[ccp4bb] Aw: Re: [ccp4bb] refmac5 problems with unnatural amino acid

[Deniz Üresin]

Hello and thanks for your answer (and sorry for the late reply)! To answer your questions:

1) Yes, I used the same dictionary for COOT and REFMAC.

 

2) Since I'm pretty new to crystallography, this is my first time working with CCP4 (for Windows) and I don't even know how to use
"REFI IDEALISE" or how to turn on "MONITOR MANY". I will take a look into that and give an update as soon as I have something new.

 

Again, thank you very much!

With kind regards,
Deniz

 

Gesendet: Mittwoch, 03. April 2019 um 13:37 Uhr
Von: "Eleanor Dodson" <eleanor.dod...@york.ac.uk>
An: "Deniz Üresin" <deniz.uere...@web.de>
Cc: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
Betreff: Re: [ccp4bb] refmac5 problems with unnatural amino acid

Qs..

1) You are using the same dictionaries for both REFMAC and COOT?

 

2) What happens in refmac if you just use REFI IDEALISE?

And turn on the option for REFMAC to

MONITOR MANY - it might tell you if there is some clash which is overriding the geometry restraints..

Eleanor

 

On Wed, 3 Apr 2019 at 12:24, "Deniz Üresin" <deniz.uere...@web.de> wrote:

Hello,

I'm trying to refine the structure of a protein mutant that has an unnatural amino acid in it. I created a restraint file for the AA and the mutation worked fine in COOT. But when I use refmac5 for refinement, it always changes the bond angle in the sidechain (an azide group, which should have a bond angle of 180°). I set the SD of the angle to 0 but that didn't help (the "refined" bond angle ends up somewhere between 120 and 150°).

Is there any other way to tell refmac5 to not alter that bond angle?

Thanks in advance,

Deniz Üresin

 

_________

Deniz Üresin

Institut für Biophysik

Johann Wolfgang Goethe-Universität Frankfurt am Main
http://www.biophys.uni-frankfurt.de/~bredenbeck/

 

 

---

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

---

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1