[ccp4bb] problem with 'generate' (cns solve)

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

Previous message:
Subject: Re: Difference Map in COOT - Possible lignad but clash with structure?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-12-28

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Subject: Re: problem with 'generate' (cns solve)
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-12-28

Subject: problem with 'generate' (cns solve)
From: Mareike Kurz m {- dot -} kurz {- at -} IMB {- dot -} UQ {- dot -} EDU {- dot -} AU
Date: 2007-12-28

I am refining a structure in which I had to model a small molecule
(done with Dundee PRODRG2 server). After fitting the small molecule
into the structure I merged the pdb's and used the merged pdb file
for "generate" (cns_solve). (Just in case: I did put the top and par
file for the small molecule into the input file).

In the obtained pdb.file from generate-the coordinates for the small
molecule have changed in a way, that by loading this pdb into Coot,
the molecule is not drawn properly anymore and appears at a random
place in the structure.
In the output file from 'generate', I get the following error message:

COOR>REMARK
COOR>HETATM 1 OAA DRG 1 6.470 4.170 1.460 1.00
20.00 O
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
COOR>CONECT 2 1 3
COOR>CONECT 3 2 4 5
COOR>CONECT 4 3
COOR>CONECT 5 3 6
COOR>CONECT 6 5
COOR>END
CHAIN> end
SEGMENT> end

and then later on:

COOR>REMARK
COOR>REMARK
COOR>HETATM 1 OAA DRG 1 6.470 4.170 1.460 1.00
20.00 O
COOR>HETATM 2 CAD DRG 1 6.320 4.540 0.090 1.00
20.00 C
COOR>CONECT 2 1 3
COOR>CONECT 3 2 4 5
COOR>CONECT 4 3
COOR>CONECT 5 3 6
COOR>CONECT 6 5
COOR>END
%READC-WRN: multiple coordinates for 6 atoms
%READC-WRN: still 886 missing coordinates (in selected subset)
CNSsolve> set echo=off end

I am fairly new to solve a structure including another small molecule
and would really appreciate if someone could give me some advice.

Thank you very much in advance,
Mareike

Mareike Kurz
m.kurz@imb.uq.edu.au

CCP4bb navigation

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

Previous message:
Subject: Re: Difference Map in COOT - Possible lignad but clash with structure?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-12-28

Next message:
Subject: Re: problem with 'generate' (cns solve)
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-12-28