Re: [ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Rezaul Karim 
If  the correct atoms are in place, resetting the b factors of those atoms/residues to a constant e.g. 5.00 and refining in phenix with individual B-factors ON should take care of these.Best,RezaSent from my iPhoneOn Aug 2, 2023, at 7:42 AM, Thomas, Leonard M.  wrote:




Hello All,


A general questions though phenix.refine is being used for refinement.  A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters.  They were given the structure to gain some experience in refinement
 and they have been asking me some questions, I was not involved in the initial work.  While everything seems to be happy and the model is correct with good refinement statistics for the most part one thing that I am unsure of is some of the heavier atoms (Phosphate
 and Sulfer) have very high temperature factors when looking at individual residues or ligands.  The temperature factors are at least twice as high as the lighter atoms they are associated with.  


I am at a loss to explain what is going on, I really have not used TLS refinement a lot so there is that.  Resolution is about 2.5 angstroms with good completeness.


Thoughts?


Thank You in advance
Len Thomas






Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price
 Family Foundation Institute of Structural Biology
University
 of Oklahoma
Department
 of Chemistry and Biochemistry
101
 Stephenson Parkway
Norman,
 OK 73019-5251
Office:
 (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl









To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Jon Cooper 
Hello, is it definitely due to the TLS refinement? I guess you have tried 
without TLS and don't see the same effect i.e. the B-factors are more 
consistent. It would be good to know.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 2 Aug 2023, 15:42, Thomas, Leonard M. wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement. A 
> student I am working with has a structure that was solved and initially 
> refined using TLS and NCS parameters. They were given the structure to gain 
> some experience in refinement and they have been asking me some questions, I 
> was not involved in the initial work. While everything seems to be happy and 
> the model is correct with good refinement statistics for the most part one 
> thing that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) 
> have very high temperature factors when looking at individual residues or 
> ligands. The temperature factors are at least twice as high as the lighter 
> atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS 
> refinement a lot so there is that. Resolution is about 2.5 angstroms with 
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
>
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Robbie Joosten 
Although the effect should be quite small, is the wavelength in your reflection 
file consistent with the actual wavelength? 

Another option is that specific filters on atom types were used in the TLS 
refinement. I would refine the models with another program 
(REFMAC/Buster/PDB-REDO) to see if the B-factor anomaly remains.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Daniel M.
> Himmel, Ph. D.
> Sent: Wednesday, August 2, 2023 17:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] High Temperature Factors with TLS
> 
> One possible explanation for high B-factors, assuming the coordinates are
> refined correctly, is partial occupancy and high mobility (dynamics) at those
> heavy atom sites.
> 
> Also, one should check Fo-Fc maps of those positions.  Are other atom types
> substituting for some of those heavy atoms (such as sulfate instead of
> phosphate)?
> 
> 
> Daniel
> 
> ___
> 
> Daniel M. Himmel, Ph. D.
> 
> Principal, Himmel Sci Med Com, LLC
> 
> E-mail:  danielmhim...@gmail.com
> <mailto:danielmhim...@gmail.com>
> 
> URL   :  https://www.HimmelSciMedCom.com
> 
> 
> 
> On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M.  <mailto:lmtho...@ou.edu> > wrote:
> 
> 
>   Hello All,
> 
>   A general questions though phenix.refine is being used for refinement.
> A student I am working with has a structure that was solved and initially 
> refined
> using TLS and NCS parameters.  They were given the structure to gain some
> experience in refinement and they have been asking me some questions, I was
> not involved in the initial work.  While everything seems to be happy and the
> model is correct with good refinement statistics for the most part one thing
> that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) have
> very high temperature factors when looking at individual residues or ligands.
> The temperature factors are at least twice as high as the lighter atoms they 
> are
> associated with.
> 
>   I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with 
> good
> completeness.
> 
>   Thoughts?
> 
>   Thank You in advance
>   Len Thomas
> 
>   Leonard Thomas, Ph.D.
>   Biomolecular Structure Core, Director
> 
>   Oklahoma COBRE in Structural Biology
>   Price Family Foundation Institute of Structural Biology
>   University of Oklahoma
>   Department of Chemistry and Biochemistry
>   101 Stephenson Parkway
>   Norman, OK 73019-5251
>   Office: (405)325-1126
>   lmtho...@ou.edu <mailto:lmtho...@ou.edu>
>   http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Thomas, Leonard M. 
So the Phosphates are actually the end of the ADP which the Sulfer atoms are 
Cystiene suffers.   The Fo-Fc maps show large positive peaks for each position 
also.  The TLS groups is the whole protein chain, there are 4 in the asymmetric 
unit as the biological unit I think is a dimer of 2 different chains.  ADP and 
FAD are bound and are separate from what I can tell.

Len


On Aug 2, 2023, at 10:05 AM, Daniel M. Himmel, Ph. D. 
mailto:danielmhim...@gmail.com>> wrote:

One possible explanation for high B-factors, assuming the coordinates are 
refined correctly, is partial occupancy and high mobility (dynamics) at those 
heavy atom sites.

Also, one should check Fo-Fc maps of those positions.  Are other atom types 
substituting for some of those heavy atoms (such as sulfate instead of 
phosphate)?

Daniel
___
Daniel M. Himmel, Ph. D.
Principal, Himmel Sci Med Com, LLC
E-mail:  danielmhim...@gmail.com
URL   :  
https://www.HimmelSciMedCom.com


On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. 
mailto:lmtho...@ou.edu>> wrote:
Hello All,

A general questions though phenix.refine is being used for refinement.  A 
student I am working with has a structure that was solved and initially refined 
using TLS and NCS parameters.  They were given the structure to gain some 
experience in refinement and they have been asking me some questions, I was not 
involved in the initial work.  While everything seems to be happy and the model 
is correct with good refinement statistics for the most part one thing that I 
am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high 
temperature factors when looking at individual residues or ligands.  The 
temperature factors are at least twice as high as the lighter atoms they are 
associated with.

I am at a loss to explain what is going on, I really have not used TLS 
refinement a lot so there is that.  Resolution is about 2.5 angstroms with good 
completeness.

Thoughts?

Thank You in advance
Len Thomas

Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Daniel M. Himmel, Ph. D. 
One possible explanation for high B-factors, assuming the coordinates are
refined correctly, is partial occupancy and high mobility (dynamics) at
those heavy atom sites.

Also, one should check Fo-Fc maps of those positions.  Are other atom types
substituting for some of those heavy atoms (such as sulfate instead of
phosphate)?

Daniel

___

Daniel M. Himmel, Ph. D.

Principal, Himmel Sci Med Com, LLC

E-mail:  danielmhim...@gmail.com

URL   :  https://www.HimmelSciMedCom.com


On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M.  wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement.  A
> student I am working with has a structure that was solved and initially
> refined using TLS and NCS parameters.  They were given the structure to
> gain some experience in refinement and they have been asking me some
> questions, I was not involved in the initial work.  While everything seems
> to be happy and the model is correct with good refinement statistics for
> the most part one thing that I am unsure of is some of the heavier atoms
> (Phosphate and Sulfer) have very high temperature factors when looking at
> individual residues or ligands.  The temperature factors are at least twice
> as high as the lighter atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Eleanor Dodson 
You need to tell us more details - is this a deposited structure?
Eleanor

On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M.  wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement.  A
> student I am working with has a structure that was solved and initially
> refined using TLS and NCS parameters.  They were given the structure to
> gain some experience in refinement and they have been asking me some
> questions, I was not involved in the initial work.  While everything seems
> to be happy and the model is correct with good refinement statistics for
> the most part one thing that I am unsure of is some of the heavier atoms
> (Phosphate and Sulfer) have very high temperature factors when looking at
> individual residues or ligands.  The temperature factors are at least twice
> as high as the lighter atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] High Temperature Factors with TLS

2023-08-02 Thread Thomas, Leonard M. 
Hello All,

A general questions though phenix.refine is being used for refinement.  A 
student I am working with has a structure that was solved and initially refined 
using TLS and NCS parameters.  They were given the structure to gain some 
experience in refinement and they have been asking me some questions, I was not 
involved in the initial work.  While everything seems to be happy and the model 
is correct with good refinement statistics for the most part one thing that I 
am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high 
temperature factors when looking at individual residues or ligands.  The 
temperature factors are at least twice as high as the lighter atoms they are 
associated with.

I am at a loss to explain what is going on, I really have not used TLS 
refinement a lot so there is that.  Resolution is about 2.5 angstroms with good 
completeness.

Thoughts?

Thank You in advance
Len Thomas

Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/