January 2013 - Chimera-users - RBVI Mailing Lists

Chimera 1.7 release candidate
by Elaine Meng 23 Jan '13

23 Jan '13

Hello, A Chimera production release candidate (version 1.7) is available; please try it and report any problems: <http://www.cgl.ucsf.edu/chimera/download.html> New features include faster loading and graphics, improvements in lighting and interactive shadows, "click-to-center" mouse mode, map display as orthogonal planes, interface to Modeller for building missing loops, Animation timeline, enhanced commands for animation, and interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. See the release notes for details: <http://www.cgl.ucsf.edu/chimera/1.7/docs/relnotes/1.7.html> Mac PowerPC and OS X 10.5 are no longer supported. 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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periodic shift of data in a Cryo EM map
by Benjamin SCHWARZ 23 Jan '13

23 Jan '13

Hi list, Sorry for the inaccurate vocabulary, I am not really from the field. I'll try to be as descriptive as I can. My problem is that I have a cryo EM map of a protein complex with the information somehow "shifted" in the "outline box". It looks like the center of my complex was placed on one corner of the outline box, and that the whole complex is thus spread over the 8 corners of the box… All the information is thus present in the map but should be periodically translated in order to place the center of my complex in the center of the box. I can think of two ways to solve my problem, and for both I need your help : 1. how to shift periodically the content of a map ? 2. how to create a new (and bigger) map by repeating and translating one map in the 9 surrounding directions ? Thanks in avance --Ben

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selection using mouse
by francesco oteri 22 Jan '13

22 Jan '13

Dear Chimera's users, I downloaded and installed version 1.7 build 38047 and I noticed that is no longer possible to select atoms through mouse. Previously, I used the 1.6 and it was still possible using mouse for selecting atoms. I am wondering whether this function has been removed or I miss something? Francesci

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(no subject)
by Jean-Francois Menetret 18 Jan '13

18 Jan '13

Hi, I am trying to restore sessions I saved about 4 months ago but I keep getting the following message: python2.7: ../../nouveau/nouveau_pushbuf.c:274: nouveau_pushbuf_flush: Assertion `0' failed. Aborted (core dumped) PS: I am currently using chimera version 1.7 (build 38083) J-F

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colour with coulombic potential
by giulia zanetti 18 Jan '13

18 Jan '13

Hi all, I am trying to colour with coulombing potential only a portion of the surface I generated, and show it together with the rest of the surface, coloured in grey. The way I've done it is to create a duplicate of the pdb model, generate surface1 from the full model, and surface2 from the selected area, and colour with coulombic potential only surface2. The issue is that sometimes surface1 is "in front" of surface2, and the only way to see surface2 is to hide surface1. This is not related to the order I create the surfaces apparently, but rather to the order I created the models. Is there a way to "bring to front" or " send to back" surfaces or models for display purposes, rather than copying models (and re-doing the selection for the residues that I want coloured?). Or a way to colour with potential only the selected area of a surface? Thanks! Giulia

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Re: [Chimera-users] Homology Modeling
by Elaine Meng 17 Jan '13

17 Jan '13

Hi CE, Different or missing chain IDs are not a problem, unless they somehow cause your specification to indicate different numbers of atoms in the two structures. The example command I gave in the previous message had one structure with chain A and the other with no chain ID. Different residue numbering is also not a problem, because you enter the numbers yourself in the match command. > match #1:482-513.A@ca #0:212-243@ca However, a structure without chain IDs could cause a problem if it contains multiple chains and thus more than one residue with the same residue number. Other common reasons for an error message like this: (a) the specification syntax is simply wrong (b) one structure has "alternate locations" (for example, 2fma residue 170.A) and thus multiple instances of the same atom/residue/chain name. If I run into this, I usually delete the alternate locations (e.g. command "delete @.b" would delete all alternate locations B) and try again. You can see how many atoms each specification generates with commands like: select #1:482-513.A@ca select #0:212-243@ca It is impossible to guess without having the actual structure and seeing the exact command that you used, sorry. However, if you think it is related to chain ID, that can be changed using "Change Chain IDs" (in menu under Tools... Structure Editing) or command "changechain" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.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 Jan 17, 2013, at 2:26 PM, Chinaza Egbuta wrote: > Hi Elaine, > > Thank you for your prompt response. Yes, the question is actually about 3D superposition. I used the match command following the atom specification syntax described in <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>. However, I have been getting the following error message "Unequal number of atoms chosen for evaluation". > > The two models I am comparing both have the same model number but the chains are different (one is "chain A" and the other is "principal chain"). This could be because the actual homology modeling was performed on the MOE platform (chemical computing) and the chain numbers are assigned differently. Please could you let me know if I the error message is as a result of this nomenclature? If yes, please could you provide me with information on how to change the chain number? > > Thank you! > > CE

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copy file command
by Rachel Kramer Green 17 Jan '13

17 Jan '13

Hi, I am trying to save an image using the cmd line in Chimera. The command that I am using is: copy file testimage.jpg jpeg width 500 height 500 It looks like it is working. The bottom bar of the display screen says "rendering high resolution image" and then "Finished saving image(s)." However, then I cannot find a created file anywhere. Any idea what is happening to the saved file? Thanks! -- ------------------------------------------------------------------------ Rachel Kramer Green, Ph.D. RCSB PDB kramer(a)rcsb.rutgers.edu

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Re: [Chimera-users] Homology Modeling
by Chinaza Egbuta 17 Jan '13

17 Jan '13

I have a protein with multiple modules that are homologous to each other. I have generated a homology model of one module based on the structure of another. However, I need to align a specific peptide that is identical between my two modules. Is there a way to do this? Thank you. CE

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Structure minimization
by Bobo Dang 15 Jan '13

15 Jan '13

Hey All, I am trying to use Chimera to minimize a small protein with a special structure, the model has nonstandard amino acid, Also the N-terminal is connected to cyclized to one Asp side chain, is it possible to minimize this modified structure by Chimera? Thanks bobo

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Ubuntu 12.10 and Chimera update #1
by Greg Couch 15 Jan '13

15 Jan '13

Ubuntu 12.10 is still buggy, but I have found a workaround to get Chimera to work if you have AMD/ATI or NVIDIA graphics. If you change the desktop environment from the default Ubuntu environment to another, e.g., Xfce, then Chimera will work. Do do that, first install xfce4: sudo apt-get install xfce4 Then logout, and you will see an circular icon to the right of your login name. Click on that icon and choose "Xfce session" and OK. Then type in your password and you'll get the Xfce desktop environment (don't use a single panel unless you know what you're doing). And then Chimera will work as before from the desktop or the command line. There are other possible desktop environments and it appears that the ones that have a compositing window manager, e.g., kde plasma, don't work. If you are using a different desktop environment in Ubuntu 12.10 that works, please tell me about it. HTH, Greg

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Chimera-users January 2013