- Chimera-users - RBVI Mailing Lists

Choose a specific rotamer
by Elisabeth Ortega 11 Feb '11

11 Feb '11

Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth Universitat Autònoma de Barcelona (Spain)

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zone
by Jean-Paul Armache 10 Feb '11

10 Feb '11

hello, there is a zone function for density maps+pdbs, which zones the map around the pdb in a certain radius. is it somehow feasible in chimera to do such thing with two pdbs ? what i mean is to zone a molecular model around another molecular model? (the reason for that is the speed, in which elaborate models are shown, sometimes zoning would be very useful for fast-checking). would be grateful for your help, best regards, jean-paul

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Showing actual electrostatic potential on surface
by Boaz Shaanan 10 Feb '11

10 Feb '11

Hi, Is there a way to show the actual potential value of a point on the electrostatic surface, say by pointing at it with the cursor, in an analogous way to the atom names that show up that way? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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3D with Nvideo
by Larry Simpson 09 Feb '11

09 Feb '11

I have a problem getting 3D with Chimera using a Quadro 600 video board on a Win7 64 computer. I am not sure what settings are required. Screen grabs are attached which show my current settings. Any assistance would be greatly appreciated. Larry

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Molecular weight of an EM map
by Tom Goddard 08 Feb '11

08 Feb '11

Hi Pu, Use the "Measure Volume and Area" dialog under menu Tools / Volume Data to show the volume in cubic Angstroms enclosed by your map contour surface. It will update automatically as the threshold changes. Make sure the voxel size of your map is set correctly in Angstroms because the reported enclosed volume uses that. That is set in the Volume Viewer dialog under the Coordinates panel. To estimate molecular weight from the volume you could use an approximate value for globular proteins from the literature of 1.21 cubic Angstroms per Dalton (Harpaz 1994). http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… Tom > Hi Tom, > > I have a question to ask you. > > I'm working on a 3D EM map from single particle reconstuction using Chimera. I > would like to know the total volumn of this 3D model or its molecular weight > when I change thresholds. How can I do it or where can I find this value? > > Best regards > > > Pu Qian

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Unrecognized command: "source"
by Pam Wang 08 Feb '11

08 Feb '11

Hi, I've just downloaded your program and was trying to run some alignments between two peptides. However, whenever I type in the command "source", I keep seeing the following error message: unrecognized command: "source" Could you please help me? I am able to run all the other commands, I just don't know why "source" is not recognized. Thank you, Pam Wang

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Script for positioning particles according the coordinates.
by Alexander MYASNIKOV 08 Feb '11

08 Feb '11

Dear colleagues, I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on? Thank you in advance, Alexander

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findclash "batch" calculations
by Elaine Meng 07 Feb '11

07 Feb '11

On Feb 4, 2011, at 2:51 AM, Julien wrote: > Hi Elaine, > I would like to find clashes between a ligand and a protein. I have around 100 000 poses of this ligands. > The information to get the poses are at the moment saved in a pdb file. Indeed three pseudo atoms are used to place the ligand in the correct position using the command match. > > The workflow would be the followin: > open ligand > open protein > open pseudo.pdb > > match ligand position1 > findclash > match ligand position2 > ... > > First, this is very slow, even in batch mode. Maybe you know a better way to do that. > Second chimera does not open more than 9999 residues, the pseudo pdb have nearly 100 000 residues. Is there a way to get around that. > > I guess the routine findclash calculates all distances brutally and compare them to a threshold. > many greetings > Julien Hi Julien, Findclash does calculate distances between atom centers, but the cutoff parameter is compared to "overlap" between the VDW spheres -- in other words, smaller atoms must be closer together than larger atoms to be considered overlapping or clashing. The output information (optional) includes both the center-center distances and the overlaps, however. You can limit the calculation to only certain atoms. There are also options to control cutoff and other settings. Details are here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> If you are really just using "findclash" without arguments, that would look at the whole structure and take more time than necessary. For example, if your ligand is model #0 and the protein model #1, one way to limit the calculation to only clashes between them and send info to the Reply Log is: findclash #0 test #1 log true Otherwise, I'm not an expert on any large-scale calculations or how you might optimize the procedure for large sets of atoms, so I'm CC-ing this question to the chimera-users list. (It is generally better to send Chimera questions to this list rather than to me personally.) The other users or developers may have good ideas. 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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Fixing registration for older versions of Chimera
by Eric Pettersen 07 Feb '11

07 Feb '11

Hi everyone, About 10 days ago I sent mail about upgrading to 1.5.2 to fix Chimera registration problems and promised a fix for older versions soon. That fix is now available from this page: http://www.cgl.ucsf.edu/chimera/fixreg/ It involves running a script on that page or, for the slightly paranoid cautious among us, downloading two files and putting them in your Chimera distribution manually. Thanks for your patience. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Rotamers
by Angelica Nakagawa Lima 03 Feb '11

03 Feb '11

Hi I can get the rotamers if I use the graphical version (when I click in tools -> Structure Editing -> rotamers). But I would like to do same thing with the comands. I used the comand swapaa (swapaa ile :10.a) and I write the pdb with the ile's rotamer (the most probable), however I would like to write the pdb file with the second most probable rotamer too. How do I do this? Thanks Angelica

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