Sean, thanks to you and to whoever else responded to my email. Yes, I'd like to get your script. Thanks in advance! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ---- Original message ----

Date: Fri, 28 Aug 2009 08:35:08 +0100 From: Wai-Ching Hon Subject: Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution To: PHENIX user mailing list

Dear Sean,

That sounds wonderful. Can I have your scripts too?

many thanks

waiching.

Sean Johnson wrote:

...

Gino,

My lab recently refined a 3.4 A structure and dealt with similar problems. We found that using secondary structure restraints was the only effective way to maintain reasonable geometry during refinement. It is kind of a daunting task to input all of the definitions by hand, so we wrote a couple python scripts that are integrated with PyMol to write the appropriate restraint definition files. All you have to do is click on the atoms that you want restrained. You are welcome to the scripts if you like. Feel free to contact me if you are interested.

Sean Johnson

Gino Cingolani wrote:

...

Hi Phenix community,

I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?

Thanks in advance for the feedback,

Gino

****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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