Re: [ccp4bb] phenix refinement about cis-proline

[Philippe BENAS]

Dear Niegel,
May be Shijun had to cancel his registration to the PhenixBB as I had to do 
since 2015 due to "too many bounces" whatever the email address I used, 
professional, yahoo or gmail ?... Has this been fixed at some point ?

All the best,Philippe
 Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Nigel Moriarty <nwmoria...@lbl.gov>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 2 mars 2018 8h25
 Objet : Re: [ccp4bb] phenix refinement about cis-proline
  


Shijun
You can ask all the questions you like about Phenix on PhenixBB. However, to 
answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification {    cis_trans_mod = cis *trans    
residue_selection = None  }
to any number of peptides.
Cheers
Nigel
---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence 
Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : nwmoria...@lbl.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
On Thu, Mar 1, 2018 at 10:58 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

Dear all    I am refining a structure which has cis-Pro and trans-Pro, the 
tans-Pro is gone when I set the "threshold degrees for cis-peptide " from 
default 45 to 65, but still has cis-Pro. While no significant change when I set 
it to 15. My question is how to set in phenix refinement to clear the Pro 
residues in cis- or trans- conformations.Best Regards shijun  



   

Re: [ccp4bb] phenix refinement about cis-proline

[Nigel Moriarty]

Shijun

You can ask all the questions you like about Phenix on PhenixBB. However,
to answer your question, you can set all peptides to trans using

apply_all_trans=True

or more specific control using

apply_cis_trans_specification {

cis_trans_mod = cis *trans

residue_selection = None

  }

to any number of peptides.

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 Thu, Mar 1, 2018 at 10:58 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
>I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro
> is gone when I set the "threshold degrees for cis-peptide " from default 45
> to 65, but still has cis-Pro. While no significant change when I set it to
> 15. My question is how to set in phenix refinement to clear the Pro
> residues in cis- or trans- conformations.
>
> Best Regards
>
> shijun
>

[ccp4bb] phenix refinement about cis-proline

[张士军]

Dear all

   I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is 
gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, 
but still has cis-Pro. While no significant change when I set it to 15. My 
question is how to set in phenix refinement to clear the Pro residues in cis- 
or trans- conformations.

Best Regards

shijun