[Chimera-users] Question about RMSD calculation of MatchMaker

[Matthias Fellner]

Good day

I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software.
A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this.

I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains).

The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains.

I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together.

Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log.

In addition a small question which I guess wont be possible - is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together?

Thank you
Matthias


[cid:image001.png at 01CFDE66.FDAB5BD0]

Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7
with these parameters:
                chain pairing: bb
                Needleman-Wunsch using BLOSUM-62
                ss fraction: 0.3
                gap open (HH/SS/other) 18/18/6, extend 1
                ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
                iteration cutoff: 2
RMSD between 191 atom pairs is 0.506 angstroms


Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1
with these parameters:
                chain pairing: bb
                Needleman-Wunsch using BLOSUM-62
                ss fraction: 0.3
                gap open (HH/SS/other) 18/18/6, extend 1
                ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
                iteration cutoff: 2
RMSD between 188 atom pairs is 0.551 angstroms


Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2
with these parameters:
                chain pairing: bb
                Needleman-Wunsch using BLOSUM-62
                ss fraction: 0.3
                gap open (HH/SS/other) 18/18/6, extend 1
                ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
                iteration cutoff: 2
RMSD between 193 atom pairs is 0.336 angstroms
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