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 script. 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 etc. 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 commands 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. --Eric 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@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