May 2009 - Chimera-dev - RBVI Mailing Lists

a request again...adjust torsion for pseudo bonds
by Jean Didier Pie Marechal 26 May '09

26 May '09

Dear all, sorry to bother you again. I want to perform a conformational search rotating residues around their chelation bond with a metal. With the adjust torsion tool, I can't rotate around pseudo bond, and I actually need to transform the different pseudo bonds in bonds. Could you authorize pseudo bonds to be rotated around? (in the contrary I'll continue with transforming pseudo bonds in bonds, but I thought that remaining with pseudo bonds is better especially when you do "add hydrogens" or other stuffs afterwards ) 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-dev-request(a)cgl.ucsf.edu Data: Dimecres, Maig 13, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 64, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. [Chimera-dev] Compiling chimera from source code (christopher > lau) 2. Re: [Chimera-dev] Compiling chimera from source code > (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 12 May 2009 21:15:56 -0700 > From: christopher lau <chris.d.lau(a)gmail.com> > Subject: [chimera-dev] [Chimera-dev] Compiling chimera from source > code > To: chimera-dev(a)cgl.ucsf.edu > Message-ID: > <f2026a300905122115w3cd5df71mdc8090670593ad94(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Madam/Sir, > > I am currently involved in a project which requires compiling the > Chimerasource code from scratch. I have been using: > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > for reference, and I understand that surfacing library is not > availabledue to licensing issues. Because I am not interested in > using this > feature, I wanted to know if it was still possible to compile the > Chimerasource code. I know that it will be difficult but any > knowledge or past > experience that may help me would be greatly appreciated. > > Thanks in advance, > > Chris >

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[Chimera-dev] Compiling chimera from source code
by christopher lau 12 May '09

12 May '09

Dear Madam/Sir, I am currently involved in a project which requires compiling the Chimera source code from scratch. I have been using: http://www.cgl.ucsf.edu/chimera/sourcecode.html for reference, and I understand that surfacing library is not available due to licensing issues. Because I am not interested in using this feature, I wanted to know if it was still possible to compile the Chimera source code. I know that it will be difficult but any knowledge or past experience that may help me would be greatly appreciated. Thanks in advance, Chris

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Re: [chimera-dev] scripting rotation around a bond
by Jean Didier Pie Marechal 06 May '09

06 May '09

Hi Eric, thanks a lot that is what I wanted. One question though: How do you inverse the part of the molecule you want to rotate? (The reverse in the GUI). 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: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Abril 29, 2009 9:16 pm Assumpte: Re: [chimera-dev] scripting rotation around a bond > On Apr 29, 2009, at 3:34 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > > > I'd like to generate from my script an ensemble of structures > > obtained by the rotation of a subgroup of the molecule around a > > given bond. Said in another way, I want to do something similar > to > > the adjust torsion tools without getting to the interfase but > > defining myself the value of the angle I want to test. > > I can't figure out what is the module to load and how to use it > and > > it seems there is no command line for this (rotation seems to > accept > > only the atom specification for the bond as an argument). Could > you > > give me a hand on this? > > Hi JD, > Basically, given a bond you want to rotate around, you create a > BondRot instance to do it: > > br = chimera.BondRot(bond) > > Then you can change it by a delta (in degrees) from it's > _original_ > (not current) position with the angle() method. You also have to > specify which side of the bond doesn't move: > > br.angle = (10, br.biggerSide()) > > You can get back to the original position with br.reset() (or with > a > delta of zero). Make sure to dispose of the BondRot with > br.destroy() > when you're done with it. > You probably want to use a daily build here, otherwise the bond- > rotation GUI will pop up as you work with the BondRot. Which can > be > kind of cool as the adjustment dial flies around like a movie clock > in > a fast-forward sequence. > > > By the way, I wanted to get the to the programmers's guide but I > > can't. You removed it from your server correct? > > > > All the best, > > JD > > The Programmer's Guide is still there, it's just not a direct link > off > the home page. Instead you have to click on the "Documentation" > link > and it's in the list on the resulting page. We removed the auto- > generated reference section since it was very big and of little > utility. > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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Re: [chimera-dev] [Chimera-users] unable to install on SLES 11
by Greg Couch 05 May '09

05 May '09

On Tue, 5 May 2009, Rajendra P. OJHA wrote: > Dear Users, > It gives the segmentation fault and icon disappear. How to rectify > the problem. > Thanks > Ojha Please send me more information. Which version of chimera did you try, which operating system are you using, and which graphics driver do you have installed? - Greg

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add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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