[Chimera-users] weighted distance
francesco oteri
francesco.oteri at gmail.com
Tue May 18 05:23:36 PDT 2010
Excuse me but the problem is at point 2:
I wrote: export LD_LIBRARY=/usr/local/chimera_15/lib:$LD_LIBRARY
buy the right way is:
export LD_LIBRARY_PATH=/usr/local/chimera_15/lib:$LD_LIBRARY_PATH
Try it!!!!
2010/5/18 Bala subramanian <bala.biophysics at gmail.com>
> 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
>>
>
>
--
Cordiali saluti, Dr.Oteri Francesco
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