Hi Herman, Strictncs is still used for viral capsids and other high NCS structures. It works very well in Refmac as long as your MTRIX records (in the PDB file) are correct and you have the identity MTRIX as well. The keyword is simply 'strictncs'. You can even combine strict and local NCS if you want in Refmac (not sure you should want to do that, but you can).
Shameless plug: PDB_REDO automatically deals with strict NCS if you work on your own structures. PDB entries with strict NCS are still checked manually because there used to be a lot of annotation errors with respect to strict NCS. It is much less common now, but I still find the odd new one :( Cheers, Robbie Date: Mon, 20 Apr 2015 08:01:26 +0000 From: herman.schreu...@sanofi.com Subject: [ccp4bb] AW: [ccp4bb] on NCS restraint To: CCP4BB@JISCMAIL.AC.UK Dear Smith, There used to be something called “strict NCS“ which meant that instead of many identical subunits, only one “average” subunit was refined, which would speed up the refinement significantly, at the expense of requiring that all subunits are exactly identical. I do not think that this option is used anymore and most refinement programs would require NCS related subunits to be similar, but not identical to each other. As Robbie Joosten pointed at, this can help a lot, especially when you do not have high resolution data. So for data with better than 2.0 Å resolution, including NCS restraints would probably not make a big difference, but otherwise I would switch them on. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu Gesendet: Freitag, 17. April 2015 06:02 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] on NCS restraint Dear Jurgen, My understanding is that NCS restraint can significantly enhance the speed of calculation, but considering the subunits even with the eactly same sequence may not be identical, to have NCS restraint may be not necessary or may be not good for the refinement, am I right? Smith At 2015-04-17 09:09:05, "Jurgen Bosch" <jbos...@jhu.edu> wrote: yes. Have two sets of NCS operators one that describe the four subunits and one describing the two subunits. If during the refinement of your structure you should find out that the subunits are not identical to each other you can relax the NCS weights. Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Apr 16, 2015, at 9:02 PM, Smith Lee <00000459ef8548d5-dmarc-requ...@jiscmail.ac.uk> wrote: Dear All, If a protein contains 6 subunits, 4 subunits from the same sequence (subunit A, B, C, D all from the same sequence), each of the 2 other subunits from 2 diffrent sequences (subunit E from the second sequence, subunit F from the third sequence), in this situation should I use NCS restraint or not? If my protein contains 2 subunits, both of the 2 subunits composed of the eaxctly same sequence, however supposing the 2 subunits have a little diffrent conformation, in this situation should we use NCS retraint or not? Smith
