Hi,
I just made a bug report for the fixed tensor issue in the mf_multimodel.py
script. Meanwhile, been testing several possibilities and this is what I
have found:
1- The script runs well in fixed tensor "mode" only when the tensor is set
to isotropic. However (!), note that the S2 values only show in the XML file
and not in the written file [I have added this line to the script
"value.write(param='s2', file='resultsPHS', force=True)", however the
created file plots zero values for the S2 of all residues].
2-The script appears to run well for a fully anisotropic tensor only when
the tensor is not set to fixed (fixed=False). However (!), when I look at
the XML results file, no S2 values show up (I am creating a bug report for
this too).
3-issue number 2 occurs both with the internal or scientific pdb reader. It
also happens even without any CONECT lines in the PDB file.
I'm sorry for all the "bugging"!
Best regards
Tiago P
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: sexta-feira, 4 de Dezembro de 2009 16:13
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: MF_Multimodel
Hi,
2009/12/4 Tiago Pais <tpais@xxxxxxxxxxx>:
Hi,
I am not really sure if I understand what you mean by a "corrupted PDB
issue"?
This just means a file that does not conform to the PDB standards
(many do not but are nevertheless not too corrupted to read). This I
can easily check if you create a bug report and attach a fragment of
the file.
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?
Molmol will delete all CONECT records from a PDB file you open, and
you then have to calculate bonds to get them back. In the file output
by Molmol, are the CONECT records in there?
Cheers,
Edward
RE: MF_Multimodel