On 12/14/17 6:38 PM, "Edward A. Berry" <ber...@upstate.edu> wrote:
>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. Actually the case in hand is a monomer in AU with biomol dimer generated by xtal symmetry. So 1) want to move close to origin then 2) get the transformation for dimer (coot + PISA seems to do fineŠ I thinkŠ wil check what happens in refinementŠ) Achesym just gave an error and didn't find any transformations for some reason - this is in F4132. No idea why it happened - will try to remember to report it. Thanks for the insights again, Tommi > >> 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 >> >> -- >> -- >> Paul Scherrer Institut >> Tim Gruene >> - persoenlich - >> OFLC/104 >> CH-5232 Villigen PSI >> phone: +41 (0)56 310 5297 >> >> GPG Key ID = A46BEE1A >>
