November 2014 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 26 Nov '14

26 Nov '14

On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > To, > Elaine Meng, > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > Debasish Banerjee Dear Debasish Banerjee, Not sure I understand your question. UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera. Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)? We haven’t heard reports of a problem. For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera. Of course, you have to be connected to the internet. Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Adding sugars to protein at specific amino acid glycosylation site
by T T 25 Nov '14

25 Nov '14

Dear Mr/Ms, Good morning. My name is Tommy from San Diego Biomedical Research Institute. I am currently learning to use the chimera software. Great work in creating a program for protein and DNA visualization. I have one question to ask regarding the subject above. Is there a way to manually add sugar component onto an existing pdb file? To be precise, I am currently working with HIV-1 envelope. I have the pdb files that features the structure of HIV-1 trimer Env. I wanted to add glycan at specific sites to show steric hindrance to antibody binding. Another question. Is there a way to superimpose 2 pdb files into one image? For example, I have one pdb file for HIV-1 Env and another pdb file for antibody. Can I "merge" these two pdb files as one image? Also, assuming that it is possible to "merge" two different pdb into one image, is there a way to rotate one protein without affect the orientation of the other protein? Any advice/tip is greatly appreciated. Thank you. Sincerely, Tommy

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ribbon options disappeared after upgrade
by Bala subramanian 25 Nov '14

25 Nov '14

Hi, Within the ribbon option under action tool: i used to have additional choices like aitch,wave, octave, etc etc. After an ubuntu upgrade, with chimera 1.9 and 1.10 (i tried both). These extra options dont appear under ribbon. What is going wrong ?. Do i need to install something ? Bala -- C. Balasubramanian

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PDB Header via command line?
by Korbin West 20 Nov '14

20 Nov '14

Hi, I'm trying to find missing atoms in certain residues. I know they are in the pdb header information, but is there a way I can use Chimera or python script to access this using the command line only? I have a large number of proteins to go through, so checking them all individually is not really efficient. Korbin West

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Split chimera screen
by Ibai Irastorza 19 Nov '14

19 Nov '14

Hello, I want to show 2 structures in chimera. I want them to be in different chimera sessions, but then, I want them to be dependant, so when I move one structure, the other structure also moves accordingly. For that matter, I would also like both structures to be in the "same perspective". How could I do that? Thanks a lot and long live chimera! Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…

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Reading Chimera source ...?
by Boris Steipe 17 Nov '14

17 Nov '14

Hi - I'm new to writing Chimera code; I've started poking around in the sample scripts and the modules but and I find it a bit slow to find my way around. For example I would like to perform some simple calculations on the coordinates of a set of selected atoms, and I see many functions that take a "sel" argument, but I can't seem to find documentation on exactly what that argument is expected to contain, or the function that would return such a selection list (is it even a list) of objects. I'm sure if I spend more time, through trial and error and dir() and grep, I'll eventually figure it out, but I wonder if there isn't a more principled approach - a document on the big picture of how the code is structured, and/or a searchable list of all functions? What's the best strategy to start reading and coding Chimera scripts? Thanks! Boris

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aligning molecules
by Elaine Meng 15 Nov '14

15 Nov '14

On Nov 14, 2014, at 7:45 PM, Bhaskar Bagchi <bhaskarbagchi(a)gmail.com> wrote: > Respected Sir > I want to align ligands after docking study. Is it possible in chimera? Please help me. > Thanking you Yours faithfully, > Bhaskar Bagchi > Cheminformatics, Bioinformatics Lab Department of Chemistry, Raiganj College Dear Bhaskar Bagchi, I may not understand your question very well, because if you align the molecules they would no longer be in their docked positions. However, there are several ways to align molecules in Chimera. If non-protein, you would probably want to use the “match” command, but this also requires specifying the atoms to use, in the right order, if the two molecules don’t have all the same atom names. See documentation for ways to align, and the “match” command specifically: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html See also related command “rmsd” and the “ViewDock” tool for looking at docking results. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) rather than to my individual address. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Can 'readstdin' capture stderr output?
by Mungo Carstairs 14 Nov '14

14 Nov '14

Hello, I am working on ?driving Chimera from Jalview using the stdin/stdout mechanism (expecting to migrate to REST in future). I have a case where a 'match' command fails, but the stdout response does not show this. Using the Chimera command line I can see a message (I guess to stderr) 'Unequal numbers of atoms chosen for evaluation' but in stdout I just see the same message as for a successful match e.g.: 'Executing match ['#1:1-69.B,96.B@CA', '#0:1-69.A,96.A@CA'], no iteration' Is there a way to detect that the match has failed and/or capture the stderr output? Thanks, Mungo Carstairs http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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Detection of sterical clashes within selection
by James Starlight 13 Nov '14

13 Nov '14

Dear Chimera users! This timeI'm writing of some automatic script aimed on the embedding of the receptors into the membrane consisted of the pre-equilibrated lipids as well as hole for the protein. The main issue that some of the receptors consist of the bulky PHE or TRP side chains on their surface which are overlap with the lipids atoms. As the result subsequent MD simulation of these systems is crushed although of long minimization stage prior to it. I'll be very thankful if someone provide me with some Chimera's command for automatic detection of these steric clashes (overlapped atoms) for a given selection (e.g protein and lipids) based on which I'll be able to write automatic python script. Thanks for help, James

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Morph conformations feature request
by Oliver Clarke 11 Nov '14

11 Nov '14

Greetings, I like the “Morph Conformations” tool in chimera, and use it a lot (as well as the equivalent tool for maps). In particular, I will often record a movie with the “encode forward then back” option selected, as I find this gives a much better looping animation that is easier to interpret. When playing the movie from within chimera (In the “MD Movie: Molecular Movement of Morph” dialog”), however, this option is not available - one can loop the animation, but it just jumps back to the start after completion, which can look rather jerky and disjointed, rather than playing forward then back, which I find gives a smoother animation that is better for analyzing the meaning of any conformational change. Would it be possible to add an alternative checkbox, next to “Loop”, to make this option available? Best, Oliver.

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Chimera-users November 2014