Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-11 Thread Yang Shi
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 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

Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Pavel Afonine
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 wrote: > Since you are using phenix.real_s

Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Nigel Moriarty
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 B

Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Gert Vriend
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.

Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Yang Shi
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 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

Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Tristan Croll
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

[ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread 师扬
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: 31.6