Re: [ccp4bb] Unusually low B factors with phenix

2012-11-04 Thread mingzhu wang
Pavel,

1.8.1-1168 also has this problem.

I found this problem existed with some dataset, but not all dataset.

1.8.1 give better map, so I built model with 1.8.1 map and go back to
1.7.3 before I deposit the structure to PDB.

When I compared the B factor from 1.8.x and 1.7.3, I found
B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem.



2012/11/3, Pavel Afonine pafon...@gmail.com:
 Joao,

 I am using the latest version of phenix 1.8.1-1168


 1.8.1-1168 should not have that problem.

 If you suspect there is still a problem, you can send me the data and model
 files off list, explain what exactly the problem is, and I will have a look
 right away.

 FYI: there is Phenix mailing list for Phenix-specific questions, where I
 can also explain in great details the behavior with the B-factors you
 observe.

 All the best,
 Pavel



[ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Demetres D. Leonidas

Hello,

I am experiencing a weird problem with B factor refinement (individual, 
isotropic) in phenix.refine (1.8.1.-1168) and  a structure at 1.9 A 
resolution. The ADP values after the refinement are very very low, less 
than 2 and sometimes 0. I am getting the same result with and without 
optimization of the X-ray/ADP weight. Has anyone else noticed that and 
is there a workaround ?


Demetres

--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Demetres,

does this affect all atoms, or only a few selected ones?

Did you compare with refmac5 (for e.g. input script errors), or did
you reset the B-factors to a reasonable value (e.g. 20-30) prior to
refinement? pdbset can do this conveniently.

Best,
Tim

On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote:
 Hello,
 
 I am experiencing a weird problem with B factor refinement
 (individual, isotropic) in phenix.refine (1.8.1.-1168) and  a
 structure at 1.9 A resolution. The ADP values after the refinement
 are very very low, less than 2 and sometimes 0. I am getting the
 same result with and without optimization of the X-ray/ADP weight.
 Has anyone else noticed that and is there a workaround ?
 
 Demetres
 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Demetres D. Leonidas

Dear Tim,

this affects all atoms and yes I did reset the B-factors to 20.00 prior 
to refinement. I have not tried REFMAC but now I will give it a try 
since phenix does not seem to do the job.


best

Demetres


On 2/11/2012 1:34 μμ, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Demetres,

does this affect all atoms, or only a few selected ones?

Did you compare with refmac5 (for e.g. input script errors), or did
you reset the B-factors to a reasonable value (e.g. 20-30) prior to
refinement? pdbset can do this conveniently.

Best,
Tim

On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote:

Hello,

I am experiencing a weird problem with B factor refinement
(individual, isotropic) in phenix.refine (1.8.1.-1168) and  a
structure at 1.9 A resolution. The ADP values after the refinement
are very very low, less than 2 and sometimes 0. I am getting the
same result with and without optimization of the X-ray/ADP weight.
Has anyone else noticed that and is there a workaround ?

Demetres

- -- 
Dr Tim Gruene

Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs
Q+SZVN6ISb0X38ZekG119/s=
=xKhB
-END PGP SIGNATURE-


--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Jeffrey, Philip D.
That sounds like the bug in Phenix.refine v1.8 that a few of us encountered - 
updating to the latest release will help.

Actually wasn't so much a bug but a feature, albeit not the best one 
imaginable.  Anyone using older v1.8 versions should update.

---
Phil Jeffrey
Princeton

On Nov 2, 2012, at 6:41 AM, Demetres D. Leonidas ddleoni...@bio.uth.gr 
wrote:

 Dear Tim,
 
 this affects all atoms and yes I did reset the B-factors to 20.00 prior to 
 refinement. I have not tried REFMAC but now I will give it a try since phenix 
 does not seem to do the job.
 
 best
 
 Demetres
 
 
 On 2/11/2012 1:34 μμ, Tim Gruene wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Dear Demetres,
 
 does this affect all atoms, or only a few selected ones?
 
 Did you compare with refmac5 (for e.g. input script errors), or did
 you reset the B-factors to a reasonable value (e.g. 20-30) prior to
 refinement? pdbset can do this conveniently.
 
 Best,
 Tim
 
 On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote:
 Hello,
 
 I am experiencing a weird problem with B factor refinement
 (individual, isotropic) in phenix.refine (1.8.1.-1168) and  a
 structure at 1.9 A resolution. The ADP values after the refinement
 are very very low, less than 2 and sometimes 0. I am getting the
 same result with and without optimization of the X-ray/ADP weight.
 Has anyone else noticed that and is there a workaround ?
 
 Demetres
 
 - -- Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
 
 iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs
 Q+SZVN6ISb0X38ZekG119/s=
 =xKhB
 -END PGP SIGNATURE-
 
 -- 
 ---
 Dr. Demetres D. Leonidas
 Associate Professor of Biochemistry
 Department of Biochemistry  Biotechnology
 University of Thessaly
 26 Ploutonos Str.
 41221 Larissa, Greece
 -
 Tel. +302410 565278
 Tel. +302410 565297 (Lab)
 Fax. +302410 565290
 E-mail: ddleoni...@bio.uth.gr
 http://www.bio.uth.gr
 ---


Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Pavel Afonine
Joao,

I am using the latest version of phenix 1.8.1-1168


1.8.1-1168 should not have that problem.

If you suspect there is still a problem, you can send me the data and model
files off list, explain what exactly the problem is, and I will have a look
right away.

FYI: there is Phenix mailing list for Phenix-specific questions, where I
can also explain in great details the behavior with the B-factors you
observe.

All the best,
Pavel