March 2010 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

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structural similarity measures in Chimera
by Elaine Meng 05 Apr '10

05 Apr '10

Dear Minming, Dr. Ferrin forwarded your question to me. We recently added calculation of structure similarity measures to Chimera. This capability is not in versions 1.4/1.4.1, but only in 1.5 (recent daily builds, which are also available from our download page). In such recent builds, the "Match -> Align" tool (under Tools... Structure Comparison in the menu) calculates two measures that have been described in previous publications, the SDM and the Q- score. The SDM has been used to construct phylogenetic trees before. I don't know if the Q-score has been used that way. Documentation for Match->Align and details of these measures: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > However, there are some issues that may affect whether you decide to use Chimera to calculate these values for your structures: (1) You would need to run Match->Align for each pair. There is no option to do all pairwise comparisons on multiple structures. You would need to script looping through all pairs (with python or shell scripting). (2) There is no Chimera command for Match->Align. Thus Match->Align would also need to be run via python. I don't have scripting expertise, so someone else would have to provide more details if you decide to try this. (3) Before you run Match->Align, the structures need to be superimposed. We purposefully made Match->Align independent of the superposition method. There are several possible ways to superimpose structures in Chimera, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> but probably the easiest in your case would be MatchMaker, which is also available as a Chimera command (matchmaker or mmaker, see that URL and links within). Usually the mmaker defaults work pretty well, for example Chimera commands: open 2mnr open 4enl mmaker #0 #1 (Then you could try running Match->Align interactively. The SDM, Q- score, etc. are reported in the Reply Log, opened with Favorites... Reply Log in the menu.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending Chimera questions to chimera-users(a)cgl.ucsf.edu (I CC'd that list here after removing the details from your original mail) > -------- Original Message -------- > Subject: A question about your software(UCSF Chimera) > Date: Tue, 23 Mar 2010 21:55:06 -0400 > > Dear Dr. Ferrin, > > I am very interested in using your software UCSF Chimera, which have > some > commands that can do the job of aligning and measuring a distance > between two > protein structures. > > I am a PhD student at Purdue University working on the evolution of > protein > structure with Professor Peter Waddell. I was hoping to use your > structure > alignment software to obtain a pairwise structure distance matrix. > This > matrix > will then be used in phylogenetic analyses, comparing the trees and > treeness > of that structural distance compared to that produced by other > published > methods. > [...] > Could you please tell me if your structural alignment software can > easily > produce a complete pairwise distance matrix for a list of ~50 > structures? I did > not see a way to do this. If not, is there any easy way to modify it > to > do this? > [...] > > Best Regards and Sincerely, > Minming Li >

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Daily build requirements
by sherden＠caltech.edu 31 Mar '10

31 Mar '10

So to get thermal ellipsoids to display from a .cif file (as opposed to a .pdb) it looks like I need version 1.50 or greater of Chimera, but it looks like versions of Chimera above 1.4x don't seem to run on my Mac (I have system 10.4.11). What OSX system version do I need so that I can run a version of chimera that I can get thermal ellipsoids to display from a .cif file? Or, conversely is there a way I can get one of the more recent daily builds to run on OSX system 10.4.11? --Nat (Nathaniel Sherden) California Institute of Technology

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Problem in Surface depiction
by Kshatresh Dutta Dubey 31 Mar '10

31 Mar '10

Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey

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Re: [Chimera-users] named selections
by Elaine Meng 30 Mar '10

30 Mar '10

Hi Ajith, We are very happy to hear you will be the "Chimera guy" for your group, and that the tutorials are useful! But sometimes it is hard to find certain things, which is why we have the chimera- users(a)cgl.ucsf.edu list (recommended rather than sending mail to me individually). It sounds like you really want to use aliases rather than named selections. See the "alias" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> and also how to specify particular models, residues, chains, etc: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierar… > For example, to alias residues 10-42 and 55 in chain A and 80-100 in chain B: alias myresidues :10-42.a,55.a,80-100.b color red myresidues These would be the residue numbers in the structure, which are not always the same as in a sequence file. Session files are not friendly/intended for viewing as text. Aliases are saved in sessions, but you would just use the alias command without arguments to list the definitions of the existing aliases. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 30, 2010, at 8:05 PM, Ajith Harish wrote: > Hi Elaine, > I will not bother you with too many questions after this last one > (at least for a while ;-)). There are a lot of features to explore > and I am playing with it and have learnt quite bit today. Also the > tutorials on the website are very helpful. I am soon going to be the > "Chimera Guy" of our group ;-) > > But there was one feature I could not figure out. Is it possible to > name sections without actually selecting the sequence from the GUI. > I need color different parts of large ensembles. Different domains > in multiple chains of a single pdb file. For now I open the sequence > of one chain at a time form the "Tools > sequence > sequence" and > then pick the residues (amino/nucleotide) based on the numbering > from the corresponding Fasta file from PDB and then name it from > "Select > Name Selection". Is it possible to assign names on a FASTA > file? > > I also looked into the session.py file. I could not relate the > numbers corresponding to my names in the session file to the residue > numbers or the residues. It would be great if I could assign names > in a file and then acess the names to color. Even better would be > assign colors to those named selections. > > Thanks much for your help. > Best wishes, > Ajith >

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Matching RGB color code from Adobe Illustrator
by Ajith Harish 30 Mar '10

30 Mar '10

Hello, I would like to color different regions of a molecule corresponding to RGB colors from Adobe Illustrator. Chimera RGB ranges from 0.000 to 1.000 where as the Illustrator RGB ranges from 0 to 255. Could you please let me know how these two scales are related? Thank you very much, Ajith

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Trouble with thermal ellipsoids
by sherden＠caltech.edu 30 Mar '10

30 Mar '10

I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes. Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations. --Nat (Nathaniel Sherden) California Institute of Technology Department of Chemistry

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RMSD
by Beale, John 29 Mar '10

29 Mar '10

What is the best way to use Chimera to compute the RMSd value of an MD trajectory snapshot relative to the crystal structure of the protein? Thanks! John M. Beale, Jr., Ph,D. Professor of Medicinal Chemistry and Pharmacognosy St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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zones and residue name/number
by Francesco Pietra 29 Mar '10

29 Mar '10

Hi: I was trying to detect all residues (or atoms) within a given distance from a single-atom ligand in model #0 (PDB file). There are several such single-atom ligand atoms in model #0 (practically invisible in chimera as they are not shown at their relative vdw size), each specified by different residue and atom numbers. I want to carry out the task for each single-atom residue. Therefore I can't use the standard command select #0:single-atom-ligand z(or za)<given.distance because that applies to all those single-atom-ligands. Unless the residue can be specified differently (the residue number in place of residue name did not work), the only way that I found to come out was to set different names for the different single-atom ligands. Is anything better? Secondary question: is there any plan to support psf/dcd format (which I am now using for MD with namd) beyond reading movies? Thanks francesco pietra

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