Dear Geoffrey,
it seems you read the manual
(http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC137),
but you didnt replace the imol and master-chain-id with a value. You
want to specify the molecule (imol, e.g. 0) and the chain from which to
copy to others (e.g. "A"), so:
|(copy-from-ncs-master-to-others /imol/ /master-chain-id/)|
e.g.
scheme/guile:
|(copy-from-ncs-master-to-others 0 "A")|
python:
|copy_from_ncs_master_to_others(0, "A")|
Another way to apply NCS is via Extensions: Extensions->NCS->Copy NCS Chain.
Hope this helps,
Bernhard
P.S. There is a Coot BB: http://www.jiscmail.ac.uk/lists/coot.html
Geoffrey Feld wrote:
This post has a question and an answer (good karma)...answer first
In response to Matt's question about periplasmic harvesting, we do an
osmotic lysis of e.coli by a series of centrifugations. First, harvest
your cells normally (4k 15 min). Then vigorously resuspend in a 20%
(w/v) sucrose, 1 mM EDTA + buffer (we use 20 mM tris). My best yields
are 1-2 mL sucrose buffer per 1 mg of protein you expect to get.
Equilibrate at RT ~20 min before centrifuging 8k 15 min. Then
resuspend the pellets in 5 mM MgSO4 same vol ratio as before (should
see foam if you did it right). Finally, spin that down 9k 15 min and
collect your periplasmic lysis. You'll want to adjust the pH of the
product, depending on what column you want to purify, ours comes out
<7 and needs to be >7 for Q sepharose. Enjoy!
And my question: I have 3 distinct NCS pairs in the structure I'm
refining, and I'd like to make my job a bit easier by applying the NCS
edit function in COOT after a round of tinkering. However, when I go
to type in the command: copy-from-ncs-master-to-others imol
master-chain-id, COOT just sits there like it doesn't know what I'm
talking about. Maybe I'm not telling it the proper syntax for
master-chain-id? I'm using COOT 0.5.2.
'Preciate it,
Geoff
--
Geoffrey K. Feld
College of Chemistry
University of California, Berkeley
"Vigilia pretium libertatis"
