[phenixbb] elbow question

[Schubert, Carsten [PRDUS]]

Nigel,

very good. I must have missed that. Did a quick dig through the web-help and did not see (or missed) these options before shooting of the suggestion.

Cheers,

	Carsten


> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Nigel Moriarty
> Sent: Friday, June 03, 2011 11:24 AM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] elbow question
> 
> Carsten
> 
> There are three levels of pH dependance in eLBOW at the moment. From
> the
> 
> phenix.elbow --help
> 
> --pH=PH               specify --pH=low to retain exact input chemistry
>                         --pH=neutral to remove hydrogens from acids ...
>                         --pH=high to add hydrogens to amines
> 
> Neutral pH (the default) also removes hydrogens from phosphates.
> 
> If you are referring to in situ pH calculations, its on the list.
> 
> Nigel
> 
> 
> On Fri, Jun 3, 2011 at 7:10 AM, Schubert, Carsten [PRDUS]
> <CSCHUBER at its.jnj.com> wrote:
> > Hi Nigel,
> >
> > picking up on that thread: Any plans in the works to add pH dependent
> protonation to elbow? I don't think this is available yet.
> >
> > Thoughts?
> >
> > Cheers,
> >
> >        Carsten
> >
> >
> >> -----Original Message-----
> >> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> >> bounces at phenix-online.org] On Behalf Of Nigel Moriarty
> >> Sent: Thursday, June 02, 2011 2:58 PM
> >> To: PHENIX user mailing list
> >> Subject: Re: [phenixbb] elbow question
> >>
> >> Wolfram
> >>
> >> There is a bug that adds the hydrogen. I corrected it and generated
> the
> >> attached file. The bug fix will be in a future nightly build very
> soon.
> >> Note that the hydrogens are not on the phosphates because eLBOW
> assumes
> >> a neutral pH. If you want them, I can provide a restraints file
> >> including them.
> >>
> >> Thanks
> >>
> >> Nigel
> >>
> >> On Thu, Jun 2, 2011 at 7:32 AM, wtempel <wtempel at gmail.com> wrote:
> >> > Dear colleagues,
> >> > am I alone in thinking that in my example phenix.elbow gave me
> more
> >> > than what I was asking for, specifically atom H11 attached to
> sulfur?
> >> > Is it added by elbow, or does it originate from the "--chem=tpp"
> >> > input?
> >> > Best regards,
> >> > Wolfram Tempel
> >> >
> >> > command line: phenix.elbow --chem=tpp --mogul phenix version:
> >> > 1.7.1-743
> >> >
> >> > _______________________________________________
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> >> > phenixbb at phenix-online.org
> >> > http://phenix-online.org/mailman/listinfo/phenixbb
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Nigel W. Moriarty
> >> Building 64R0246B, Physical Biosciences Division Lawrence Berkeley
> >> National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709
> >> Email : NWMoriarty at LBL.gov Fax   : 510-486-5909       Web  :
> >> CCI.LBL.gov
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
> 
> 
> 
> --
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
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