Re: [ccp4bb] elbow and compound library

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

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Subject: Re: elbow and compound library
From: Eric Larson larsonet {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-03-03

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Subject: Re: elbow and compound library
From: Nigel W Moriarty NWMoriarty {- at -} LBL {- dot -} GOV
Date: 2009-03-03

Eric

Staurosporine is a standard ligand in the Monomer library in PHENIX and
will work directly with phenix.refine.

I should mention that if you have the atom names different from the
monomer library

phenix.ready_set model_including_stau.pdb

will run eLBOW on the ligands in the model using all the best options.
ReadySet! also adds hydrogens to the model which is a good thing.

Nigel

On 3/3/09 11:17 AM, Eric Liu wrote:
> Hi All,
>
> I downloaded a stausporine PDB file and used elbow to generate the cif
> file for my ccp4 refinement. It gave the following error message:
>
>
> 0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise
> Bondise B
>
> Failed to determine the bonding of a fragment of the molecule.
>
> PDB file elbow.stau_pdb.001.pdb written.
> Bonding file elbow.stau_pdb.001.bonding.py
> written.
>
> Edit bonding file to reflectALTERNATIVELY
>
> Re-run eLBOW with the --reel option and the molecule wil be loaded
> into REEL. Edit the bonds and save the results as "fixed.cif" to
> allow eLBOW to load the bonding. the desired bond.
>
>
>
> I guess stausporine was quite complicated molecule. How do I rerun the
> elbow with reel option? What other programs you can use to generate
> compound library file?
>
>
> Thanks!
>
> Eric

--
Nigel W. Moriarty, Ph.D.
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty@LBL.gov
Web : CCI.LBL.gov

CCP4bb navigation

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

Previous message:
Subject: Re: elbow and compound library
From: Eric Larson larsonet {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-03-03

Next message:
Subject: Announcement: Fragment Screening Library for X-ray Crystallography
From: John Badger jbadger1 {- at -} SAN {- dot -} RR {- dot -} COM
Date: 2009-03-03