[phenixbb] input initial TLS parameters

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Sun Feb 24 10:39:39 PST 2008

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).


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