November 2007 - Chimera-dev - RBVI Mailing Lists

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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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Re: [chimera-dev] Chimera-dev Digest, Vol 46, Issue 7
by Jean-Didier Maréchal 28 Nov '07

28 Nov '07

Hi Eric, both information have been of great interest for me. I actually read Walt mail when it came to the list, though, I forgot about it afterward... Thanks JD On Tue, 2007-11-27 at 12:00 -0800, chimera-dev-request(a)cgl.ucsf.edu wrote: > 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. Re: Different models (Thomas Goddard) > 2. Re: Molecular Editing: metal ion chelation (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Nov 2007 14:27:08 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Different models > To: Marco Mernberger <mernberger(a)Mathematik.Uni-Marburg.de> > Cc: chimera-dev(a)cgl.ucsf.edu > Message-ID: <474B483C.3050804(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Marco, > > The Chimera volume path tracer tool has some similarity to your > proposed Chimera tool. It allows you to place markers on volume data > and connect them up. The markers could represent molecules, domains, > ... and are implemented as a Chimera molecule, so all the coloring, > selecting, hiding/displaying capabilities of molecules are available to > the user. > > The volume path tool is implemented all in Python in directory > > chimera/share/VolumePath > > Look specifically at the markerset.py file which defines classes > Marker_Set, Marker, and Link that are wrappers for Chimera Molecule, > Atom and Bond. > > Tom > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Nov 2007 15:59:09 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Molecular Editing: metal ion chelation > To: Jean-Didier Mar?chal <jeandidier.marechal(a)uab.es> > Cc: chimera-dev(a)cgl.ucsf.edu > Message-ID: <629CBC57-7D4F-4612-A50E-DD80312697D9(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi JD, > Unfortunately, Chimera isn't really being as smart here as you are > giving it credit for. Many PDB files specify coordination bonds in > CONECT records. Chimera identifies those bonds and converts them to > pseudobonds (otherwise its atom-typing code, which depends on correct > covalent bonding, would get the bonded atoms wrong). So PDB files > that do not identify the coordination bonds with CONECT records (e.g. > 1lwx) will not have any coordination bonds in Chimera. > I'm wondering if what you are hoping to do is along the lines of > this previous mail to chimera-users: > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001529.html > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Nov 23, 2007, at 9:30 AM, Jean-Didier Mar?chal wrote: > > > Hi Eric, > > > > Thanks for that. I have been able to get a bit further. > > > > To follow with my problem, I have one question more though. > > Basically, I > > would like to know how chimera "Recognizes" metal chelation and > > coordination bounds. > > > > What I see is that when you open a pdb with a metal ion, the program > > places correctly "semi bounds" corresponding to coordination > > interactions. Unfortunately, I work with a series of protein > > structures > > where metals do not adopt a typical geometries (ex: 1lwx). First, I > > would like to be able to improve the number of acceptable metal > > geometries, but my questions are: how does chimera recognize the right > > geometry of the metal ions? Is it implemented in a python module? > > It is > > a C++ code? > > > > All the best, > > JD > > > > > > > > > >

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Molecular Editing
by Jean Didier Pie Marechal 26 Nov '07

26 Nov '07

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Different models
by Marco Mernberger 26 Nov '07

26 Nov '07

Hi there, i have a question concerning a kind of extension, i'm considering ... I'm a PhD student using chimera for the depiction and comparison of chemical and protein structures. I'm wondering if i could implement an extension that would allow me a self-defined type of molecule model, where the atoms are replaced by self-defined centers representing specific functional groups in a molecule. Could you give me a hint, how to do that? I mean, what kind of class do i have to change in order to define such a model and to load a corresponding file type? Thanks in advance, Marco Mernberger

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Re: [chimera-dev] [Chimera-users] Angles
by Eric Pettersen 06 Nov '07

06 Nov '07

On Nov 6, 2007, at 7:38 AM, Greg Pintilie wrote: > yes, try: > > chimera.selection.currentAtoms() > > this will return a list of the currently selected atoms in the > Chimera viewer. > > > For your purposes, it sounds like you want vectors between every two > atoms that you subsequently select. Watch out however, that the list > returned by the above command need not be in the order that you made > the selection. I noticed that in general the selection routines return > atoms in arbitrary order, independent of the selection order or their > position in the structure. Not sure if there is any way to enforce any > kind of order? chimera.selection.currentAtoms(ordered=True) This returns the atoms in the order they were selected. It's not the default since it involves a possibly-expensive sorting operation and because many uses of the current selection don't care about the ordering. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Chimera-dev November 2007