[Chimera-users] structural similarity measures in Chimera

[Eric Pettersen]

Dear Dr. Li,
	I'm sorry, but that would not be feasible.  It is not a "plug and  
chug" situation, where the exact series of tasks you need is already  
known.  As mentioned previously, the structures would first need to be  
superimposed before Match->Align is used to calculate similarity  
scores.  Although Chimera provides several ways to superimpose  
structures (Superimposing Structures), you would need to evaluate  
which method and parameters work on your structures of interest, using  
your own knowledge of this family of proteins.  After superimposing,  
getting the scores, and building a phylogeny, if there were any  
discrepancies from what you were expecting, you would probably want to  
re-evaluate some of the superpositions and possibly recalculate them,  
again based on your own detailed knowledge of these proteins.
	We are willing to provide tools for your research, but actually  
performing this part of your study with Chimera would go far beyond  
that role.  It sounds like you may need to take a simpler approach,  
such as using some other program that both superimposes proteins and  
provides a similarity score in the same step (as opposed to the  
decoupled approach in Chimera, which would also require python  
scripting knowledge).  However, I'm not aware of any program that will  
do all pairwise comparisons automatically, so you would need to find a  
program that you can download for local use and then somehow (shell or  
other) script looping through all the pairs.
	Here is an informal list of superposition programs, some of which are  
available for download: Online Structure Alignment Resources
	If you recruit someone familiar with Python to your team, I'd be  
willing to make the scriptability improvements to Match->Align that I  
mentioned previously and provide guidance on the basic scripting  
outline you would need.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Apr 3, 2010, at 2:09 PM, Minming Li wrote:

>
> Dear Dr. Pettersen and Dr. Meng,
>
> Thank you for your last email. I'm sorry that I am not so familiar  
> with
> Python, so could you help me to use the Chimera to produce the  
> distance
> matrix of the listed 45 pdbs below? Otherwise, is there any easy way  
> to do this
> just by running the program instead of using the Match->Align by  
> hand? Thank
> you so much!
>
> The list of the 45 pdbs:
> 1il2a,1asza,1kmmc,1adyb,1adjb,1b76b,1efwa,11asb,1j5wb,1bbwa,
> 1lylb,1e1oa,1pysa,1b8aa,1httb,1kmna,1qe0b,1g51a,1evlc,1evka,
> 1nj8d,1kmmb,1c0aa,1j5wa,1serb,1h4qa,1eqrc,1sera,1nj1a,1h4sb,
> 1atib,1h4vb,1b70a,1eqra,1kmnb,1adya,1adjc,1hc7a,1httc,1eqrb,
> 1g51b,1qe0a,1b76a,1atia,1efwb.
>
> Best regards!
>
> sincerely,
> Minming Li
>
> --------------------------
> Minming Li
> PhD student,
> Interdisciplinary Life Science Program (PULSe Program),
> Purdue University,
> West Lafayette, IN. USA.
> Email: li362 at purdue.edu
>
>
> Quoting Eric Pettersen <pett at cgl.ucsf.edu>:
>
>> On Mar 30, 2010, at 9:04 PM, Elaine Meng wrote:
>>
>>> However, there are some issues that may affect whether you decide to
>>> use Chimera to calculate these values for your structures:
>>>
>>> (1) You would need to run Match->Align for each pair.  There is no
>>> option to do all pairwise comparisons on multiple structures.  You
>>> would need to script looping through all pairs (with python or shell
>>> scripting).
>>>
>>> (2) There is no Chimera command for Match->Align.  Thus Match->Align
>>> would also need to be run via python. I don't have scripting
>>> expertise, so someone else would have to provide more details if you
>>> decide to try this.
>>
>> Given that you said you wanted a complete pairwise matrix of ~50
>> structures, that would be ~1200 unique pairs, which is obviously way
>> too many to do by hand.  Currently Match->Align is awkward to script,
>> even in Python, since all the important code is internal to the  
>> Match-
>>> Align dialog and basically impossible to call externally.  If you
>> are sure that you would like to use Chimera for this computation I  
>> can
>> reorganize the Match->Align code so that it could be called
>> externally.  I don't think the reorganization will be difficult.  You
>> would still need to resort to a Python script to make the Match- 
>> >Align
>> calls and loop through your models, so you would need some  
>> rudimentary
>> familiarity with Python.  Let me know.
>>
>> --Eric
>>
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu
>>
>>
>>



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