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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]
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: [email protected] [mailto:phenixbb- [email protected]] 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
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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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov