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
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
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
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.
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
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
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