Hi, The purpose of NCS is to reduce the degrees of freedom in order to avoid over refinement -not only to expedite refinement. Strict or restrained NCS should be applied at lower resolutions (<2.7Å) or data completeness. Forgo NCS If you have a complete and better than 2.5Å dataset. Also, you can define the regions where NCS is applied and thus avoid loops/regions where the NCS is violated.
Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York 160 Convent Ave, MR-1135 New York, NY 10031 (212) 650-6070 rkha...@ccny.cuny.edu<mailto:rkha...@ccny.cuny.edu> On Apr 20, 2015, at 4:01 AM, herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> wrote: 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<mailto: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<mailto: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<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu<http://lupo.jhsph.edu/> On Apr 16, 2015, at 9:02 PM, Smith Lee <00000459ef8548d5-dmarc-requ...@jiscmail.ac.uk<mailto: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
