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Re: [ccp4bb] PDBSET bug with unusual (but legal) atom names
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: PDBSET bug with unusual (but legal) atom names
From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-09-05		Next message:
Subject: PhD Position in Structural Biology
From: Clemens Grimm Clemens {- dot -} Grimm {- at -} BIOZENTRUM {- dot -} UNI-WUERZBURG {- dot -} DE
Date: 2008-09-05


Subject: Re: PDBSET bug with unusual (but legal) atom names
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-09-05

even though I also don't fully understand the code, your interpretation
seems to make sense. I don't know a fix for the code. Yet, when I used
pdbset from ccp4-6.0.99e, this error did not occur (but did with pdbset
from ccp4-6.0.2). So if it's an option you might simply update to the
latest beta-Version of ccp4.
$CCP4/lib/src/mmdb/mmdb_rwbrook.cpp seems completely rewritten in the
beta-version since that code and your excerpt hardly share any similarity!

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Thu, 4 Sep 2008, Borhani, David wrote:

> I believe I found the bug, but I don't understand enough to know how to
> fix the code correctly.
>
> In $CCP4/lib/src/mmdb/mmdb_rwbrook.cpp, lines 1546-1561:
>
> if (FTN_STR(ID)[0]==' ') {
> atomName[0] = char(0);
> if ((FTN_STR(AtNam)[1]=='H')


> ((FTN_STR(AtNam)[1]=='D') && (FTN_STR(ID)[2]=='D'))) {
> i = 0;
> while ((i
> (FTN_STR(AtNam)[0]!=HydAtomName[i][0])) i++;
> if (i
> GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
> }
> if (!atomName[0]) {
> atomName[0] = ' ';
> GetStrTer ( &(atomName[1]),FTN_STR(AtNam),3,4,FTN_LEN(AtNam) );
> }
> } else
> GetStrTer ( atomName,FTN_STR(AtNam),4,5,4 );
>
> This code snippet is in subroutine MMDB_F_ATOM, which is called from
> $CCP4/lib/src/rwbrook.f S/R XYZATOM, which is called (multiple places
> for both input & output) from pdbset.
>
> The logic here, which I don't understand fully (in part because I don't
> really understand c++, but also because the code is so sparsely
> commented), seems to me to be wrong.
>
> It seems to be testing whether the first character of the "ID", which I
> think is the two-character atomic element name, is a space or not. If a
> space, do something special for hydrogen/deuterium, AND importantly (and
> incorrectly) ensure that the 4-character atom name on output also begins
> with a space; if not a space (correct for ALL atoms, no???), simply copy
> the input 4-character atom name (without adjustment to its
> justification) to output.
>
> Could someone more in the know confirm that this logic is flawed or not,
> and also please suggest a proper code fix?
>
> Thanks!
> Dave
>
> David Borhani, Ph.D.
> D. E. Shaw Research, LLC
> 120 West Forty-Fifth Street, 39th Floor
> New York, NY 10036
> David.Borhani@DEShawResearch.com
> 212-478-0698
> http://www.deshawresearch.com
>
> ========================================================================
> =========
>
> I used PDBSET (ccp4-6.0.2; linux; script at end of email) to generate
> symmetry-related chains (with chain renaming).
>
> Certain atom names get mangled. Specifically, the NAP residue, which as
> many of us are painfully aware is named unusually, comes out wrong:
>
> Example input:
> ATOM 12107 AOP1 NAP G1001 22.769 33.214 214.847 1.00 34.14
> O
> ATOM 12108 AP2* NAP G1001 21.800 33.997 213.998 1.00 37.32
> P
> ATOM 12109 AOP2 NAP G1001 22.509 35.058 213.208 1.00 32.04
> O
> ATOM 12110 AOP3 NAP G1001 20.909 33.196 213.051 1.00 31.50
> O
>
> INCORRECT output:
> ATOM 12107 AOP NAP M1001 22.769 33.214 214.847 1.00 34.14
> M O
> ATOM 12108 AP2 NAP M1001 21.800 33.997 213.998 1.00 37.32
> M P
> ATOM 12109 AOP NAP M1001 22.509 35.058 213.208 1.00 32.04
> M O
> ATOM 12110 AOP NAP M1001 20.909 33.196 213.051 1.00 31.50
> M O
>
> Note the incorrect one-character rightward shift of the atom name, and
> thus loss of the last character of the atom name.
>
> ALSO, the bug has nothing to do with the symmetry generation/chain
> renaming: I re-ran PDBSET, simply requesting translation of all
> coordinates by [0.00001,0,0], and I get the same incorrect atom name
> output.
>
> I waded through pdbset.f, rwbrook.f, and the new MMDB lib routines, but
> I must admit that the bug location remains totally opaque to me! Any
> help in locating the bug would be much appreciated!
>
> Thanks,
> Dave
>
> David Borhani, Ph.D.
> D. E. Shaw Research, LLC
> 120 West Forty-Fifth Street, 39th Floor
> New York, NY 10036
> David.Borhani@DEShawResearch.com
> 212-478-0698
> http://www.deshawresearch.com
>
> PDBSET scripts used (via ccp4i gui):
>
> symgen X, Y, Z
> symgen -Y+1/2, X+1/2, Z
> symgen Y-1/2, -X+1/2, Z
> symgen -X, -Y+1, Z
> chain symmetry 1 -
> B A
> chain symmetry 2 -
> B D
> chain symmetry 3 -
> B C
> chain symmetry 4 -
> B B
> chain symmetry 1 -
> A E
> chain symmetry 2 -
> A H
> chain symmetry 3 -
> A G
> chain symmetry 4 -
> A F
> chain symmetry 1 -
> H I
> chain symmetry 2 -
> H L
> chain symmetry 3 -
> H K
> chain symmetry 4 -
> H J
> chain symmetry 1 -
> G M
> chain symmetry 2 -
> G P
> chain symmetry 3 -
> G O
> chain symmetry 4 -
> G N
> End
>
> remark test
> shift -
> 1e-05 0.0 0.0
> end
>
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