[chimera-dev] distance measurements

[Feixia]

Thank you, Eric!
I am still downloading PDB files through Bio.python. I am just interested  
in the overall distance distribution of residues, say Lys alpha carbon.  
NMR entries might end up over-representing due to their multiple models.   
Thank you for pointing it out.  Is there a quick way to distinguish  
crystal structures from NMR structures?

Best,
Feixia

On Wed, 19 Aug 2015 14:17:35 -0400, Eric Pettersen <pett at cgl.ucsf.edu>  
wrote:

> Hi Feixia,
> 	You could certainly use Chimera to do that.  You need to know some  
> Python.  Take a look at the Programmer’s Guide:
>
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html
>
> In particular, the “basic primer” discusses how to loop over files in a  
> directory and do things to them one by one.
> 	Here’s some example code for printing the lysine CA-CA distances for a  
> single open file.  You could take that and move it into the loop  
> >described in the basic primer — customizing it as you wish…
>
> from chimera import openModels, Molecule
> # opening NMR files can produce multiple models, so use a loop...
> for mol in openModels.list(modelTypes=[Molecule]):
> 	lysCas = [a for a in mol.atoms if a.name == “CA” and a.residue.type ==  
> “LYS”]
> 	for i, ca1 in enumerate(lysCas):
> 		for ca2 in lysCas[i+1:]:
> 			print mol.name, ca1, ca2, ca1.coord().distance(ca2.coord())
>
> —Eric
>
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>
>> 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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