Re: [phenixbb] elbow question

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: [email protected] [mailto:phenixbb- [email protected]] 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

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Hi Nigel,

picking up on that thread: Any plans in the works to add pH dependent

On Fri, Jun 3, 2011 at 7:10 AM, Schubert, Carsten [PRDUS] wrote: protonation to elbow? I don't think this is available yet.

...

Thoughts?

Cheers,

       Carsten

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-----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

...

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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:

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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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb