[Chimera-users] Analysis of dihedral angles

sette at uniroma2.it sette at uniroma2.it
Tue Apr 13 02:24:14 PDT 2010

Hi all,

my reply is not really related but similar.
I work with NMR data and often we need list of distances or dihedral  
angles for the whole molecule, like distances between a NH protons and  
the rest of the molecule, or list of the chi1 dihedral angles. It  
seems that at present there is no way to get this. Scripts are possible?


Def. Quota "Eric Pettersen" <pett at cgl.ucsf.edu>:

> On Apr 12, 2010, at 9:12 AM, eduardo.troche at uvigo.es wrote:
>> Hi all,
>> I'm a new Chimera user. I'm performing some molecular dynamics with  
>>  a more or less simple system with Amber,and now that I have them   
>> done, I would like to analyze some specific data,like changes in a   
>> dihedral angle during the dynamic process, or distances between   
>> pairs of atoms. If I select several dihedral angles in Chimera and  
>> I  play the dynamic movie, I can see these changes, but is it  
>> possible  to get a table of results that shows the value of this  
>> angle for  each step of the dynamic process?
> Hi Eduardo,
> 	You can get this information by defining some actions to perform at  
>  each frame.  To do this use MD Movie's Per Frame->Define Script...   
> menu item.  This will bring up a dialog that allows you to define   
> Chimera commands or Python code to execute at each frame (controlled  
>  with the "Interpret script as..." menu at the top of the per-frame   
> dialog).  The Chimera command "angle" can be used to report  
> dihedrals  to the reply log, so something like:
> 	angle #0:5 at o4',c1',n9,c4
> would report the specified dihedral angle to the reply log.   
> Something  similar can be done with the "distance" command but it's  
> a little  trickier since the distance command sets up a distance  
> monitor and it  won't let you set up a duplicate monitor, so you  
> need to clear  existing distance monitors first (with "~dist").  So  
> something like  this:
> 	~dist all
> 	dist #0:6 at o4',h8
> would report the given distance to the reply log.  If you are   
> reporting many distances/angles you might consider using the "echo"   
> command to insert additional text into the reply log to help you  
> keep  track of things.  Also, you can use the "help" command (e.g.  
> "help  echo") to get more info on any command.
> 	I hope this helps.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette at uniroma2.it
e-mail:        m77it at yahoo.it
Tel.:          +39-0672594424
Fax:           +39-0672594328

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