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problem with new Chimera 1.4 and 1.4.1 OSX Aqua
by Miriam Gochin 10 Apr '10

10 Apr '10

Dear Chimera team, I am not sure what I am doing wrong, but the new version does not open correctly on my Mac (OS-X-10.6.2). I get a small black square surrounded by white space that will not enlarge. Is there some setting I should adjust? Best wishes, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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[Re: Residue exposition cutoff]
by Yasser Almeida Hernández 07 Apr '10

07 Apr '10

Thanks for your answer... About this i have an idea resumed in two question: In principle an solvent-exposed residue must have in average high value of b-factor, so will be very flexible. 1 - Can i say that those residues that have and average b-factor up to a cutoff value AND an areaSAS (or % of that area) superior than a other cutoff value, will be exposed to the solvent??? 2 - There is a cutoff value of b-factor for the residues flexibility? Best regards -------- Forwarded Message -------- From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-to: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Residue exposition cutoff Date: Mon, 5 Apr 2010 11:22:37 -0500 Hi Yasser, Actually you don't have to use DMS ... if you show a surface in Chimera it also automatically computes the SES (solvent-excluded surface) and SAS area per atom and per residue, attributes named areaSES and areaSAS. For more details, see these previous posts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html > Some notes about areaSES and areaSAS: (1) if you don't want to include inside bubbles in the surface area calculations, after creating the surface(s) remove the inside bubbles with the command: setattr s allComponents false (2) the surface that Chimera displays is the SES (also known as Connolly surface or molecular surface), not the SAS, although both sets of areas are calculated Actually Tom Goddard mentioned the areaSAS attribute briefly in an earlier reply to you: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/003995.html> As to what cutoff should be used for classifying atoms or residues as buried or exposed, I'm not aware of any commonly used value. It is a more philosophical issue that depends on your ultimate purpose. You might try coloring by different cutoffs to try to decide what is appropriate for your research (keeping in mind that the SES is what Chimera actually displays), or read publications of similar work to see what other researchers have used. In publications, I have seen residues classified by "fraction" or % of the surface area of a residue in the structure divided by the area of that same type of residue in a hypothetical fully exposed state, but I don't remember the exact cutoffs used, and Chimera does not provide the fully exposed values. An example of a program that does provide such values is GetArea: <http://curie.utmb.edu/getarea.html> 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 Apr 3, 2010, at 1:38 PM, Yasser Almeida Hernández wrote: > Hi all.... > I have 2 question, beyond Chimera's issues. > > 1 - There is some cutoff value to consider a residue or more > strictly, an atom exposed to the solvent?. > > 2 - Could i set a this cutoff using the area values and types (SR0, > SC0 and SS0) from the DMS program output? > > 3 - Wich program you recommend to compute SAS? > > Thanks, > best regards ----- Terminar mensaje reenviado ----- -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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amino acid clashes
by Kirys, Tatsiana 06 Apr '10

06 Apr '10

Dear All, i'm trying to figure out scheme for calculating protein amino acid clashes. I've read in User's Guide that 1) The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs: overlapij = rVDWi + rVDWj dij allowanceij 2) It has an option: Ignore contacts of pairs [ N ] or fewer bonds apart (N=4 by default). i calculated rotamer clashes from "Penultimate rotamer library" according to 1) and there are clashes between N ans C N and CB N and CG CA and CG CA and OD1 etc. i'm sure i do something wrong because "Penultimate rotamer library" was checked for the clashes. I dont understand why 2) option exists, what is the physical meaning of it? and why N can be cosed arbitrary? many thanks Tania

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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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Residue exposition cutoff
by Yasser Almeida Hernández 05 Apr '10

05 Apr '10

Hi all.... I have 2 question, beyond Chimera's issues. 1 - There is some cutoff value to consider a residue or more strictly, an atom exposed to the solvent?. 2 - Could i set a this cutoff using the area values and types (SR0, SC0 and SS0) from the DMS program output? 3 - Wich program you recommend to compute SAS? Thanks, best regards -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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Possible bug in Chimera RMSD calculation
by Yasser Almeida Hernández 03 Apr '10

03 Apr '10

Hi all.... In Chimera , i selected a single pair of atoms for RMSD calculation with the command rms (rms #1:221.A@NE #0:221.A@NE) and it return the distance between the atoms ???? It would be a bug??? Please check this.... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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Coloring model represented as PipesAndPlanks
by Ibrahim Moustafa 01 Apr '10

01 Apr '10

Dear Chimera team, I have a problem with coloring different regions of the protein presented as PipesAndPlanks. I know I can change the colors of the SS elements from the menu of PipesAndPlanks. But, this is not what I want: I want to color different regions of the protein with different colors and not to be limited with the colors given to the SS. Before, I had no problem in doing so. I think this problem appeared in the recent updates. Something I noticed and could be related is that to change the presentation from the default chimera to PipesAndPlanks the new presentation assigned the same model# as the original model. I think, in previous versions the new presentation used to be given a new model#. Similarly, if I want to create a map for the model using (molmap) it is given the same model # rather than a new model# as used to be. I run Chimera version 1.4.1 (build 30282) on a Mac OSX 10.4 (PPC). Thanks for help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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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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