On 12/14/2017 04:34 AM, Tim Gruene wrote:
Dear Tommi,
1.
if you only need to consider translations, and not other symmetry operations,
you can use moleman2, convert coordinates to fractional ones and add or
substract the integer that brings the centre of mass closest to 0.
2.
In case you want to take the symmetry operations into account, you would have
to check for each operator, which one brings the centre of mass closest to 0.
This could most likely be scripted with moleman2.
3. If you also want to consider origin shifts (in spacegroups where alternate
origins exist) the achesym site does that. (If you can't bring the molecule to
the origin, bring the origin to the molecule)
4. If you also want to pack multiple chains that may have been built in various
locations into a compact multimer, the achesym site does that.
But no, it's not a simple script.
And I believe the achesym site works not so much to put the center of mass near the
origin, but to put as many atoms as possible in first unit cell (0<x,y,z<1;
fractional). Moving closer to the origin within the unit cell is then a secondary
priority.
Best,
Tim
On Thursday, December 14, 2017 8:39:48 AM CET Kajander, Tommi A wrote:
Dear Paul,
Yes thank you. This was the best answer i think. Someone else already also
suggested that also. Coot is very handy indeed.
(Would still be curious of knowing how to find the "closest to origin" copy
otherwise - but this solves my problem)
Thanks to all who responded.
Cheers,
Tommi
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley
<pems...@mrc-lmb.cam.ac.uk> Sent: Thursday, December 14, 2017 3:25:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coordinate transformation
On 13/12/2017 13:50, Kajander, Tommi A wrote:
Hello,
If someone could point this out would be very helpful... Wasnt there a
simple script somewhere that would transfer coordinates close to origin -
if they for some reason are not? Just cant find anything right away.
At the risk of not answering the question because it's not a simple script,
my I recommend Coot?
File -> Open -> yourcoords.cif
Draw -> Cell & Symm -> Master Switch -> Yes
Show Unit Cells -> Yes
OK
Drag the View to the Origin # it's marked with an "O"
Middle-mouse click on an Symmetry-related Atom # that's close to the origin
Extensions -> Modelling -> Symm Shift Reference Chain Here
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Tim Gruene
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