Re: [ccp4bb] refmac5 issues: C-terminal amidation and maltose library file

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
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Subject: Re: refmac5 issues: C-terminal amidation and maltose library file
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-07-23

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: augie.pioszak@vai.org
>
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Stop the new PDB format!
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-07-23

Next message:
Subject: Re: Stop the new PDB format!
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-07-23