[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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