[Chimera-users] pdb-l: structure based sequence alignment

Eric Pettersen pett at cgl.ucsf.edu
Fri Mar 16 13:18:24 PDT 2007

Hi Sona,
	Before getting to your question, just wanted to mention that the  
post you quoted isn't accurate anymore:  Chimera can incorporate  
structureless sequences into alignments as of the last production  
release (October).  Once you have a structure-based alignment (or any  
alignment really) showing in Multalign Viewer you can add sequences  
to it using MAV's Edit menu.
	I don't know of any non-madness-inducing way in Chimera of  
superimposing 50+ ligands without writing a script.  There are two  
kinds of scripts you could write.  One is a text file containing the  
exact same commands you would type at Chimera's command line.  You  
would give the file a suffix of .com or .cmd and open it using  
File...Open or the "open" command.  The other type is a Python  
script, also a text file, which requires a little bit of learning but  
offers the ability to use loops -- quite helpful in this scenario.  A  
Python script file would have a .py suffix and can be opened the same  
way as a Chimera-command script.
	For purposes of the example scripts below, I'm going to assume the  
ligands have the same residue name (FMN in the example), that there  
is only one occurrence of the residue per file, and the ligand atoms  
have the same name.  PDBs you want to use that don't match these  
criteria you could do by hand -- hopefully there would just be a  
few.  On the assumption that you have a mix of NMR and  
crystallographic structures, the script will delete hydrogens,  
yielding a heavy-atom only RMSD (probably a good idea anyway if there  
are any methyl groups).  Lastly, I'll assume you have a reference  
structure to match onto already open in model #0 before you run the  
	The Chimera-command script would be something like this:

open 1jhf; del H; match #1:FMN #0:FMN; close 1
open 1kef; del H; match #1:FMN #0:FMN; close 1
open 1rd9; del H; match #1:FMN #0:FMN; close 1

	For the Python version I'll make one further assumption:  that you  
have the PDB IDs listed in a file named "pdbs".  The Python version  
would be:

from chimera import runCommand # use runCommand to execute Chimera  
f = open("pdbs", "r") # open file containing PDB IDs
for line in f:  # read through file
	pdbID = line.strip()  # remove trailing newline from text
	runCommand("open " + pdbID + "; del H; match #1:FMN #0:FMN; close 1")
f.close()  # close file

The indentation for the lines that follow the "for" statement  
indicate that they are to be executed as the loop.  The lack of  
indentation for the f.close() indicates that it is not part of the  
loop -- it is executed once the loop finishes.


On Mar 15, 2007, at 6:54 PM, Sona Vasudevan wrote:

> Hello Eric,
> Have a few questions about Chimera. I would like to superimpose  
> just the ligands bound to complexes. In this case I would like to  
> basically get a rms deviation of 50+ ligand co-ordinates (same  
> ligand from different PDBs). I now Chimera's match could do it but  
> is there a way a easier way to superimpose ligands?
> Thanks!
> Sona
> On 2/6/06, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Sona,
>        UCSF Chimera (www.cgl.ucsf.edu/chimera) can certainly  
> construct a
> structure-based sequence alignment, but can't incorporate  
> structureless
> sequences into the alignment so maybe it's not what you're looking  
> for.
> But just in case, here are the URLs for Chimera's Match->Align tool
> (which creates the alignment) and MatchMaker tool (which superimposes
> structures):
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/
> matchalign.html
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/
> matchmaker.html
> --Eric
>        Eric Pettersen
>        UCSF Computer Graphics Lab

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