Hmm - I use this quite a bit.
ifier.
You cant start Autoamore for a particular model until that has been
entered into the model database - the first Q you are asked from the GUI
is "Which model?" But you can certainly close the model database once
you have entered the model name with a unique identifier.
The orde of operations is:
sortfun to reformat the observed data
tabfun to generate SFs from the model
rotfun
trafun
fitfun
However if you have already run sortfun or tabfun with that input the
gui will not repeat the steps.
Could you have used the same name for different models perhaps - that
will get the software well confused!
Eleanor
On 04/27/2011 04:26 PM, Chris Richards: on wrote:
On 27 Apr 2011, at 15:02, Edward A. Berry wrote:
No, that would be the TABFUN step. You are running SORTFUN which takes your
experimental data and puts in the the .tab format required by the subsequent
routines. And with the HKLIN command line variable you are telling it to
get data from AmoreModel_MR_trial.mtz . Does that file exist, is it
readable, and path name correct?
The file doesn't exist, it's a figment of the GUI's imagination. After some
poking around, I've now got it to work properly.
The problem seems to be that the GUI is very sensitive to the order in which
you enter data. When you choose to run AMoRe, it pops up an AMoRe window and a
Model Database window. If you enter data into these in the order specified in
the tutorial, it will run the scripts for a model in the form of SFs from an
MTZ, even though the Model Database window claims to be using a model in the
form of coordinates.
The trick to getting it to work seems to be:
1) Open the Model Database window. Enter your pdb filename. Don't even think about clicking "Close",
despite what the tutorial says. Click "Save&Exit", and never open the window again. If you do
have to open it again, "Restore Default Parameters" and start from scratch.
2) Open the AMoRe window, set up the job parameters and run the job.
Doing this will get it to run TABFUN on your pdb file rather than SORTFUN on a
non-existent mtz file. Most of the time.
Thanks to Stefano Trapani and Jorge Navaza for pointing us in the direction of
the standalone AMoRe.
Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
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