Hi,
I am not really sure if I understand what you mean by a "corrupted PDB
issue"?
The PDB that I am using was created with MolMol (Version 2K.2 - old version
probably) from an original PDB that was deposited at the Protein data bank
server, which indeed does not have the CONECT lines. I used MolMol because I
needed to add the hydrogen atoms to the structure. Probably some other
programs do not introduce the CONECT lines...?! Do you think MolMol is
actually "corrupting" the PDB during the process of H addition?
Cheers
TP
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: sexta-feira, 4 de Dezembro de 2009 15:02
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: MF_Multimodel
Hi,
Do you know if this is a corrupted PDB issue as well? I don't really
have the time, let alone the interest, to expand the internal reader
to handle all possible PDB corruptions (it would have to be hundreds
of times bigger than the current code size). If it is not, then
please submit a bug report, attaching the smallest possible set of
lines from the PDB which causes this issue.
Cheers,
Edward
P. S. This is open source so if anyone has interest in adding PDB
corruption handling code to relax, that would be most welcome.
2009/12/4 Tiago Pais <tpais@xxxxxxxxxxx>:
The internal reader accepts
these CONECT records perfectly. An easy test is to read in the PDB
file with CONECT records with the internal reader and then write it
out again. They should be preserved. If not, this is a bug which can
be reported at https://gna.org/bugs/?func=additem&group=relax which I
can then repair.
I think the mf_multimodel script uses the internal reader...what is the
command to read with the internal reader?
This is an argument to the structure.read_pdb() user function. This
now defaults to the internal reader.
I have executed the command structure.write_pdb() and the pdb file written
does not keep the lines with CONECT. This seems to be a similar to the
problem that Michael has reported a couple of days ago when using
modelsel.py.
I have tried to read the pdb with parser='scientific' and the problem
about
the "CONECT lines" disappears.
Do you want me to write a bug report anyway?
Regards,
TiagoP
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RE: MF_Multimodel