Q2
Copy the MAL entry into your own directory
cp $CLIBD/monomers/m/MALcif ./
Then correctt it in your directory
And assign LIBIN ./MAL.cif
The program will read your corrected version and ignore the distributed
one.
Q1
If you run REFMAC the GUI under review restraints, it will detect and
make a LINK entry for you
Then you will need to use the GUI task - merge monomer library to
combine your corrected MAL with the new LINK
Run refmac again with XYZIN the output from "review restraints " task (
that will include a LINK record)
and it should/might! work..
Eleanor
Pioszak, Augie wrote:
Hello All,
I have two questions about refinement with Refmac5.
1. I have a protein structure that is C-terminally amidated. What is
the best way to handle this?
I was trying to use the sketcher to create my own library definition
for the modifed amino acid, but then I had issues with the modified
amino acid not being covalently linked to the rest of the protein. I’m
guessing there is a better way, such as creating a definition for just
the additional NH2 group and telling refmac how to covalently link it
to the last amino acid, but I’m not sure how to do this.
2. I have a structure with maltose in it. The refmac library
definition for maltose has atoms “O1” and “O1,” mislabeled as Carbons.
How can I correct this?
I know I can change it with the sketcher, but then it tells me the
name MAL is already taken and I have to use another. I’d prefer to
leave it as the standard MAL name.
Thanks for any help. I apologize if these issues have been covered before.
Augie
Augen Pioszak, Ph.D.
Postdoctoral Fellow
Laboratory of Structural Sciences
Van Andel Research Institute
333 Bostwick Ave. N.E.
Grand Rapids, MI 49503
phone: (616) 234-5399
email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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