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> 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 > > On Tue, Oct 10, 2017 at 9:03 AM, Gert Vriend <gerrit.vri...@radboudumc.nl> > wrote: > >> Look at 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> <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 >> >> >> >
