[Chimera-users] Writing alignment and RMSD out

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 10 14:54:50 PST 2007

Hi Zhiya,
	I've attached an enhanced version of the script that covers your  
additional needs.  Changes are:

1) writes out # of residues pairs involved in RMSD
2) appends list of those residue pairs
3) does the Match->Align step and writes that alignment instead of  
MatchMaker alignment
4) writes out transformed version of second PDB
5) if alignment file is named xxx.msf, then RMSD file is xxx.rmsd  
(instead of xxx.msf.rmsd) and PDB file is xxx.pdb

	Note that in a Python script if you know how to do something with a  
Chimera command you can do the same thing in the script by using the  
"runCommand" function.  So for instance if you look in the script you  
can see that I write the PDB file by using runCommand with an string  
argument that is the same as the "write" command that you would use  
at the Chimera command line to write the PDB file.
	Also, you may want change the script to use different values in the  
calls to the MatchMaker and Match->Align functions than what I used.   
For instance, the call to Match->Align uses a distance cutoff of 4.0  
(same as the 2005 script) whereas the default cutoff nowadays is 5.0.
	In regards to Match->Align producing a different number of aligned  
columns than the MatchMaker "core" even with the same cutoff value,  
that is totally believable.  You will get situations where loop  
residues happen to cross each other within the cutoff distance but  
those residues were not in the same column of the MatchMaker  
alignment [nor should they be really] and therefore could not be in  
it's final "core".


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On Dec 10, 2007, at 2:54 AM, "" <shengzhiya at nibs.ac.cn> wrote:

> Dear Eric,
> Thank you very much for your reply and I apologize for this late  
> ?thank you?! I am out of town and can not touch the internet during  
> the weekend.
> I still got several questions here. Would you please help me?
> 1. The significance of RMSD varies with the numbers of atom pairs,  
> so maybe it makes more sense if I can write out the number of atom  
> pairs at the same time. Is this possible?
> 2. I think I need the alignment from Match->Align, which better  
> represents the structure alignment. Sorry I kind of got stuck on  
> the output problem, and forgot what I need in the first place. And  
> I am curious about which residues are included in the ?core?  
> regions and used for RMSD calculation after turning on the  
> ?iterate? option. Can I see this from the Match->Align output? It  
> seems that even if I choose the same cutoff in Match->Align as in  
> iteration, the number of aligned residues is still not the same as  
> the number of atom pairs in RMSD calculation.
> 3. Also, I am really sorry for not mention this in my first letter  
> -- can I write the transformed PDB file out at the same time? I can  
> only do this with a ?.com? file but not a python script.
> Thank you very much for your help!
> Have a nice day!
> Best wishes,
> Zhiya

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