Hi,
Thank you very much for your email. One question about the
consistency_tests.py file, when using consistency_tests.py to extract
J (0) from one field strength data R1/R2/NOE, following parameter is
needed to set:
# Set the angle between the 15N-1H vector and the principal axis of
Hi Mengjun,
All of your questions are answered by the literature behind this
analysis. There are three key references as stated in chapter 2 of
the relax manual:
- Fushman, D., Tjandra, N., and Cowburn, D. (1999). An approach to
direct determination of protein dynamics from 15N NMR relaxation
Hi Edward,
Thank you very much for your suggestions. I will read these papers
carefully. Thank you.
Regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Hi Mengjun,
All of your questions are answered by the literature behind this
analysis. There are three key references
Update of bug #20674 (project relax):
Category:relax sample scripts = relax's source code
Status: Confirmed = Fixed
Open/Closed:Open = Closed
Summary:
Hi Mengjun,
This bug has now been fixed. The problem was with the very first
residue, as the PDB file has no H atom for it. Normally this is not
an issue because the first atom should normally not be visible in a
nitrogen HSQC. So there are 3 ways of fixing the problem. You could
wait until a
Hi Edward,
Thank you very much. I am a little bit confused, the pdb file
2QFK_MONOMERHabc5.pdb have been added H by software reduce, I also
check the first residue GLY, which has 5 H atoms. Perhaps I
misunderstand your meanings, do you mean the 2QFK_MONOMERHabc5.pdb
file (I have
Hi,
The script you use is trying to extract the atom with the name 'H'
from the file. You will not find this for GLY1. This PDB file has
atoms H1, H2, H3, etc, but no 'H'. Therefore you won't be able to
define the N-H bond in this way. Also note that the nitrogen is not
in a peptide bond, and
Hi Edward,
Thank you so much for your explanations, now it is clear for me that
the 5 H of the first reside GLY is not from peptide bond, perhaps it
is better to deselect the first residue as you suggested. Thank you
very much.
Regards,
Mengjun
Quoting Edward d'Auvergne
Hi Edward,
Thank you so much for your suggestions. I will read it carefully.
Regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Hi,
The best way would be to read the manual. Sebastien Morin has written
a nice guide with step-by-step instructions on what you need to do in
URL:
http://gna.org/bugs/?20674
Summary: UnboundLocalError in consistency_tests.py
Project: relax
Submitted by: None
Submitted on: Thu 28 Mar 2013 03:37:52 PM UTC
Category: relax sample scripts
Severity: 3
Additional Item Attachment, bug #20674 (project relax):
File name: T1 dhp 700.txt Size:74 KB
File name: T2 dhp 500.txt Size:67 KB
File name: T2 dhp 700.txt Size:68 KB
File name: logconsistency Size:371 KB
Hi Mengjun,
Could you also attach the PDB file? I need it to be able to run the
script and replicate the problem.
Cheers,
Edward
On 28 March 2013 16:39, anonymous no-reply.invalid-addr...@gna.org wrote:
Additional Item Attachment, bug #20674 (project relax):
File name: T1 dhp 700.txt
Hi again,
I was wondering if you have read the consistency testing part of the
relax manual written by Sebastien Morin (the person who implemented
this analysis). Specifically this section:
http://www.nmr-relax.com/manual/Consistency_testing_script_mode_relaxation_data_lo.html
Note the text,
Additional Item Attachment, bug #20674 (project relax):
File name: 2QFK_MONOMERHabc5.pdb Size:282 KB
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Update of bug #20674 (project relax):
Status:None = Confirmed
Assigned to:None = bugman
Operating System: Microsoft Windows = All systems
Hi Edward,
Thanks. I have submitted the pdb file. I understand that the
consistency test is for 2 field nmr data, for example, by comparing
the J(0) at 500 MHz and J(0) at 700 MHz, so I loaded the two field
data when using consistency_tests.py. I am confused that if one field
data is
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