[ccp4bb] Refmac dictionary problem

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

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

Previous message:
Subject: Re: Reindexing Orthorhombic
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2009-04-17

Next message:
Subject: Re: close Cl contacts and poor Cl density
From: "H {- dot -} Raaijmakers" hraaijmakers {- at -} XS4ALL {- dot -} NL
Date: 2009-04-17

Subject: Refmac dictionary problem
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2009-04-17

Dear ccp4bb,

I've finally gotten around to updating my ccp4 to version 6.1.1 with
the default refmac 5.5.0072 that comes with this from the ccp4
downloads site. I am working on relatively high resolution structures
with a number of alternate conformers for certain amino acids which I
put in using the mac version of Coot 0.6-pre-1, something else I
updated last week. However, when I now run refmac on a pdb file with
two conformers for certain amino acids it seems that refmac doesn't
recognise them and distorts the bond angles/lengths. I've checked the
format of the pdb file outputted by coot and this seems normal (see
below), which suggests to me that the new refmac doesn't like the A
and B suffix on the residue name. Is this a known bug, and if so is
there an easy fix?

Thanks,

Simon

ATOM 860 N ASER A 107 -1.909 -4.393 -14.018 0.50
10.31 N
ATOM 861 N BSER A 107 -1.942 -4.416 -14.064 0.50
8.93 N
ATOM 862 CA ASER A 107 -0.633 -3.962 -14.010 0.50
6.64 C
ATOM 863 CA BSER A 107 -0.669 -4.036 -13.974 0.50
5.74 C
ATOM 864 CB ASER A 107 -0.549 -2.697 -13.710 0.50
7.45 C
ATOM 865 CB BSER A 107 -0.505 -2.657 -13.639 0.50
6.94 C
ATOM 866 OG ASER A 107 -0.877 -1.986 -12.787 0.50
16.90 O
ATOM 867 OG BSER A 107 -0.869 -1.863 -14.924 0.50
3.17 O
ATOM 868 C ASER A 107 -0.612 -4.590 -12.892 0.50
15.50 C
ATOM 869 C BSER A 107 -0.533 -4.683 -12.889 0.50
12.17 C
ATOM 870 O ASER A 107 -0.999 -5.055 -11.781 0.50
7.08 O
ATOM 871 O BSER A 107 -1.003 -5.114 -11.813 0.50
7.22 O

CCP4bb navigation

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

Previous message:
Subject: Re: Reindexing Orthorhombic
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2009-04-17

Next message:
Subject: Re: close Cl contacts and poor Cl density
From: "H {- dot -} Raaijmakers" hraaijmakers {- at -} XS4ALL {- dot -} NL
Date: 2009-04-17