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A question re: unresolved residues. Is it necessary to list unresolved residues in this file if no data was supplied for these residues? Example r1 file (made up):
1 2 3 2.7114 0.05 4. 2.6151 0.04
Do residues 1 and 2 need to be listed in the unresolved file?
Thanks, Doug
On Jan 10, 2008, at 3:59 PM, Sebastien Morin wrote: Thanks Ed !
Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not having any file for unresolved residues...
The lines :
=============
# The file containing the list of unresolved residues to exclude from the analysis.
UNRES = 'unresolved'
=============
could become :
=============
# The file containing the list of unresolved residues to exclude from the analysis (set this to None if no residue is to be excluded).
UNRES = 'None'
=============
and the lines :
=============
# Unselect unresolved residues.
unselect.read(name, file=UNRES)
=============
could become :
=============
# Unselect unresolved residues.
if not UNRES:
unselect.read(name, file=UNRES)
=============
This would avoid using an empty file for (non existant) unresolved residues or commenting 2 different lines in the code...
If you agree, I could make the change right away...
Ciao !
Sébastien
Edward d'Auvergne wrote: Done! See https://mail.gna.org/public/relax-commits/2008-01/msg00376.html.
The current version of the script in the 1.2 line will now properly
handle not having a PDB file if you set the value of PDB_FILE to None.
Nevertheless, I would be very careful with the conclusions. If there
are regions appearing to exhibit chemical exchange or slow nanosecond
motions - check very carefully that these motions are also present in
the local tm model MI results. If not, there is a good chance that
you have artificial motions!
Regards,
Edward
On Jan 10, 2008 8:20 PM, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi,
I am now helping someone to start with relax and got into a question
about the full_analysis.py script.
In the full_analysis.py script, the following code appears at line 550 :
# Load the PDB file.
if not local_tm:
pdb(name, PDB_FILE)
For a local tm, no PDB file is needed. That's logic. However, I would
have thought that no pdb file would also be needed for an isotropic
diffusion tensor (sphere).
Am I right ?
Can someone with no 3D structure use the full_analysis.py script to
optimize an isotropic diffusion tensor ?
Thanks !
Sébastien :)
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Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530
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Re: The use of a pdb with the sphere diffusion tensor