 |
 |
Dear all, Many thanks for all of your suggestions - it seems that I was looking with the wrong search terms (perturb => shake) and there are indeed many tools out there for performing this. Problem solved :-) Best wishes Graeme > On 17 Aug 2017, at 18:18, Victor Lamzin <[log in to unmask]> wrote: > > Dear Graeme, > You can also type the following on a command line, optional commands are given in square parentheses. > Victor > > $warpbin/arp_warp > mode shakemodel allatoms > files ccp4 xyzin FILENAME.pdb xyzout FILENAME.pdb > symmetry SPACEGROUP > shakemodel [ bexclude B1 ] [ breset B1 B2 ] [ randomise X ] [ shift X Y Z ] > end > > > On 17/08/2017 17:17, Graeme Winter wrote: >> Dear All, >> >> Is there a protocol out there to gently perturb atomic positions so that re-running refinement can essentially put them back without bias from the original refinement? In particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I do not want to run the lower resolution refinements with the "memory" of the weak high resolution data present... and only have the refined structure to work from... >> >> Am using refmac5, but any pdb randomizer would hit the spot >> >> Many thanks Graeme >> > -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom