[chimera-dev] distance measurements

[Elaine Meng]

Hi Feixia!
Yes, you could use Chimera to measure all lysine CA-CA distances in many structures, but it would require some scripting to loop through the structures, find the lysines, and do the measurements.

There is some information on looping through structures and running Chimera commands here:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

Now, for each structure, you might imagine the script should first find all the lysines and then use the “distance" command on each pairwise combination, substituting in the proper residue numbers.  However, there is an easier way with the “findclash” command.  You can use it for multiple distance measurement in a single command. For example:

open 2gbp
findclash :lys at ca test self overlap -1000 log true

… will measure all distances among lysine CA atoms in structure 2gbp and list results in the Reply Log (open from Favorites menu).  The -1000 in the command says to measure the distance even if the atoms are “overlapping” by -1000 (more than 1000 angstroms apart).  The last column in the results is the atom-atom distance, and they are given in order of increasing distance, in this case:

464 contacts
atom1  atom2  overlap  distance
LYS 191.A CA  LYS 189.A CA  -1.802  5.562
LYS 227.A CA  LYS 223.A CA  -2.137  5.897
LYS 300.A CA  LYS 246.A CA  -2.800  6.560
LYS 169.A CA  LYS 164.A CA  -4.676  8.436
LYS 270.A CA  LYS 276.A CA  -4.677  8.437
[… several lines removed …]
LYS 276.A CA  LYS 203.A CA  -53.705  57.465
LYS 276.A CA  LYS 137.A CA  -56.756  60.516
LYS 61.A CA   LYS 137.A CA  -56.829  60.589
LYS 58.A CA   LYS 137.A CA  -59.598  63.358
464 contacts

The log contents can be saved to a text file, for example see
 <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html>

However, your log would have a huge amount of results for all structures and it might be hard to tell which results go with which structures, so another possibility would be to save a separate file of results for each structure, and in that case your script would need to substitute in an output filename, e.g.

findclash :lys at ca test self overlap -1000 saveFile ~/Desktop/2gbp.log

See findclash documentation for all the options.  Then you can embed the command in the python looping script as described in the first link above.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.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 Aug 18, 2015, at 8:36 AM, Feixia <feixia.chu at unh.edu> wrote:

> Hi there,
> I am interested in retrieving distance information from large dataset in an automatic fashion.  For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries.  Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time.  I wonder if we can do that with Chimera.  Your advice will be highly appreciated.
> Best,
> Feixia