[Chimera-users] StrucMeasure and distance

Wed Jul 23 09:21:05 PDT 2008

Dear all,

a small question. I know how to calculate the distance between two atoms calling the "distance" command and I generally use it embedded in the scripts I write. However, this time, I'd like to have access through my script only to the values of the distances (nothing related to the display) in order to stock them. I thought I would find my way through by using the StructMeasure module, but I am not able to do so. How could I just have a return of the distances between two atoms in the shell?

Thanks a lot,

JD

Dr. Jean-Didier Maréchal
Professor Lector
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: chimera-users-request at cgl.ucsf.edu
Data: Dimecres, Agost 8, 2007 9:00 pm
Assumpte: Chimera-users Digest, Vol 52, Issue 6

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> Today's Topics:
> 
>   1. writing translation/rotation (Thomas C. Marlovits)
>   2. Re: writing translation/rotation (Elaine Meng)
>   3. Re: writing translation/rotation (Eric Pettersen)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Wed, 8 Aug 2007 14:19:43 +0200
> From: "Thomas C. Marlovits" <marlovits at imp.univie.ac.at>
> Subject: [Chimera-users] writing translation/rotation
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <BAFCFCAA-D911-4E0C-8F5E-B41430E8E1B6 at imp.univie.ac.at>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi,
> 
> am looking for an analysis tool in Chimera  that would write out -  
> let's say a matrix for translation/rotation of a pdb-file in 
> respect  
> to another one.
> 
> Usage:  would like to align chain A and chain B present in a pdb-
> file  
> and want to know which translation/rotation matrix has to be 
> applied  
> in order to convert  the non-aligned pdb-coordinates of chain B to  
> the 'new" aligned pdb-coordinates.
> 
> Thanx for your help,
> -Thomas
> 
> 
> 
> --------------------------------------------------------------------
> ---- 
> -------
> 
> Thomas C. Marlovits, PhD, M.A.S.
> 
> 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 at imp.univie.ac.at
> 
> 
> 
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> ------------------------------
> 
> Message: 2
> Date: Wed, 8 Aug 2007 10:14:38 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] writing translation/rotation
> To: "Thomas C. Marlovits" <marlovits at imp.univie.ac.at>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <047E2934-FDD1-496C-A784-EF7A126301E4 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
> 
> Hi Thomas,
> (1) Currently to transform one structure relative to another, they  
> need to be in separate files, so first put chain A in one PDB file, 
> 
> chain B in another.
> 
> (2) Then, decide how to match (superimpose) the structures.  There  
> are several options - MatchMaker (which will figure out the  
> correspondences for you by doing a sequence alignment and then  
> matching alpha-carbons), the "match" command which will allow you 
> to  
> name the specific atoms you want to use for fitting, both with or  
> without fit iteration (pruning far-apart pairs from the fit). 
> Usually  
> the MatchMaker defaults, which include fit iteration, work quite 
> well  
> - thus I usually try those first.  (specific example below)  Make  
> note of how the match was done once you are happy with it.
> 
> (3) Assuming you have rotated and translated things around in order 
> 
> to look at the match, you next want to reset to untransformed  
> positions (at least of the A chain) and re-match with the approach  
> worked out earlier.  Then write the matrices to a file or the Reply 
> 
> Log as desired.
> 
> Specific example:  PDB entry 1zik is a leucine zipper with A and B  
> chains.  With text editing, I created zika.pdb (just the A chain) 
> and  
> zikb.pdb (just the B chain).
> In chimera:
> - open zika.pdb
> - open zikb.pdb
> command: mm #0 #1
> 
> (this is the command version of MatchMaker, using defaults and  
> zika=#0 reference, zikb=#1 structure to match)  I decide this match 
> 
> looks good by rotating/translating and visual examination.  Then  
> reset, re-match, write matrices.
> 
> command: reset     (now don't rotate/translate!)
> command: mm #0 #1
> command: matrixget -     (the "-" sends the info to the Reply Log.  
> 
> could also write to file)
> 
> Here is the info pasted from the Reply Log, which is under 
> Favorites  
> in the menu:
> Model 0.0
> 	1 0 0 0
> 	0 1 0 0
> 	0 0 1 0
> Model 1.0
> 	0.318155 -0.0547522 0.946456 7.3815
> 	0.0202055 -0.997713 -0.0645095 35.85
> 	0.947823 0.0396477 -0.316321 -9.44741
> 
> The "matrixget/matrixset" man page has more information on the 
> matrices:http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> On Aug 8, 2007, at 5:19 AM, Thomas C. Marlovits wrote:
> 
> > Hi,
> > am looking for an analysis tool in Chimera  that would write out -
>  
> > let's say a matrix for translation/rotation of a pdb-file in  
> > respect to another one.
> >
> > Usage:  would like to align chain A and chain B present in a pdb- 
> > file and want to know which translation/rotation matrix has to be 
> 
> > applied in order to convert  the non-aligned pdb-coordinates of  
> > chain B to the 'new" aligned pdb-coordinates.
> >
> > Thanx for your help,
> > -Thomas
> > ------------------------------------------------------------------
> ---- 
> > ---------
> > Thomas C. Marlovits, PhD, M.A.S.
> > 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
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 8 Aug 2007 10:58:25 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] writing translation/rotation
> To: "Thomas C. Marlovits" <marlovits at imp.univie.ac.at>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <54D65DC0-D5D1-451C-8386-7AF2B7EA8847 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
> 
> On Aug 8, 2007, at 10:14 AM, Elaine Meng wrote:
> 
> > Hi Thomas,
> > (1) Currently to transform one structure relative to another, they
> > need to be in separate files, so first put chain A in one PDB file,
> > chain B in another.
> 
> Another alternative is to simply open two copies of the file, in  
> which case you would have to use the specific-chain-to-specific-
> chain  
> pairing method in MatchMaker.  Elaine's method does have the  
> advantage of making it easy to inspect the quality of the match  
> without having to undisplay/delete other chains.
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         pett at cgl.ucsf.edu
>                         http://www.cgl.ucsf.edu
> 
> 
> 
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