[Chimera-users] measuring multiple distances at once

sette at uniroma2.it sette at uniroma2.it
Thu May 29 05:25:10 PDT 2014


Hi Elaine,

thanks a lot!!!
Very useful command :)

Marco


Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Marco,
> Yes, you can even do it in a single step, but not with the distance  
> command, which takes only two things at a time (two atoms, or one  
> atom and one axis, etc.):
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
>
> To get multiple atom-atom distance measurements at once you would  
> use Find Clashes/Contacts (in menu under Tools... Structure  
> Analysis) or the "findclash" command.  Although the cutoff you  
> specify is the VDW overlap (distance between surfaces of VDW  
> spheres, which can be positive or negative), it will output not only  
> the overlaps but also the center-center distances.  The output can  
> be written to Reply Log or to a file.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>
> For example, to measure distances between atoms named HN in model #0  
> and nearby atoms named HA in model #1:
>
> findclash #0 at hn test #1 at ha overlap -4 hbond 0 log true
>
> would find all HN-HA pairs with VDW surfaces within 4 angstroms of  
> each other (make sure those are the correct atom names, and you  
> could use larger negative cutoff to find pairs farther apart) and  
> write all the overlaps and center-center distances of those pairs to  
> the Reply Log.  There's another example in this previous post:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008741.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On May 28, 2014, at 3:14 AM, sette at uniroma2.it wrote:
>
>> Hi Elaine,
>> thanks a lot.
>> It is possible, in the last version to measure distances from one  
>> (or more) single atoms and other groups of atoms?
>> for example HN of a protein and ha of that proteins?
>> Thanks,
>> Marco
>
>



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

www.rete29aprile.it


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