May 2009 - Chimera-users - RBVI Mailing Lists

unable to install on SLES 11
by Rajendra P. OJHA 05 May '09

05 May '09

Dear Users, It gives the segmentation fault and icon disappear. How to rectify the problem. Thanks Ojha

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Fwd: Coulombic Surface Coloring
by Francesco Pietra 04 May '09

04 May '09

---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sun, May 3, 2009 at 11:01 PM Subject: Re: [Chimera-users] Coulombic Surface Coloring To: Eric Pettersen <pett(a)cgl.ucsf.edu> On Sun, May 3, 2009 at 10:50 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Francesco, > How did you find the page describing Coulombic Surface Coloring, did > you Google it? Yes, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi… Anyway, that tool is only in the daily build, and not in > whatever version you are using. You can get a daily build by going to the > Chimera home page (www.cgl.ucsf.edu/chimera) and following the "Daily > Builds" link. You can install in a location different from your current > version if you like. That way you can use the daily build for the surface > coloring, but use the other version if needed (i.e. if you run into a bug). I'll first see if a program to furnish data for Chimera's Electrostatic Surface Coloring is available. Any suggestion? I forgot that have both apbs and delphi executables as components of an installed docking program. > If your protein consists only of standard residues then I see no > reason for you to use your calculated charges -- the pre-computed Amber > charges should be fine. If there are non-standard residues then it's up to > you if you want to use Define Attribute to add the charges to the structure > or instead rely on Chimera's charge-computation capabilities. My "have a file with calculated charges" was misleading, It was a mol2 file saved with Chimera. thanks francesco > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > On May 3, 2009, at 12:07 PM, Francesco Pietra wrote: > >> Hi: >> I would like to simply color the surface of a protein by the Coulombic >> Surface Coloring method. I can show the surface, have a file with >> calculated charges if useful, but i am unable to implement the >> indications below >> >> >> "There are several ways to start Coulombic Surface Coloring, a tool in >> the Surface/Binding Analysis category. >> >> The molecular surface(s) should first be displayed (using Actions... >> Surface... show or the command surface) and then chosen from the list >> of Surfaces to color by ESP. " >> >> which tool should be opened from Surface/Binding Analysis? Of those >> related, I can only see Electrostatic Surface Coloring and that - in >> my hands - does not bring to the simple Coulombic method. >> >> Thanks for clearing >> francesco pietra >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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NMRCLUST
by Austin B. Yongye 04 May '09

04 May '09

Dear chimera users, Does the NMRCLUST algorithm in the Ensemble Cluster tool use Kelley penalty values (Kelley et al. Protein Engineering, 1996, 9(11), 1063-1065) to determine the optimum number of clusters during a clustering procedure? Thanks, Austin-

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Merging models
by Elaine Meng 04 May '09

04 May '09

On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote: > Hi everybody, > > I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz > ) made of two models. I need to merge this two models into one. How > can I do that? > > Thanks in advance, > > Maziar S. Ardejani > Lab 9, The Orner Lab > Division of Chemistry and Biological Chemistry > School of Physical and Mathematical Sciences > 21 Nanyang Link > Nanyang Technological University > Singapore 637371 > Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? <http://www.rcsb.org/pdb/explore/explore.do?structureId=2VXI> There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols. Please send Chimera questions to chimera-users(a)cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Coulombic Surface Coloring
by Francesco Pietra 03 May '09

03 May '09

Hi: I would like to simply color the surface of a protein by the Coulombic Surface Coloring method. I can show the surface, have a file with calculated charges if useful, but i am unable to implement the indications below "There are several ways to start Coulombic Surface Coloring, a tool in the Surface/Binding Analysis category. The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP. " which tool should be opened from Surface/Binding Analysis? Of those related, I can only see Electrostatic Surface Coloring and that - in my hands - does not bring to the simple Coulombic method. Thanks for clearing francesco pietra

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recording operations
by Fajer 03 May '09

03 May '09

Dear All, Does Chimera record the "menu" selected operations that can be played back in a manner analogous to storing "command" entered operations ? I'd rather avoid having to modify python script of the stored session. Peter Fajer

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My Chimera 1.4 build 27395 is not keeping 2D Labels when saving images except if Pov-Ray tracing is turned on
by Victor Alves 02 May '09

02 May '09

Hi When I save a picture with 2D Labels, they don't show up in the saved image. I tried with different image types (jpg, tiff, png) and even a new image just with some 2D Labels in it. I don't know if this is important but all of them have a white background. The only way I managed to see the labels was to turn on Pov-Ray tracing! Any ideas? Thank you in advance Victor Alves

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Chimera-users May 2009