I use PISA for the compact molecule construction - it works very well, and probably should be the default at the end of every MR - it also tries to choose a sensible symm op which allows assemblies to be generated easily.
But then you would have to think about how to position that assembly as close to the origin as possible. One way to buld on my script would be to search distances between the centre of mass and all alternate origins - easy fenough or non-polar SGs .. Eleanor On 14 December 2017 at 16:38, 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. > > > 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 >> >>
