[phenixbb] segmented rigid body refinement

[Gino Cingolani]

thanks for the prompt reply!

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:   gino.cingolani at jefferson.edu
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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine [pafonine at lbl.gov]
Sent: Thursday, July 12, 2012 12:42 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] segmented rigid body refinement

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:   gino.cingolani at jefferson.edu<mailto:gino.cingolani at jefferson.edu>
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: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>] on behalf of Nathaniel Echols [nechols at lbl.gov<mailto:nechols at lbl.gov>]
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 <Gino.Cingolani at jefferson.edu<mailto:Gino.Cingolani at jefferson.edu>> 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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