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

[Feixia]

Thanks a lot!
Best,
Feixia

On Wed, 19 Aug 2015 21:37:11 -0400, Repic Matej <matej.repic at epfl.ch>  
wrote:

> Hi Feixia,
>
> While the findclash in chimera will do, I believe you need a more
> lightweight tool suitable for high-throughput jobs. Chimera has a lot of
> overhead parsing the structure and also the python backend is not
> super-efficient for numerous calculations as is necessary in your case.
> The pdb has ~110,000 structures and even if it takes 1s to parse one
> structure it will still take about a day and a half to loop through all
> the structures. Therefore, I suggest you apply the right tool for the  
> job,
> which in this case is the "ncont" tool from the ccp4 crystallographic
> suite available for free from http://www.ccp4.ac.uk/download/
>
> For my test set of 20 pdbs it was about 15 times faster than chimera.
>
> A ncont input file for checking all :LYS at CA against all :LYS at CA would  
> look
> like:
> ------ncont.inp-------
> source //(LYS)/CA
> target //(LYS)/CA
> maxdist 1000
> sort distance inc
> ----------------------
>
> You can run this file with the command:
> ncont xyzin structure.pdb < ncont.inp > ncont.out
>
> If you want to run it on every pdb file in the folder just run a loop:
> for f in *.pdb; do ncont xyzin "$f" < ncont.inp > "$f".dist; echo "$f
> finished"; done
>
>
> For doing the same thing in chimera I used this script:
> ---------------------------dist.py---------------------------------
> # The script loops over all pdb files in the same folder as the
> # script is residing in and saves all distances between
> # lysine C-alpha atoms to a file.
> #
> # This script should be run with the following command:
> # chimera --silent --nogui dist.py
>
> import chimera
> from chimera import runCommand as rc
> from os import listdir
>
> # Make sure we only get pdbs from the current folder
> files = [ f for f in listdir('.') if f.endswith(".pdb")]
>
> # Loop over pdb files
> for f in files :
>     rc('open %s' % f)
>     rc('findclash :lys at ca test self overlap -1000 bondSeparation 1
> saveFile %s.dist' % f)
>     rc('close 0')
>     print('%s done' % f)
> --------------------------------------------------------------------
>
>
>
>
> Best,
> Matej
>
>
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique Fédérale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC  LCBC
> BCH 4108
> CH - 1015 Lausanne
>
> ------------------------------------------------------
>
>
>
>
>
>
> On 8/19/15, 19:55, "chimera-users-bounces at cgl.ucsf.edu on behalf of  
> Elaine
> Meng" <chimera-users-bounces at cgl.ucsf.edu on behalf of 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 ³distance" command on each pairwise
>> combination, substituting in the proper residue numbers.  However, there
>> is an easier way with the ³findclash² 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
>>
>> Š 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
>> ³overlapping² 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
>> [Š several lines removed Š]
>> 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.htm
>> l>
>>
>> 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
>>
>>
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>


-- 

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