Here is a VERY oldfashioned solution. Find the centre of mass of your molecule.
pdbset xyzin mol.pdb end tells you that Make a mini PDB with the CRYST1 record, and two "atoms" - one at 0 0 0, the other at the centre of mass with some atom type say C then distang xyzin min.pdb radi C 20 say dist all end This will give you the symmetry equalent for the Centre f Mass transformed by all symmetry operators Then apply that symmetry operator to your coordinates.. BUT this will NOT have checked the best origin shift.. That is another problem.. Eleanor And Yes Randy - I am sure this could be done more easily and elegantly in Python.. On 14 December 2017 at 09:34, Tim Gruene <tim.gru...@psi.ch> wrote: > Dear Tommi, > > 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. > > 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. > > 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 >
