Hi folks,
Been sitting here getting a little confused with the seemingly endless
possibilities of the fit and align commands. What I want to do is a
pairwise alignment of the ca atoms of protein portion of some HIV
complexes ie 2 chains of 99 residues).
When I use the command
align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
pinched from robert campbells website (ta) I get the following results:
Match: read scoring matrix.
Match: assigning 208 x 209 pairwise scores.
MatchAlign: aligning residues (208 vs 209)...
ExecutiveAlign: 195 atoms aligned.
ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=2.49).
ExecutiveRMS: 6 atoms rejected during cycle 2 (RMS=0.67).
Executive: RMS = 0.475 (184 to 184 atoms)
I know how to turn off the refinement so thats and that aligns 195 atoms
without refinement. (This can be also complicated when the 2 chains are
A and B or 1-99 and 101-199). So what I am after is the protein
alignment which will align 198 atoms (2 x chain of 99 residues) to give
me a pairwise alignment to compare _multiple _structures.
Could someone point me in the right direction please.
Many thanks
Joel
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
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Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
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