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[ccp4bb]: Re:[ccp4bb] SUMMARY loop lmsd's, was tricking TOPP
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Thank you to everyone who replied. Sorry to take so long to
send the summary...
Summary of the question:
I want to calculate rmsd's of specific loops in the active site.
1) CNS rmsd.inp: rmsd for each residue, but both structures have
to be described by the same .mtf file, so I can't evaluate same
protein from different species or mutants easily.
2) DALI gives a single overal rmsd for the whole protein, but I
am interested in certain loops. can't look at segments of protein
3) TOPP breaks the rmsd's down into 2nd structure, calculating
rmsd's for each alpha-helix and beta-strand, but not for loops.
NOTE: You can trick TOPP by making fake 'HELIX' cards
where there are really loops (not helices), but
if the rmsd's of those fake helices <2 ... rejected!
Summary of the suggestions with my comments from trying them...
1) Edit .pdb's to only have the loops of interest, send to DALI:
Argh! I have 9 complexes of dimers with a TIM barrel
and 8 loops of interest in each active site!
That's 144 edited .pdb files pairwise to DALI. ;-)
Also: if I send edited loops to DALI, the overall superposition
of the protein is not possible and rmsd's are isolated
numbers with little meaning.
2) LSQMAN: http://xray.bmc.uu.se/usf/welcome2usf.html:
This is a nice program, but with 144 loops to compare, an
interactive program can't be left to run overnight.
3) CCP4's LSQKAB or COMPAR: These seem convenient, but I didn't
try them, because I found another one I liked before I got
to this suggestion.... sorry!
4) ALIGN (Cohen, NIH; J. Appl. Cryst, 1997, 30:1160-1161) or
I tried to find these to download from the web, but the names
are not unique enough ...too many hits... so I gave up after
half hour or so.
4) ProFit: http://www.biochem.ucl.ac.uk/~martin/swreg.html
This one I liked the best!!!
-It's very flexible!
-It's script-run... so I wrote the script once and just
changed the filenames to compare different protein pairs.
-You can specify exactly which residues to use for the
LSq-superposition, and exactly which ones to calculate
the rmsd, and they can be different.
-You can specify 'C-alpha' or 'all atom' rmsd, so in the CA
mode, it overlooks mutations (not like CNS).
NOTE: I can't find a reference for ProFit now that I used
it and want to put the results in a paper...???
thanks for all the responses!
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