Yeah, it's the relaxation of the 15N so the spin name should be 'N'.
It might give strange results having vectors of zero length ;)
Edward
On Fri, Oct 24, 2008 at 2:38 AM, Tyler Reddy [EMAIL PROTECTED] wrote:
Maybe I need to use 'N' for the spin_name column because the extracted
vector is
Hi Tyler,
If you want all output from relax to go to a log file, use the option
'-l'... (relax -l script.py)
If you want all output from relax to go to a file AND the terminal
(display), use the option '-t'... (relax -t script.py)
These options are visible when typing : ./relax --help (or
Oh... Sorry... It's still early in the morning here (Quebec City)...
...
Dont' forget to specify a log file...
LOG - relax -l LOG script.py
TEE - relax -t LOG script.py
If you just specify the script, the script will be erased by the log...
Cheers,
Séb
Sébastien Morin wrote:
Hi
:S It overwrites a pre-existing file! And the important script of
all things!!! That'll have to be fixed. Seb, could you submit a bug
report for that?
Cheers,
Edward
On Fri, Oct 24, 2008 at 2:12 PM, Sébastien Morin
[EMAIL PROTECTED] wrote:
Oh... Sorry... It's still early in the morning
Thanks Seb.
It looks like my 'prolate' iterations in the 2nd round are maxing out and this
is causing an error output (even though the first round seemed okay):
k: 311 xk: array([ 2.60992216e-11, 5.0957e+02])
fk: 2254.7254621187344
Entering sub-algorithm.
Hi,
This is a strange bug if it only occurred in the second round. I
can't see what the problem is right now so I will have to think about
this one for a bit. In the mean time, would you be able to create a
bug report for this issue? Additional information may be required to
solve this one.
The aic results file should be attached to the bug report. It looks like it's
there when I check it.
Quoting Edward d'Auvergne [EMAIL PROTECTED]:
Hi,
I've tried the PDB file and it seems to be fine. There are no strange
formatting issues there. Therefore it is caused by the loaded
Right, got it and can reproduce the bug. I think I know what the
issue is, but would you be able to attach the full_analysis.py script
to the bug report so I can confirm it? Well, actually there are
probably two issues, the first being a problem with the full analysis
script not setting the spin
Ok, I updated to the latest build and made the adjustment. Presumably
since the
heteronucleus is set to 'N', 'H' is enough info for that column in the
sequence
file? It's working now for 'prolate' in any case.
I see that you can change the bug report display to show 'closed'
reports, sorry
Maybe I need to use 'N' for the spin_name column because the extracted
vector is
H-H, which is very weird. It took 10 rounds for the 'prolate' script to
converge:
RelaxWarning: The XH bond vector for residue ':[EMAIL PROTECTED]' is of zero
length.
Extracted H-H vectors for ':[EMAIL PROTECTED]'.
Okay, I submitted the report. Let me know if there's more information you need
or a better way to submit bug reports in general.. haven't done this before.
Also, I had to manually copy/paste the output, and while it looks fine, if
there is a problem with the same pdb structure getting read twice
Hi Tyler,
Do you get the same error when trying the 'oblate' or 'ellipsoid'
diffusion tensors ?
Sébastien
Tyler Reddy wrote:
I'm having an issue with the full_analysis.py script. It seems to work
fine when
DIFF_MODEL = 'local_tm' or 'sphere' (converges on 4th round) but for 'prolate'
I
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