[Chimera-users] weighted distance

[francesco oteri]

Dear bala, to invoke chimera as a python module ( Question 2) you should
execute the following steps:

1) Finding the root directory  of the chimera installation
(example:/usr/local/chimera )
2) export LD_LIBRARY=/usr/local/chimera/lib:$LD_LIBRARY
3) export
PYTHONPATH=/usr/local/chimera/lib:/usr/local/chimera/share:$PYTHONPATH

The result is:

oteri at priestley:~$ python
Python 2.6.4 (r264:75706, Dec  7 2009, 18:43:55)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import chimera
>>>




2010/5/18 Bala subramanian <bala.biophysics at gmail.com>

> Dear Eric and Elaine,
>
> *Thank you so much for your inputs*. I could implement the 'weighted
> distance' representation. I have certain queries. I would appreciate your
> inputs for the same.
>
> 1) When i type help(object) in chimera's python shell, it shows the help
> message, is there any to way to make the help information to be displayed in
> a separate window. I tried in config setting but i couldnt make it.
>
> 2) Is there any way to invoke chimera within normal python interpreter. I
> am able to do this for pymol. But i dnt know if i can do the same with
> chimera. I tried to set PYTHONPATH, but it vain.
>
> [cbala at RAMANA ~]$ python
> Python 2.5.2 (r252:60911, Sep 30 2008, 15:41:38)
> [GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import pymol
>
> 3) In the following code, i am collecting Cbeta atoms from two groups of
> residues and calculating the cb-cb distance. If instead of Cbeta, i have to
> calculate the side chain COM-COM (center of mass) distance between two
> groups of residues, how can i do it or which module should i use.
>
> 4)What is the syntax to change the color of pseudobonds ?
>
> *I am pasting the script below so that it may be useful to someone who
> wants to do a similar thing.
> *
> >>> import chimera
> >>> from StructMeasure.DistMonitor import *
>
> >>> model=chimera.openModels.open('trial.pdb')
> >>> res=model[0].residues
> >>> don_atom=[];acp_atom=[]
>
> #collecting CB atoms of donor and acceptor residues
>
> >>> for x in res:
>     if x.type in ['ARG','GLN']: don_atom.append(x.atomsMap['CB'][0])
>     elif x.type=='GLU': acp_atom.append(x.atomsMap['CB'][0])
>     else: continue
>
> #open the distance weight data
>
> >>> weight={}
> >>> for line in open('rad.dat'):
>     line=line.split()
>     weight[float(line[0])]=line[1]
>
> >>> b=[]
> #pseudo bond list
>
> >>> for v1 in don_atom:
>                for v2 in acp_atom:
> b.append(distanceMonitor.newPseudoBond(v1,v2))
>
> #changing pseudo bond features
> >>> for pb in b:
>                pb.drawMode=1
>                chi=round(pb.length())
>                if chi in weight: pb.radius=float(weight[chi])
>
>
> Thanks,
> Bala
>
> On Mon, May 10, 2010 at 8:07 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Oops.  The module name is "StructMeasure", not "StructureMeasure", so the
>> correct line of Python would be:
>>
>> from StructMeasure.DistMonitor import distanceMonitor
>>>
>>
>> --Eric
>>
>>
>> On May 10, 2010, at 3:36 AM, Bala subramanian wrote:
>>
>> Dear Elaine and Eric,
>> Thanks for the inputs. I started the chimera interface and tried to use
>> the StructureMeasure module using the IDLE that is present in chimera but it
>> shows me import Error. I dnt understand why. I am using chimera 1.5 alpha
>> version 29904. Do i need to set some path to use the module.
>>
>> >>> from StructureMeasure import *
>> Traceback (most recent call last):
>>   File "<pyshell#8>", line 1, in <module>
>>     from StructureMeasure import *
>> ImportError: No module named StructureMeasure
>>
>>
>> Bala
>>
>> On Wed, May 5, 2010 at 8:37 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>
>>> On May 5, 2010, at 10:28 AM, Elaine Meng wrote:
>>>
>>> With Chimera commands, you can create a distance monitor and set its
>>> stick thickness, color, etc.:
>>> open 1zik
>>> alias pair1 #0:22.a at oe2:25 at ne
>>> dist pair1
>>> setattr p drawMode 1 pair1
>>> setattr p radius .05 pair1
>>> setattr p color hot pink pair1
>>> setattr p label " " pair1
>>>
>>> However, it sounds like python will be necessary to conditionally set
>>> radius or color depending on the value of the distance.
>>>
>>>
>>> A little more info on this possibility.  You can get the distance-monitor
>>> pseudobond group in Chimera with:
>>>
>>> from StructureMeasure.DistMonitor import distanceMonitor
>>>
>>> and run through the distance-monitor pseudobonds with:
>>>
>>> for pb in distanceMonitor.pseudoBonds:
>>> ...do something that sets pb.radius based on pb.length()...
>>>
>>> --Eric
>>>
>>>                          Eric Pettersen
>>>                         UCSF Computer Graphics Lab
>>>                         http://www.cgl.ucsf.edu
>>>
>>>
>>>
>>
>>
>
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>


-- 
Cordiali saluti, Dr.Oteri Francesco
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