Dear Cindy,
cindy wrote:
I am running Coot 0.1.1 on an SGI.
Ah, I am getting forgetful about how things worked in 0.1.1
I'm trying to incorporated methylated lysines into my model, but it is not working. I've
done the following
File=>Get monomer
placed the methylated lysine where I want then
File=>Merge molecules
when I try to regularize it, or use real space refine I get a message telling me there are no
restraints found. I then import the CIF file generated by coot and it tells me that the CIF
dictionary contains no restraints.
I have not seen a dirty mmCIF file message
OK, this could well be because there are indeed no "proper" restraints
in the cif file. What does your cif file look like? Like that for ALA
(complete)? or ATT (minimal)? If minimal, you need to run
libcheck/sketcher (or something) to get a complete restraints description.
With more modern versions, coot will do that for you, so you'd do (for
example):
(mutate-by-overlap 0 "A" 56 "MLZ")
Section 5.14.3:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC118
We have not kept up to date with providing binaries for sgi, the latest
one I can see is here:
http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/old/0.3.3/coot-0.3.3-binary-IRIX.tar.gz
Paul.
p.s. Do consider trying Coot on a Mac or PC - it's somewhat nicer there
(IMHO).
