[phenixbb] input initial TLS parameters

[Engin Ozkan]

The recently-rolled out version of the TLSMD server not only produces a 
.tlsin file for refmac, but also a .phenix file.  This file contains 
only TLS groups info, and nothing else. Here is an example.

refinement.refine {
 adp {
    tls="(chain A and resid 21:28)"
    tls="(chain A and resid 29:45)"
    tls="(chain A and resid 46:65)"
    tls="(chain A and resid 66:105)"
    tls="(chain A and resid 106:128)"
}
}

So, users of phenix.refine can use this file, and rely on phenix for TLS 
values...

Engin

Pavel Afonine wrote:
> 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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>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>>
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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
>> http://cci.lbl.gov/paul
>>
>> Lawrence Berkeley Laboratory
>> 1 Cyclotron Road, BLDG 64R0121
>> Berkeley, CA 94720, USA.
>>   
>> ------------------------------------------------------------------------
>>
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>>   
>>     
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