[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
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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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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


Re: [ccp4bb] Rpim and how its related to anomalous signal

2012-11-02 Thread Jim Pflugrath
In my opinion Rpim is not related directly to anomalous signal, so perhaps that 
is why there is some confusion.

Also I think some folks confused Rpim with Rrim.  The latter is also called 
Rmeas.  But once again, these are not related directly to anomalous signal.  I 
do not find Rpim very useful for anything since when the data has high 
multiplicity Rpim gets very low, but as Michael Blum told me, Precision does 
not trump accuracy.  I would personally rather have accurate data than highly 
redundant but inaccurate data.

I like to look at the deltaF / sigma(deltaF) value reported by SHELXC and other 
programs, where deltaF is ||F+| - |F-||.
This might also be called d/sig.  There are other things to look at as well.

Jim

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vijayakumar.B 
[vijaybioscie...@gmail.com]
Sent: Tuesday, September 18, 2012 4:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rpim and how its related to anomalous signal

Dear CCP4BB users,

I am very much interested to work in Anomalous scattering technique for 
macromolecular structure determination. I have already gone through some 
literature in which they have explained about a parameter called “Rpim”.  I am 
little bit confused about Rpim values.

Can anyone tell me about the use of this parameter in structure determination 
by anomalous techniques and how Rpim is related to anomalous signal?  Thanks in 
advance

With kind regards

B. Vijayakumar