Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

Re: [ccp4bb] a question about procheck
- Protein crystallography

Main steps:

   - Protein purification
   - Crystallisation

Special:

   - Programs for crystallography
   - X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

   - CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: a question about procheck
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-08-10		Next message:
Subject: Re: SAD: Refine against anomalous data
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-08-10


Subject: Re: a question about procheck
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-08-10

Dear Eleanor:
But in my structure, the atom labelles are all right.
Such as GLU A 15 :

ATOM 55 N GLU A 15 -59.930 -39.249 -9.123 1.00 30.10
N
ATOM 56 CA GLU A 15 -60.573 -38.776 -7.889 1.00 30.54
C
ATOM 57 CB GLU A 15 -61.533 -37.599 -8.146 1.00 31.08
C
ATOM 58 CG GLU A 15 -61.014 -36.528 -9.124 1.00 35.70
C
ATOM 59 CD GLU A 15 -61.459 -36.784 -10.589 1.00 40.21
C
ATOM 60 OE1 GLU A 15 -60.561 -36.946 -11.467 1.00 40.16
O
ATOM 61 OE2 GLU A 15 -62.701 -36.815 -10.851 1.00 41.17
O
ATOM 62 C GLU A 15 -61.334 -39.901 -7.182 1.00 29.34
C
ATOM 63 O GLU A 15 -61.335 -39.989 -5.947 1.00 29.37
O

I think the labbels are all right.

Thanks.

On 8/10/07, Eleanor Dodson wrote:
>
> There are conventions on which atoms is labelled OE1 and which OE2 for
> example
>
> It doesnt change the electron density of structure calns an iouta but
> conventions are conventions!
>
> Eleanor
>
> Jiamu Du wrote:
> > Dear All:
> > I have refined a structure. When I run procheck, a messege apears in
> > the log file as below:
> >
> > Average value of CA-N-C-CB angle is 33.83
> > Standard deviation is 1.85
> > * Side chain atoms swapped for residues:
> > * GLU A 15 ARG A 24 TYR A
> >
> > I have checked the density and the geometry of these residues. All
> > this residues are all right.
> > Is there anyone who have the same experience? How to deal with this
> > situation?
> >
> > Thanks.
> >
> > --
> > Jiamu Du
> > State Key Laboratory of Molecular Biology
> > Institute of Biochemistry and Cell Biology Shanghai Institutes for
> > Biological Sciences
> > Chinese Academy of Sciences (CAS)
>
>


--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd