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RE: [ccp4bb]: Abnormal residues in procheck



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Toby,

I had a similar problem with Antiamoebin I. I got around the problem by
reducing the non-standard residues to the nearest standard residue, ie Hyp
to Pro, D-Iva to Ala, Aib to Ala and Phe-OH (Phol) to Phe. These alterations
will allow Procheck to deal with the main chain torsion angles etc.

Regards

Chris
**********************************************
Chris F. Snook, Ph.D.                     email : snookc@missouri.edu      
Dept Biochemistry                        phone : (573)-884-2302         
Univ. of Missouri                           FAX   : (573)-884-4812         
117 Schweitzer Hall

Columbia

MO 65211

______________________________________________


> ----------
> From: 	Boggis
> Sent: 	Monday, August 7, 2000 12:08 PM
> To: 	ccp4bb@dl.ac.uk
> Subject: 	[ccp4bb]: Abnormal residues in procheck
> 
> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> Apologies if this has been asked/explained before:
> 
> Procheck doesn't seem to like my abnormal residues. This is quite a
> problem for me since the peptide I'm working on only has 3 non-glycine, 
> non-proline residues (out of 16)! It has 1 Gly and 1 Pro, but all the rest
> are not in the "Top 20" hit parade. They are Aib, Iva, Hyp and Phe-OH
> (terminal alcohol).
> 
> Is there any way of telling procheck what these residues are so that it
> can deal with them reliably? I'm worried that some of the stats/graphs
> will be misleading.
> 
> When I run procheck I only get 1 error message about an unknown atom type,
> but there could be more wrong than I can see, couldn't there?
> 
> Thanks for any help/advice!
> 
> Toby
> 
> ------------------------------------------------------------
> Toby Galbraith 
> Birkbeck College, London
> email: t.galbraith@mail.cryst.bbk.ac.uk
> ------------------------------------------------------------
> 
>