Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Nicholas Keep]

I must also credit Robbie with the easiest (most elegant?) solution to 
my question.


You run 0 cycles of refmac with the mixed B factor model.

Thanks all for your inputs.

Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Robbie Joosten]

Hi Eleanor,

This is covered in PDB_REDO: we figure out whether the B-factors are totals or 
residuals. Wouter Touw has made the BDB (http://www.cmbi.ru.nl/bdb/) a databank 
in which all B-factors are represented as the isotropic component of the total 
B-factor. This is quite useful if you want to study patterns in B-factors.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Eleanor Dodson
> Sent: Wednesday, March 08, 2017 15:35
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Removing TLS component of B factor of deposited PDB
> files to input to refmac
> 
> Actually I think it is pretty dangerous to trust the TLS stuff in the PDB 
> header -
> there is a muddle between B_residual and B_merged and no adequate
> description in the header.
> 
> 
> Unless you are planning on doing many many repeats I would re-refine
> before checking the map...
> 
> eleanor
> 
> 
> On 8 March 2017 at 14:16, Eleanor Dodson 
> wrote:
> 
> 
>   TLSANL?
> 
>   Eleanor
> 
> 
>   On 8 March 2017 at 14:08, Nicholas Keep
>  wrote:
> 
> 
>   It would be nice to be able to run zero cycles of refmac to get
> a map etc direct from a PDB file.
> 
>   However due the PDB requiring the TLS component of B
> factor to be included this does not work.
> 
>   Is there software to remove the TLS component so a zero
> cycle of refmac can be run.
> 
>   Best wishes
> 
>   NIck
> 
> 
>   --
>   Prof Nicholas H. Keep
>   Executive Dean of School of Science
>   Professor of Biomolecular Science
>   Crystallography, Institute for Structural and Molecular
> Biology,
>   Department of Biological Sciences
>   Birkbeck,  University of London,
>   Malet Street,
>   Bloomsbury
>   LONDON
>   WC1E 7HX
> 
>   email n.k...@mail.cryst.bbk.ac.uk
>   Telephone 020-7631-6852  (Room G54a Office)
> 020-7631-6800  (Department Office)
>   Fax   020-7631-6803
>   If you want to access me in person you have to come to the
> crystallography entrance
>   and ring me or the department office from the internal
> phone by the door
> 
> 
> 

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Pavel Afonine]

Normally, these days at least, a model that is result of TLS refinement
contains total B factor in ANISOU records and its TLS component in TLS
records (REMARK3), with Btotal = Btls+Bresidual.

If TLS matrices are available, it's trivial to calculate Btls from TLS
matrices in REMARK3 and subtract it from Btotal (ANISOU), which will give
you Bresidual.

Some of older PDB files are likely to have Bresidual in ATOM records and
TLS component in REMARK3 as TLS matrices. In this case, to get total
Btotal, you need to compute Btls from TLS and add to Bresidual.

I guess TLSANAL is the CCP4 tool to do this, and phenix.tls will do
conversion both ways as well.

Pavel

On Wed, Mar 8, 2017 at 6:34 AM, Eleanor Dodson 
wrote:

> Actually I think it is pretty dangerous to trust the TLS stuff in the PDB
> header - there is a muddle between B_residual and B_merged and no adequate
> description in the header.
>
> Unless you are planning on doing many many repeats I would re-refine
> before checking the map...
> eleanor
>
> On 8 March 2017 at 14:16, Eleanor Dodson 
> wrote:
>
>> TLSANL?
>> Eleanor
>>
>> On 8 March 2017 at 14:08, Nicholas Keep 
>> wrote:
>>
>>> It would be nice to be able to run zero cycles of refmac to get a map
>>> etc direct from a PDB file.
>>>
>>> However due the PDB requiring the TLS component of B factor to be
>>> included this does not work.
>>>
>>> Is there software to remove the TLS component so a zero cycle of refmac
>>> can be run.
>>>
>>> Best wishes
>>>
>>> NIck
>>>
>>>
>>> --
>>> Prof Nicholas H. Keep
>>> Executive Dean of School of Science
>>> Professor of Biomolecular Science
>>> Crystallography, Institute for Structural and Molecular Biology,
>>> Department of Biological Sciences
>>> Birkbeck,  University of London,
>>> Malet Street,
>>> Bloomsbury
>>> LONDON
>>> WC1E 7HX
>>>
>>> email n.k...@mail.cryst.bbk.ac.uk
>>> Telephone 020-7631-6852  (Room G54a Office)
>>>   020-7631-6800  (Department Office)
>>> Fax   020-7631-6803
>>> If you want to access me in person you have to come to the
>>> crystallography entrance
>>> and ring me or the department office from the internal phone by the door
>>>
>>
>>
>

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Eleanor Dodson]

Actually I think it is pretty dangerous to trust the TLS stuff in the PDB
header - there is a muddle between B_residual and B_merged and no adequate
description in the header.

Unless you are planning on doing many many repeats I would re-refine before
checking the map...
eleanor

On 8 March 2017 at 14:16, Eleanor Dodson  wrote:

> TLSANL?
> Eleanor
>
> On 8 March 2017 at 14:08, Nicholas Keep 
> wrote:
>
>> It would be nice to be able to run zero cycles of refmac to get a map etc
>> direct from a PDB file.
>>
>> However due the PDB requiring the TLS component of B factor to be
>> included this does not work.
>>
>> Is there software to remove the TLS component so a zero cycle of refmac
>> can be run.
>>
>> Best wishes
>>
>> NIck
>>
>>
>> --
>> Prof Nicholas H. Keep
>> Executive Dean of School of Science
>> Professor of Biomolecular Science
>> Crystallography, Institute for Structural and Molecular Biology,
>> Department of Biological Sciences
>> Birkbeck,  University of London,
>> Malet Street,
>> Bloomsbury
>> LONDON
>> WC1E 7HX
>>
>> email n.k...@mail.cryst.bbk.ac.uk
>> Telephone 020-7631-6852  (Room G54a Office)
>>   020-7631-6800  (Department Office)
>> Fax   020-7631-6803
>> If you want to access me in person you have to come to the
>> crystallography entrance
>> and ring me or the department office from the internal phone by the door
>>
>
>

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Eleanor Dodson]

TLSANL?
Eleanor

On 8 March 2017 at 14:08, Nicholas Keep  wrote:

> It would be nice to be able to run zero cycles of refmac to get a map etc
> direct from a PDB file.
>
> However due the PDB requiring the TLS component of B factor to be included
> this does not work.
>
> Is there software to remove the TLS component so a zero cycle of refmac
> can be run.
>
> Best wishes
>
> NIck
>
>
> --
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852  (Room G54a Office)
>   020-7631-6800  (Department Office)
> Fax   020-7631-6803
> If you want to access me in person you have to come to the crystallography
> entrance
> and ring me or the department office from the internal phone by the door
>

[ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Nicholas Keep]

It would be nice to be able to run zero cycles of refmac to get a map 
etc direct from a PDB file.


However due the PDB requiring the TLS component of B factor to be 
included this does not work.


Is there software to remove the TLS component so a zero cycle of refmac 
can be run.


Best wishes

NIck


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door