[Chimera-users] measuring multiple distances at once
sette at uniroma2.it
sette at uniroma2.it
Thu May 29 05:25:10 PDT 2014
thanks a lot!!!
Very useful command :)
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.):
> 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.
> 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:
> I hope this helps,
> 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?
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
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