November 2009 - Chimera-dev - RBVI Mailing Lists

Rotation about the axis of symmetry
by Liam Browne 23 Nov '09

23 Nov '09

Hi all, I want to rotate a model by 90 degrees about the axis of symmetry, but I seem to be having problems setting the axis correctly. After two identical models are superimposed I use measure rotation and get the following: Matrix rotation and translation -0.04092271 -0.36724445 0.92922379 -82.20183653 -0.91203666 0.39354649 0.11537022 -54.21831923 -0.40806183 -0.84276490 -0.35104539 11.47082481 Axis -0.55288898 0.77167664 -0.31437070 Axis point -56.22800779 0.00000000 25.47389901 Rotation angle (degrees) 119.94780111 Shift along axis 0.00338820 What should I do to rotate the model at the same axis but by 90 degrees? Many thanks, Liam _________________________________________________________________ View your other email accounts from your Hotmail inbox. Add them now. http://clk.atdmt.com/UKM/go/186394592/direct/01/

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writing atom information using the mol2 atom order.
by Jean Didier Pie Marechal 03 Nov '09

03 Nov '09

Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could 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

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writing atom information using the mol2 atom order.
by Jean Didier Pie Marechal 03 Nov '09

03 Nov '09

Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could 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-dev-request(a)cgl.ucsf.edu Data: Dilluns, Octubre 26, 2009 8:00 pm Assumpte: Chimera-dev Digest, Vol 69, Issue 1 > 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. thank you so much (Corey Fugate) > 2. Re: thank you so much (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 23 Oct 2009 16:57:11 -1000 > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] thank you so much > Message-ID: <D445EAAC-78D8-4394-85E0-997DBED43CD8(a)hawaii.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > I started using Chimera a few weeks ago. It is wonderful, I love it. > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Oct 2009 11:03:55 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Corey Fugate <fugate(a)hawaii.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] thank you so much > Message-ID: <26F83250-86D7-4E19-8B17-304418C8169D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > So glad you like it. And always struggling to make it better. > Thanks! :-) > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Oct 23, 2009, at 7:57 PM, Corey Fugate wrote: > > > I started using Chimera a few weeks ago. It is wonderful, I > love it. > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >

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Chimera-dev November 2009