average temperature factor

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Ursula Schulze-Gahmen

11 Jul 2012 11 Jul '12

4:32 p.m.

Is there an easy way to calculate average temperature factors in phenix or another program after ADP + TLS refinement in phenix? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Pavel Afonine

11 Jul 11 Jul

6:58 p.m.

Hi Ursula,

...

Is there an easy way to calculate average temperature factors in phenix or another program after ADP + TLS refinement in phenix?

yes. If you PDB file is after phenix.refine run, then the average ADP is reported in PDB file header as well as in refinement log file. For a PDB file you can calculate average ADP using this command: phenix.pdbtools model.pdb model_statistics=true It does not matter where PDB file come from as long as ATOM or/and ANISOU records contain the correct ADPs. Pavel

Ursula Schulze-Gahmen

12 Jul 12 Jul

4:24 p.m.

Hi Pavel, Yes, I see the baverage in the header of the pdb file. But I would like to get the baverage for the different chains in the structure. I tried using "phenix.pdbtools model.pdb model_statistics=true" on separate chains, but I don't get a value for Baverage from this. Ursula On Wed, Jul 11, 2012 at 11:58 AM, Pavel Afonine wrote:

...

Hi Ursula,

Is there an easy way to calculate average temperature factors in phenix

...
or another program after ADP + TLS refinement in phenix?

yes. If you PDB file is after phenix.refine run, then the average ADP is reported in PDB file header as well as in refinement log file. For a PDB file you can calculate average ADP using this command:

phenix.pdbtools model.pdb model_statistics=true

It does not matter where PDB file come from as long as ATOM or/and ANISOU records contain the correct ADPs.

Pavel ______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

Christian Roth

4:31 p.m.

Hi Ursula, probably there exist also a trick in phenix, but another option would be moleman from Uppsala. It prints B values for chains or for the type of atom/residue. Christian Am Donnerstag 12 Juli 2012 18:24:48 schrieb Ursula Schulze-Gahmen:

...

Hi Pavel,

Yes, I see the baverage in the header of the pdb file. But I would like to get the baverage for the different chains in the structure. I tried using "phenix.pdbtools model.pdb model_statistics=true" on separate chains, but I don't get a value for Baverage from this.

Ursula

On Wed, Jul 11, 2012 at 11:58 AM, Pavel Afonine wrote:

...
Hi Ursula,

Is there an easy way to calculate average temperature factors in phenix

...
or another program after ADP + TLS refinement in phenix?

yes. If you PDB file is after phenix.refine run, then the average ADP is reported in PDB file header as well as in refinement log file. For a PDB file you can calculate average ADP using this command:

phenix.pdbtools model.pdb model_statistics=true

It does not matter where PDB file come from as long as ATOM or/and ANISOU records contain the correct ADPs.

Pavel ______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online .org/mailman/listinfo/phenixbb>

-- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

David Cobessi

4:43 p.m.

Hi Ursula, Have you tried Baverage from CCP4? I think that it is doing it. Kind regards, David On 07/12/2012 06:24 PM, Ursula Schulze-Gahmen wrote:

...

Hi Pavel,

Yes, I see the baverage in the header of the pdb file. But I would like to get the baverage for the different chains in the structure. I tried using "phenix.pdbtools model.pdb model_statistics=true" on separate chains, but I don't get a value for Baverage from this.

Ursula

-- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122

Pavel Afonine

4:49 p.m.

Hi Ursula, here is a solution, not nice though: step 1: get a pdb file with chain in question: phenix.pdbtools model.pdb keep="chain A" output.file_name="chain_A.pdb" step 2: then this will give you average B phenix.pdbtools chain_A.pdb model_statistics=true Other suggestions (by David & Christian) might work too, but I have no idea how these programs handle TLS contribution to ADP and ANISOU records. Though since phenix.refine outputs total ADPs I guess this should be just fine. Pavel On 7/12/12 9:24 AM, Ursula Schulze-Gahmen wrote:

...

Hi Pavel,

Yes, I see the baverage in the header of the pdb file. But I would like to get the baverage for the different chains in the structure. I tried using "phenix.pdbtools model.pdb model_statistics=true" on separate chains, but I don't get a value for Baverage from this.

Ursula

On Wed, Jul 11, 2012 at 11:58 AM, Pavel Afonine mailto:[email protected]> wrote:

Hi Ursula,

Is there an easy way to calculate average temperature factors in phenix or another program after ADP + TLS refinement in phenix?

yes. If you PDB file is after phenix.refine run, then the average ADP is reported in PDB file header as well as in refinement log file. For a PDB file you can calculate average ADP using this command:

phenix.pdbtools model.pdb model_statistics=true

It does not matter where PDB file come from as long as ATOM or/and ANISOU records contain the correct ADPs.

Pavel _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nathaniel Echols

13 Jul 13 Jul

7:10 p.m.

On Thu, Jul 12, 2012 at 9:49 AM, Pavel Afonine wrote:

...

here is a solution, not nice though:

step 1: get a pdb file with chain in question:

phenix.pdbtools model.pdb keep="chain A" output.file_name="chain_A.pdb"

step 2: then this will give you average B

phenix.pdbtools chain_A.pdb model_statistics=true

Other suggestions (by David & Christian) might work too, but I have no idea how these programs handle TLS contribution to ADP and ANISOU records. Though since phenix.refine outputs total ADPs I guess this should be just fine.

Since this question has come up before, I've added a window for displaying this in the GUI. Clicking the magnifying glass icon next to any PDB file will already open a panel showing an overview of the model contents, and now there will also be a button labeled "B-factors by chain" for any file with multiple chains. Clicking this button will display the isotropic B-factors statistics by chain. Under the circumstances, I'm assuming the B-factor field in the PDB file is already the total B-factor. This will be available in the next nightly build. -Nat

Felix Frolow

15 Jul 15 Jul

6:09 a.m.

I get it! in my case it is a right click!!! :-) On Jul 13, 2012, at 22:10 , Nathaniel Echols wrote:

...

On Thu, Jul 12, 2012 at 9:49 AM, Pavel Afonine wrote: here is a solution, not nice though:

step 1: get a pdb file with chain in question:

phenix.pdbtools model.pdb keep="chain A" output.file_name="chain_A.pdb"

step 2: then this will give you average B

phenix.pdbtools chain_A.pdb model_statistics=true

Other suggestions (by David & Christian) might work too, but I have no idea how these programs handle TLS contribution to ADP and ANISOU records. Though since phenix.refine outputs total ADPs I guess this should be just fine.

Since this question has come up before, I've added a window for displaying this in the GUI. Clicking the magnifying glass icon next to any PDB file will already open a panel showing an overview of the model contents, and now there will also be a button labeled "B-factors by chain" for any file with multiple chains. Clicking this button will display the isotropic B-factors statistics by chain. Under the circumstances, I'm assuming the B-factor field in the PDB file is already the total B-factor.

This will be available in the next nightly build.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nathaniel Echols

9:41 a.m.

On Sat, Jul 14, 2012 at 11:09 PM, Felix Frolow wrote:

...

I get it! in my case it is a right click!!! :-)

You can change what happens when you click this button in the Preferences (under Files); I changed the default (which used to be to open the PDB file in a text editor) maybe a year ago, but that wouldn't override any existing settings. -Nat

...

On Jul 13, 2012, at 22:10 , Nathaniel Echols wrote:

Since this question has come up before, I've added a window for displaying this in the GUI. Clicking the magnifying glass icon next to any PDB file will already open a panel showing an overview of the model contents, and now there will also be a button labeled "B-factors by chain" for any file with multiple chains. Clicking this button will display the isotropic B-factors statistics by chain. Under the circumstances, I'm assuming the B-factor field in the PDB file is already the total B-factor.

This will be available in the next nightly build.

-Nat _______________________________________________

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participants (6)

Christian Roth
David Cobessi
Felix Frolow
Nathaniel Echols
Pavel Afonine
Ursula Schulze-Gahmen