[phenixbb] input initial TLS parameters

[Pavel Afonine]

The only information that is vital for phenix.refine are the selections 
for TLS groups, for example:

TLS grop #1: "chain A and resseq 1-200"
TLS grop #2: "chain B and resseq 34-500"
etc...
This information is obtained from TLSmd server. Sometimes though it is 
very easy just to have a look at your model to say what your TLS groups are.

The actual values of TLS matrices that TLSmd is producing as well are 
useless for phenix.refine simply because it has its own extremely 
sophisticated algorithm for finding these values. And this algorithm is 
much more powerful since it uses the experimental data. As an 
illustration, I re-refined 350 TLS containing structures from PDB using 
phenix.refine and I never observed any kind of refinement instability.

Pavel.



> This was my understanding, so TLSmd is still very useful
> for assigning the initial groups, which seems better than
> picking  by eye. Its interesting to know than phenix 
> then generates its own set of starting parameters
> Refmac uses the TLSmd parameter values as the
> input for further refinement, and in my experience
> is sometimes unstable.
>
> -----Original Message-----
> From: Paul Adams [mailto:PDAdams at lbl.gov]
> Sent: Sun 2/24/2008 3:31 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] input initial TLS parameters
>  
> 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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>
> --
> 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
> http://cci.lbl.gov/paul
>
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