Hi again ccp4bb. Thanks for your help and sorry for the spam! I've chased
down the variables and figured out how to export them as full floats with a
simple print command. I'll put together a script for anyone who wants to do
so in the future.
Cheers,
Shane
On Wed, Apr 15, 2015 at 12:21 PM, Shan
Dear Shane,
It's not CCP4, but Tom Terwilliger's find_ncs program works conveniently. Like
coot, it's only returning 4 decimal places, if that's a problem (though adding
a 5th decimal place would only typically change the result of a rotation by
hundredths of an Angstrom). I've just tried it:
>
> good enough to pass the orthonormal test.
.. scratch that, it passes sometimes and still fails for other
structures/chains. So I'm still in search of a higher-precision export
Shane
On Wed, Apr 15, 2015 at 11:44 AM, Shane Caldwell wrote:
> Hi Bernhard, thanks for the pointer. It looks lik
Hi Bernhard, thanks for the pointer. It looks like most of the coot ncs
functions don't print the matrix values, which made exporting them tricky,
especially because I'm pretty new to scripting in Python.
I have 4 chains, and
ncs_ghosts(0) just spits out
result is [['NCS found from matching Chain
Just for completeness, of course (!?) you can get something like this in
Coot. In terms of return value and accuracy (>>3 digits) I would use the
scripting function:
ncs_ghosts(imol) - pythonic
(ncs-ghosts imol) - schemey
imol - your protein with NCS
Bernhard
Alright, thanks! It
On 04/01/2015 08:47 PM, Shane Caldwell wrote:
I guess the next, probably more general question for the bb is: which utilities
export an NCS transformation matrix with more precision?
TAJones' "O" program allows you to specify output format like
write .LSQ_RT_m2m ncs.odb (3f16.10)
which gives
On Wed, 1 Apr 2015 17:52:44 -0400, Shane Caldwell
wrote:
>Hi ccp4bb,
>
>I'm trying to solve a problem I never quite figured out in the past. I'd
>like to use the *sortwater* utility to send my picked waters to various
>protein chains, and to give them the same residue number if they are
>NCS-equ
the test limit is perhaps over-tight
data eps/0.0001/
Phil
On 2 Apr 2015, at 00:34, Dale Tronrud wrote:
> I think you are on the right track - There are not enough decimal
> points in your matrix elements to pass the orthonormal test. This test
> checks that the length of each row (x^2+y^2
I should maybe add some code to orthonormalise the matrix if it's not too far
off (which would be approximate). I haven't looked at this program for a long
time (nor indeed used it), so don't hold your breath
Phil
On 1 Apr 2015, at 22:52, Shane Caldwell wrote:
> Hi ccp4bb,
>
> I'm trying to
Alright, thanks! It's a good thing, then, I spent the afternoon brushing up
on matrices.
I guess the next, probably more general question for the bb is: which
utilities export an NCS transformation matrix with more precision?
*superpose* and *gesamt* only export three decimals, though I'm sure the
I think you are on the right track - There are not enough decimal
points in your matrix elements to pass the orthonormal test. This test
checks that the length of each row (x^2+y^2+z^2) is equal to one and the
dot product of each row with every other row is equal to zero. If the
values on your
Hi ccp4bb,
I'm trying to solve a problem I never quite figured out in the past. I'd
like to use the *sortwater* utility to send my picked waters to various
protein chains, and to give them the same residue number if they are
NCS-equivalent, as the manual outlines.
http://www.ccp4.ac.uk/html/sortw
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