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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 <[log in to unmask]> 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 <[log in to unmask] <mailto:[log in to unmask]>> 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 : [log in to unmask] > Fax : 510-486-5909 Web : CCI.LBL.gov <http://cci.lbl.gov/> > > On Tue, Oct 10, 2017 at 9:03 AM, Gert Vriend <[log in to unmask] <mailto:[log in to unmask]>> 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 <[log in to unmask]> <mailto:[log in to unmask]> 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> > > >