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@purdue.edu

Quoting Eric Pettersen <pett@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