[Chimera-users] weighted distance
Bala subramanian
bala.biophysics at gmail.com
Tue May 18 04:46:50 PDT 2010
Hai oteri,
I tried the way you had suggested but still i get some error. chimera comes
with its own python and i dnt know if there is a clash. Could you please
write me why this ImportError happens.
[cbala at RAMANA ~]$ export
PYTHONPATH=/usr/local/chimera_15/lib:/usr/local/chimera_15/share:$PYTHONPATH
[cbala at RAMANA ~]$ export LD_LIBRARY=/usr/local/chimera_15/lib:$LD_LIBRARY
[cbala at RAMANA ~]$ 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 chimera
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.5/site-packages/PIL/__init__.py", line 15, in
<module>
ImportError: libgfxinfo.so: cannot open shared object file: No such file or
directory
---------------------------------------------------------------------------------------------------------------------
On Tue, May 18, 2010 at 1:39 PM, francesco oteri
<francesco.oteri at gmail.com>wrote:
> 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
>>>>
>>>>
>>>>
>>>
>>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
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