And here is a more compact/elegant version courtesy of Paul that accomplishes a
similar function in half the code - morphing with a radius decreasing from 12
to 6 Å over an arbitrary number of cycles, using a map initially blurred with a
B-factor of 100, decreasing incrementally to 0 (the
On 30/12/13 17:42, Oliver Clarke wrote:
And here is a more compact/elegant version courtesy of Paul that accomplishes a
similar function in half the code - morphing with a radius decreasing from 12
to 6 Å over an arbitrary number of cycles, using a map initially blurred with a
B-factor of
OK - so the following will redirect the console output to a file, then look for
a matching chain from the sequence in test.fasta - after that I can grep
testing.log for the appropriate pattern and assign it to a best_chain_id
variable of some sort:
import subprocess
import sys
so =
On 30/12/13 22:45, Oliver Clarke wrote:
Great! Next scripting question that I’m puzzling over - how to take a set of
sequences (present in a single fasta file), in arbitrary order, match and align
them to their corresponding homologous subunits in a PDB file, and use
align_and_mutate to
After I sent that I did find a way to redirect the console output to a file -
not pretty but it works:
import sys
import os
import subprocess
so = open(testing.log, 'w', 0)
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0)
os.dup2(so.fileno(), sys.stdout.fileno())
And then I can grep the
Hi Mark,
You can use the Fixed atoms... widget in the toolbar (below regularize) to do
just that - click on it and you can set the fixed atoms.
The regularize command (without a map) tends to move things more than I think
they should. Perhaps the end atoms should be fixed. How would one
Oliver,
Thanks for the reply. I am familiar with the widget. But that wouldn't
restrain (rather than constrain) the other atoms. Perhaps just fixing ends
will work. I'll have to play around with it next time I'm fitting. Many
thanks for your ideas.
-Mark
On 31/12/13 01:39, Mark A Saper wrote:
The regularize command (without a map) tends to move things more than I think they
should. Perhaps the end atoms should be fixed. How would one restrain atoms to their
starting coordinates? From the old days I recall Frodo's REFI command being
better
