[Chimera-users] Is it possible?
Ahir Utsav Pushpanath
a.pushpanath at mail.cryst.bbk.ac.uk
Wed Feb 4 02:55:52 PST 2009
Hello Dear Sir/Madam,
I am very fond of chimera, and everytime I have
looked at scripts for doign things, I find that chimera has them already
inbuilt as features. There is one particular problem that I am sure
chimera has the capability of doing but I am struggling to do it.
1) I want to use structural superposition servers such as Mammoth etc to
produce a structural alignment of two proteins, 2nadA and 1ybaB.
However, some of these servers do not produce a sequence alignment
output in a format compatible with chimera (i.e such as .aln or aligned
fasta). But they do produce a .pdb file showing the superposition.
2) If I load the .pdb onto chimera, sometimes in "model list" window, i
see the two proteins, wheras in others I only see 1 model(yet there is
clearly 2 models there)
3) I was wondering whether you can load the superposition onto chimera,
and see the sequence alignment that gives rise to that structural
superposition, so that I may save it as a .aln format using multialign
viewer. How do I do this?
Apologies if this is a very straightforward scenario.
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