December 2010 - Chimera-users - RBVI Mailing Lists

center of rotation
by Bill Montfort 30 Dec '10

30 Dec '10

I'm returning to chimera after many years away and am quite impressed with the program, save for one issue: rotating about the screen center. My favorite way of viewing structures is for the rotation to be about a center of my choosing, as is common in many graphics programs (e.g. COOT). I would prefer to pick an atom on the screen and have this become the rotation center. Is there a simple way to accomplish this in chimera? A small point perhaps, but one that is frustrating for me....... Bill Montfort

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Quiero ser tu amigo en Quepasa.com
by Sergio Garay 27 Dec '10

27 Dec '10

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average structure of superimposed models
by Sumitro Harjanto 23 Dec '10

23 Dec '10

Hi Elaine, I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an 'average' structure as a representative model of these proteins. Can I achieve this through Chimera..? Cheers, Sum Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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[chimera-users]about "color key"
by C.J. 22 Dec '10

22 Dec '10

Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.

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CASTp .poc
by S. Shunmugasundararaj 22 Dec '10

22 Dec '10

Hi Everybody, I loaded the CASTp *.poc file in Chimera and saved as a *.py file. When I open the .py file later, I do not see the .poc details. Is it hidden somewhere or how do I get that details? I do not see the "instance" item in the Tools menu. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html page does not seem to have the details about that. Thanks Raj

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File conversion: strange behaviour
by George Tzotzos 22 Dec '10

22 Dec '10

Hi everybody, I'm attaching a pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres. Any explanation for this behaviour? Many thanks and best regards George

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File conversion: strange behaviour
by George Tzotzos 22 Dec '10

22 Dec '10

Hi everybody, I'm attaching a pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres. Any explanation for this behaviour? Many thanks and best regards George

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Re: [Chimera-users] [chimera-dev] Coloring
by Elaine Meng 21 Dec '10

21 Dec '10

Hi Hajeung, To color all carbons green the command would simply be color green,a C whereas "byatom" means to use the built-in element coloring scheme, not a specific color <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> and @ means atom name, not element, so "@C" would only get the atoms named C (not CA,CB, etc.). General user questions should probably go to chimera-users(a)cgl.ucsf.edu (chimera-dev is for development/programming questions). 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 Dec 19, 2010, at 5:36 AM, Hajeung Park wrote: > Hello, I want to color “C” to a certain color. The manual is not very clear bout it. > My understanding is > > Color green byatom ,a @C > > But it give me error. > > Thanks.

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Curves+ graphics of DNA
by Richard LAVERY 21 Dec '10

21 Dec '10

I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera? Richard LAVERY richard.lavery(a)ibcp.fr http://web.mac.com/laveryr/Homepage Institut de Biologie et Chimie des Protéines 7 passage du Vercors, Lyon 69367, France Tel: +33 (0)4 72 72 26 37, Cell 06 62 76 84 47

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changing HIS to HIP
by Francesco Pietra 16 Dec '10

16 Dec '10

Hello: I need to change several histidine residues (both HIS and HIE, although both called HIS) to HIP. I tried manually. In case of monoprotonation at NE2: modify structure element N bonds 3 geom trigonal connect to preex atoms color by element change modified residue's name to HIP set atom names to ND1 or retain current atom names In both cases the proton attached to ND1 takes the name "H1" instead of the expected HD1. Is that error in the above procedure or chimera bug? (chimera alpha version 1.5 (build 30702) on GNU/LINUX 32bit) Addendum: is there any other method of accomplishing the task with chimera? It is rather troublesome to go through all monoprotonated histidines of this large homomer (in different chains HIS of the same number have been differently protonated by reduce). A problem with reduce (if not my misuse of reduce) is that all histidines become monoprotonated, while the experimental pH is such that all should be diprotonated. I must add that I am bound to reduce because the program that I use subsequently goes through reduce. thanks for help francesco pietra

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