- Chimera-users - RBVI Mailing Lists

adding pseudo bonds
by Jean Didier Pie Marechal 12 May '09

12 May '09

Dear all, what is the way to add pseubond between metal and chelating atoms? if you could tell me what are the "mouse driven" and "script driven" manner I'll be very pleased.... all the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Diumenge, Maig 10, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 11 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Protonate heteroatoms only (Francesco Pietra) > 2. Re: Protonate heteroatoms only (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Sat, 9 May 2009 23:35:37 +0200 > From: Francesco Pietra <chiendarret(a)gmail.com> > Subject: [Chimera-users] Protonate heteroatoms only > To: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: > <b87c422a0905091435q4a1671e2td61284cf092e7fb6(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi: > Is there a command in Chimera to protonate (Sybyl-type) the > heteroatoms only (or deprotonate the other elements from a fully > protonated protein)? > thanks > francesco pietra > > > ------------------------------ > > Message: 2 > Date: Sat, 9 May 2009 15:27:55 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Protonate heteroatoms only > To: Francesco Pietra <chiendarret(a)gmail.com> > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > del HC > > will delete all hydrogens bonded to carbons (their IDATM types are > HC). > --Eric > > Eric Pettersen > USCF Computer Graphics Lab > > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote: > > > Hi: > > Is there a command in Chimera to protonate (Sybyl-type) the > > heteroatoms only (or deprotonate the other elements from a fully > > protonated protein)? > > thanks > > francesco pietra > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 73, Issue 11 > ********************************************* >

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chimera performance
by Bala subramanian 11 May '09

11 May '09

Friends, Is there any way to check the performance of chimera. I have been using chimera without any problems but now it is very slow, in opening even a small dna molecule and manipulating. Is there any way that i can check the root of the problem. Thanks, Bala

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any aid for dock3.5 score?
by Francesco Pietra 11 May '09

11 May '09

Hi: I am considering to use dock3.5 score in DOCK6.2, which makes use of Delphi. Is any aid in chimera for builing the grid? thanks francesco

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Protonate heteroatoms only
by Francesco Pietra 09 May '09

09 May '09

Hi: Is there a command in Chimera to protonate (Sybyl-type) the heteroatoms only (or deprotonate the other elements from a fully protonated protein)? thanks francesco pietra

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changing diameter of the cylinders in bs representation
by Jean Didier Pie Marechal 08 May '09

08 May '09

Dear all, I know how to change the size of the balls using the vdwdefine, but I don't see the command/option to change the diameter of the cylinder in bs representation. Can I do this? best JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Maig 7, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 7 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: chimera performance (Greg Couch) > 2. volume filtering (Thomas C. Marlovits) > 3. Re: volume filtering (Tom Goddard) > 4. Re: any aid for dock3.5 score? (Elaine Meng) > 5. Re: chimera performance (Bala subramanian) > 6. Re: chimera performance (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 6 May 2009 12:23:38 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera performance > To: Bala subramanian <bala.biophysics(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0905061215200.1920327(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Wed, 6 May 2009, Bala subramanian wrote: > > > Friends, > > > > Is there any way to check the performance of chimera. I have been > using> chimera without any problems but now it is very slow, in > opening even a > > small dna molecule and manipulating. Is there any way that i can > check the > > root of the problem. > > > > Thanks, > > Bala > > So it was formerly fast on the same computer? This could happen on > a > Linux computer if you updated the kernel and forgot to reinstall > the > graphics driver (from ATI or NVidia, the open source 3D drivers > still need > work, but are improving). Another possibility, on all operatings > sytems, > is that there is a background process that is using a lot of CPU or > memory, so chimera doesn't have the resources it used to. > > If you just want to check the graphics performance, then you can > use the > Benchmark tool in Tool / Utilities to guage the current > performance. And > then you can compare to the reported scores to see if your graphics > performance is reasonable (the Show button in the Benchmark tool > brings up > the web page). > > - Greg > > > ------------------------------ > > Message: 2 > Date: Tue, 5 May 2009 22:34:45 +0200 > From: "Thomas C. Marlovits" <marlovits(a)imp.ac.at> > Subject: [Chimera-users] volume filtering > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: <019F22EC-BFF8-4612-A1B9-BE4DDA9471E3(a)imp.ac.at> > Content-Type: text/plain; charset="us-ascii" > > HI, > > I am trying to look for the various filtering options as descibed > on > the Chimera webpage (guide to volume data display). Indicated are > Gaussian filtering, Fourier filter, Hide dust, etc ... > unfortunately, > I can only find the Gaussian filter option under TOOLS/VOLUME DATA > > but cannot find the others ... can you point me to these other > options, in particular the Fourier filter ? (am using version 1.3 !) > Tx. > -Thomas > > > > -------------------------------------------------------------------- > ----------- > > Thomas C. Marlovits, PhD, M.A.S. > Research Group Leader > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences > (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits(a)imp.univie.ac.at > > > > >

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volume filtering
by Thomas C. Marlovits 06 May '09

06 May '09

HI, I am trying to look for the various filtering options as descibed on the Chimera webpage (guide to volume data display). Indicated are Gaussian filtering, Fourier filter, Hide dust, etc ... unfortunately, I can only find the Gaussian filter option under TOOLS/VOLUME DATA but cannot find the others ... can you point me to these other options, in particular the Fourier filter ? (am using version 1.3 !) Tx. -Thomas ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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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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