June 2014 - Chimera-users - RBVI Mailing Lists

rename a residue?
by Julian Tirado-Rives 18 Jun '14

18 Jun '14

Dear Chimera team, thanks for all the work you put in into a very, very, useful program. I just have a question that I am hoping is just my inability to find the proper command ... is there a way to rename a residue before writing a PDB? I often use chimera as pre-preparation step before getting into some particular calculation packages, which often require different names for residues to indicate tautomers, protonation, etc. and it would be nice to do it from chimera rather than take the PDB's through a rather annoying set of scripts, sed's, or even text editors! Thanks in advance, - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Attaching a Probe to Modify an Existing Amino Acid
by Shana Burstein 18 Jun '14

18 Jun '14

Hello, I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? Sincerely, Shana Burstein Haverford College '15

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delete atoms based on their coordinates
by Aranha, Michelle 18 Jun '14

18 Jun '14

Hi , I wanted to know if there is a way in chimera to select and delete atom/atoms based on their position/coordinates in the simulation box. For example delete water 150 at (x, y, z). I tried zone sel, but I couldnt get it to work. Regards, Michelle ?

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com files & animation
by Dougherty, Matthew T 16 Jun '14

16 Jun '14

When executing a com file for animation production, I would like to see the line that is being executed display in the reply log. Is there a way to do that? I would prefer not using echo commands because of the large number of lines in the file being executed. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Chimera Plugins
by Eric Bell 16 Jun '14

16 Jun '14

Hello, Does a list exist somewhere of plugins developed for Chimera, or would we need to find them posted separately on a host site? Also, I found recently a software that gives preset .stl mesh resolutions for all atoms of the same element so that when they are 3d-printed, the atoms can all be distinguished from one another: http://cad4.cpac.washington.edu/WinXMorphHome/Cif2VRMLHome/Cif2VRML.htm However, the rest of the software seems lacking in reference to chimera's capabilities, is there any way that Chimera could have a similar feature? Ideally it would allow the "subdivisions" property of the viewing effects apply to every element, similar to how radius applies to all atoms of the same element. Thanks, Eric

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Adding residue to two sides of DNA
by Mehdi Bagherpour 16 Jun '14

16 Jun '14

Dear Chimera Users, I want to add 3 base-pairs to two side of DNA. I tried more about that but I couldn't. Could some one any idea about doing that in chimera or another programs. Best Regards, Mahdi

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QUESTION
by Eifler, Jay Q. (UMKC-Student) 16 Jun '14

16 Jun '14

Wanting to know if we can use charges assigned by define attribute in a file for the purpose of adding ions. Seems like the Add Ions feature will not do this and will only use the built in methods Gasteigter, etc. I have a HYP residue that the Add Charge feature won't do.

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About direct fetching biological assemblies into Chimera
by Boaz Shaanan 16 Jun '14

16 Jun '14

Hi Tom, This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think? Cheers, Boaz Message: 6 Date: Mon, 2 Jun 2014 16:53:06 -0700 From: Tom Goddard <goddard(a)sonic.net> To: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Fetch biological unit? Message-ID: <0086EC78-81D4-4892-9A22-A4177426F74D(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Darrell, I added a Chimera Fetch dialog entry ?PDB biounit? that will fetch all the biological assembly files for a pdb id ? there can be more than one. Also they can be fetched using the Chimera command: open pdbbuID:2bbv Will be in tonight?s daily build. Tom Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Color by RMSD for multi-chain structure?
by Oliver Clarke 13 Jun '14

13 Jun '14

Hi all, Is there an easy way to color two superimposed structures by RMSD (per C-alpha pair)? I had a quick look through the manual and the mailing list and I couldn’t find any easy way to do so for a structure that consists of more than one chain. I think this would be a very useful addition to either render by attribute or the calculation of a morph (because presumably the paired CA-CA distances are already calculated in the process of generating the morph). I have aligned based on one chain in a complex, and would like to color the entire complex by RMSD (to highlight the parts that move the most between two states of the same complex). I can calculate the per CA RMSD using “rmsd #1 #2”, but I can’t see any obvious way to assign that to a residue attribute using the attribute calculator or setattr etc. Many thanks, Oliver.

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easy way to make alignments in chimera
by Michał Kadlof 13 Jun '14

13 Jun '14

Hello, I would like to ask if there is any quick way to make aligment (with secondary structure score included) beetwen two homologous protein structures, and save them in Stockholm format (information about missing residues is needed). I have houndreds of such pairs, and it would be very helpfull to do it by script for headless Chimera. -- yours sincerely Michael Kadlof University of Warsaw

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Chimera-users June 2014