[phenixbb] input initial TLS parameters

[Paul Adams]

Hi Mark,

   if I understand Pavel correctly I think he is saying that TLSmd can 
provide both group definitions and initial values for the TLS 
parameters. In phenix.refine the only information that is required is 
the group definitions - the values for the TLS parameters will be 
refined using a procedure that discards any of the input values anyway. 
This is one of the things that has been done to make the procedure more 
stable. The TLS parameter values from TLSmd are, in many cases, probably 
good estimates for the true parameters, but they would need to be 
refined anyway.

   Cheers,
	Paul

Mayer, Mark (NIH/NICHD) [E] wrote:
> Hi Pavel,
> 
> I thought one of the main advantages for using the TLSmd server
> was that it provided the crystallographer with suggestions
> for the TLS staring groups (as well as the TLS values for
> these groups) avoiding the need to make somewhat arbitrary
> choices about the TLS group boundaries. 
> 
> If phenix then refines the TLS values for the groups picked
> with help pf the TLSmd server analysis which is this less
> good that starting TLS refinement in phenix without input
> from the MD server?
> 
> 
> -----Original Message-----
> From: Pavel Afonine [mailto:pafonine at lbl.gov]
> Sent: Sun 2/24/2008 12:44 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] input initial TLS parameters
>  
> Hi Jorge,
> 
>>     I tried to find a way to input initial TLS parameters for the 
>> groups into phenix. 
> 
> There is absolutely no need to give phenix.refine a start input values 
> for TLS groups: phenix.refine determines them automatically. All you 
> need to provide are the selections for TLS groups.
> 
>> I know many times this is not advisable, but I wanted to test what 
>> comes out from TLSmd server. 
> 
> This is not advisable, indeed (and not possible to do as well). 
> phenix.refine must do a better job in finding TLS parameters than TLSmd 
> server simply because phenix.refine uses the experimental data + very 
> sophisticated and robust refinement protocol, while the TLSmd server 
> relies on the B-factors in input PDB file (as far as I know, correct me 
> if it's not true).
> 
> Pavel.
> 
> 
> 
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> 
> 
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--
Paul Adams
Deputy Division Director, Physical Biosciences Division, LBL
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
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