[Chimera-users] Questions about Matchmaker and GDT

[Ralph Loring]

Hi,
I don't know if there's a special user group for Matchmaker but this also
involves other aspects of Chimera.
1) I'm looking at AlphaFold structures of RIC-3, a chaperone for nicotinic
receptors that is also an intrinsically disordered protein.  There are pdbs
for six species in the AlphaFold database: Human, mouse rat, fish, fly and
worm.  These differ tremendously in terms of sequence, size and predicted
secondary structures but they all have a putative signal sequence and a
transmembrane domain.  I used Matchmaker to align the human pdb to each of
the others.  The results of combining all 6 looks like a bowl of spaghetti
until the parts before the putative signal sequence and the C-terminal
tails are deleted.  Then I can see that the putative signal sequences and
the transmembrane domains are in the same plane as if they are in a
membrane.  I just want to confirm that this is merely a lucky coincidence
and that Matchmaker has no preference for aligning hydrophobic alpha
helices into a planar space corresponding to a membrane. The coincidence,
if it is one, is striking and I just want to make sure.  Note that I have a
similar question for AlphaFold, the source of the pdbs.
2) Does Chimera do Global Distance Testing (GDT)?  For that matter, does
ChimeraX (I've been thinking about switching and if it does, this may be
what it takes to get over the activation energy barrier)? I can't find GDT
in any of the directions.  When Matchmaker runs, for instance comparing
human and fly RIC-3, the sequence alignment score is only 270 but the RMSD
is 1.6 angstroms (but only for 7 pruned atom pairs and when all 233 atom
pairs are considered, the RMSD is 55 angstroms, so clearly not much
overlap).  I've heard that GDT corrects somewhat better than RMSD for not
having precise superimposition.  However, I don't know that it would make a
lot of difference in this case but I'd like to find out. The mystery is
that drosophila RIC-3 works almost as well as human RIC-3 in helping
assemble human pentameric nicotinic receptors even though the structures
are so different.
Thanks for your help,
Ralph Loring
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