[Chimera-users] [chimera-dev] distance measurements

Feixia feixia.chu at unh.edu
Wed Aug 19 21:00:13 PDT 2015

Thank you, Elaine!

On Wed, 19 Aug 2015 13:55:48 -0400, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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


Feixia Chu, Ph.D.
Associate Professor
Molecular, Cellular & Biomedical Sciences
University of New Hampshire
Gregg Hall, Rm436
35 Colovos Rd
Durham, NH 03824
Tel 603 862 2436

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