Thanks for all the suggestions, and I will try them immediately! Best
Yang > 在 2017年10月11日，上午8:55，Pavel Afonine <pafon...@gmail.com> 写道： > > And I should add this works just great! (given we are on the same page > defining 'great'). > > I used this for Cryo-EM model challenge; Nigel added this functionality at > that time to make this possible. > > Pavel > > On Wed, Oct 11, 2017 at 2:17 AM, Nigel Moriarty <nwmoria...@lbl.gov > <mailto:nwmoria...@lbl.gov>> wrote: > Since you are using phenix.real_space_refine, there is a rather brutal > parameter > peptide_link.apply_all_trans=True > > that will restrains all peptide links to be trans. It can help with moving > all cis to trans but you should check them as best you can at 4.3A. > > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : nwmoria...@lbl.gov > Fax : 510-486-5909 Web : CCI.LBL.gov <http://cci.lbl.gov/> > > On Tue, Oct 10, 2017 at 9:03 AM, Gert Vriend <gerrit.vri...@radboudumc.nl > <mailto:gerrit.vri...@radboudumc.nl>> wrote: > Look at http://swift.cmbi.ru.nl/servers/html/index.html > <http://swift.cmbi.ru.nl/servers/html/index.html> under "structure > validation" you will find a server that predicts which peptide planes most > likely need to be flipped. This server is the implementation of: > > Detection of trans-cis flips and peptide-plane flips in protein structures. > <https://www.ncbi.nlm.nih.gov/pubmed/26249342> > Touw WG, Joosten RP, Vriend G. > Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1604-14. doi: > 10.1107/S1399004715008263. Epub 2015 Jul 28. > > Good luck, > Gert > > On 10-10-2017 15:28, Yang Shi wrote: >> Hi, Tristan Croll, >> >> Thanks for your suggestion.I will consider to rebuild these first. >> >> Yang >> >>> 在 2017年10月10日，下午9:18，Tristan Croll <ti...@cam.ac.uk> >>> <mailto:ti...@cam.ac.uk> 写道： >>> >>> Relying on refinement to fix cis peptide bonds for you is unlikely to end >>> well. It looks to me like you really need to spend some time investigating >>> and manually rebuilding these first. >>> >>> On 2017-10-10 13:52, 师扬 wrote: >>>> Dear all, >>>> I am refining a model based on a 4.3A EM density map,and there are >>>> some cis-peptides in the beginning model. >>>> By using phenix.real_space_refine with a very low cis-peptide >>>> threshold (0), all the cis-peptide become to the twisted. >>>> The start Omega angle: >>>> cis-proline: 31.63 % >>>> twisted proline: 0.00 % >>>> cis-general: 11.11 % >>>> twisted-general: 0.05 % >>>> The final Omega angle: >>>> cis-proline: 0.00 % >>>> twisted proline: 27.55 % >>>> cis-general: 0.00 % >>>> twisted-general: 6.04 % >>>> My questions are: >>>> 1) What is the twisted peptide? >>>> 2) Is the amount acceptable at the current resolution? >>>> 2) How to refine it? >>>> Thanks in advance! >>>> Yang Shi >>>> 【网易自营|30天无忧退货】仅售同款价1/4！MUJI制造商“2017秋冬舒适家居拖鞋系列”限时仅34.9元>> >>>> [1] >>>> Links: >>>> ------ >>>> [1] http://you.163.com/item/detail?id=1165011&from=web_gg_mail_jiaobiao_9 >>>> <http://you.163.com/item/detail?id=1165011&from=web_gg_mail_jiaobiao_9> > > >
