The latter....something more analytical to split individual chains into smaller groups (e.g. like to define tls groups). Thanks, 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] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________ From: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] Sent: Thursday, July 12, 2012 12:19 PM To: PHENIX user mailing list Subject: Re: [phenixbb] segmented rigid body refinement On Thu, Jul 12, 2012 at 9:16 AM, Gino Cingolani mailto:[email protected]> wrote: I'm refining a large oligomeric structure at low res (~6A). I'd like to define groups to use for 'segmented rigid body refinement'. Is there any rational way to define 'segments'? My macromolecule is already an oligomer on its own, so, intuitively, each protomer is a segment. Not sure I understand the question - do you mean you want to split the individual chains into smaller groups, and you're looking for an analytical method for determining these groups? -Nat

Hi Gino, you could use phenix.find_tls_groups but the tool requires meaningfully refined B-factors and more or less good geometry so the secondary structure can be identified automatically. If this is your case then phenix.find_tls_groups might work for you. Pavel On 7/12/12 9:33 AM, Gino Cingolani wrote:

The latter....something more analytical to split individual chains into smaller groups (e.g. like to define tls groups).

Thanks,

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] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

------------------------------------------------------------------------ *From:* [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] *Sent:* Thursday, July 12, 2012 12:19 PM *To:* PHENIX user mailing list *Subject:* Re: [phenixbb] segmented rigid body refinement

On Thu, Jul 12, 2012 at 9:16 AM, Gino Cingolani mailto:[email protected]> wrote:

I'm refining a large oligomeric structure at low res (~6A). I'd like to define groups to use for 'segmented rigid body refinement'. Is there any rational way to define 'segments'? My macromolecule is already an oligomer on its own, so, intuitively, each protomer is a segment.

Not sure I understand the question - do you mean you want to split the individual chains into smaller groups, and you're looking for an analytical method for determining these groups?

-Nat

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