Re: [ccp4bb] Refmac5 question

2020-02-04 Thread Robbie Joosten 
Hi Joern,

The logic behind it this is that those are hydrogen position that are uncertain 
due to possible flips and free rotation (tyr, thr, ser). You should probably 
only set these occupancies to 1.00 after you have studies the local hydrogen 
bonding network.

Cheers,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Joern
> Krausze
> Sent: Tuesday, February 4, 2020 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac5 question
> 
> Dear all,
> 
> I've got a Refmac5 question. When I refine my protein structure in Refmac5
> with the options make hydrogen ALL and make hout yes, some of the
> hydrogen atoms in the output file have zero occupancies. At a first glance,
> only the the H-atoms attached to OG1 of Ser, ND2 of Asn, and NE2 of Gln are
> affected. These hydrogen atoms were present in the input file with their
> occupancies matching that of the residues they are attached to. Is there a
> reason for this behavior that I might be missing? I am currently running
> Refmac version 5.8.025.
> 
> 
> 
> 
> Best regards,
> 
> Joern
> 
> 
> --
> *
> Address:
> 
> Joern Krausze
> Department of Plant Biology
> Braunschweig University of Technology
> Spielmannstr. 7
> 38106 Braunschweig
> Germany
> 
> Email:  j.krau...@tu-braunschweig.de <mailto:j.krausse@tu-
> braunschweig.de>
> Phone:  +49 (0)531 3915858
> *
> 
> 
> 
> 
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Re: [ccp4bb] Refmac5 question

2020-02-04 Thread Huw Jenkins 
> On 4 Feb 2020, at 09:24, Joern Krausze  wrote:
> 
> These hydrogen atoms were present in the input file with their occupancies 
> matching that of the residues they are attached to. 

What happens with make hydrogen YES?

That should keep all hydrogens present in the input file 
(http://www.ccp4.ac.uk/html/refmac5/keywords/restraints.html#make_hydr)


Huw



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[ccp4bb] Refmac5 question

2020-02-04 Thread Joern Krausze 

Dear all,

I've got a Refmac5 question. When I refine my protein structure in 
Refmac5 with the options make hydrogen ALL and make hout yes, some of 
the hydrogen atoms in the output file have zero occupancies. At a first 
glance, only the the H-atoms attached to OG1 of Ser, ND2 of Asn, and NE2 
of Gln are affected. These hydrogen atoms were present in the input file 
with their occupancies matching that of the residues they are attached 
to. Is there a reason for this behavior that I might be missing? I am 
currently running Refmac version 5.8.025.



Best regards,

Joern

--
*
Address:

Joern Krausze
Department of Plant Biology
Braunschweig University of Technology
Spielmannstr. 7
38106 Braunschweig
Germany

Email:  j.krau...@tu-braunschweig.de
Phone:  +49 (0)531 3915858
*




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