation etc.) would be synchronized between both windows, whereas other functionality such as Zone select, find Hbonds etc. would not. Is such a feature available for the current release, or is it planned for ChimeraX? Thanks and Cheers Markus

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Laptop to run Chimera
by Christianson, David T 04 Oct '16

04 Oct '16

Good afternoon, I would like to purchase a laptop for Chimera use, I am open to either an Apple or Windows based computer. Might any of you have a model that you would suggest? Thanks very much for your time, Dave

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comparing maps with different orientations
by Cathy Lawson 03 Oct '16

03 Oct '16

Dear USCF Chimera Team, I’m looking for suggestions on how to go about the following: For the EMDataBank map challenge we have sets of EM maps of the same molecule that have been submitted in different orientations. We’d like to automate production of images for each set of maps with a common orientation/scale so that they can be readily compared. Models fitted to each map are in principle available, so this could be part the process if needed (e.g., to define transformations between map positions/orientations). Many thanks, Cathy ****************** Catherine Lawson, Ph.D. EMDataBank, RCSB PDB Center for Integrative Proteomics Research Rutgers University cathy.lawson(a)rutgers.edu USA +1 (848) 445 5494 http://emdatabank.org

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Chimera-users October 2016