[phenixbb] segmented rigid body refinement

Pavel Afonine pafonine at lbl.gov
Thu Jul 12 09:42:27 PDT 2012


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
> 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 Nathaniel Echols 
> [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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