Re: [phenixbb] elbow question

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

_______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov