I think it may well be a problem with the scaling.
It is hard to get a reasonable estimate of the Wilson B at 3A -
especially in a small cell.
Look at the Log Graph plots - one associated with R factor gives you
and v resolution. They SHOULD overlap pretty well, but
sometimes they dont and someti
Greetings,
We've been working on a number of related structures. Crystals are in
P64 with fairly small unit cell (40,40,55) and only diffract to around
2.5-3.0, so we aren't working with a lot of reflections. For several of
these data sets the maps look very reasonable but Refmac refinement
g
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(
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 l
Hi,
I am using the latest version of phenix 1.8.1-1168 for the MacOSX and I
see a similar behaviour with the B-factors.
Which version do you suggest to update to?
There might be a problem with over-refinement and one workaround might be
to limit the Rfree-R=0.05, but your Rfree will likely to incr
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,
It could be a problem with your data, e.g. many overloaded reflections
not being removed or F and F^2 mixed up. What is your Wilson B-value?
George
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-30
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:
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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 convenientl
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
opti
Regards,
Mitch
---
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kyle Dolan
Sent: Friday, May 07, 2010 3:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unusually low B factors after refinement
Hello,
I am trying to run restrained refinement with Refmac5 (v
Hello,
I am trying to run restrained refinement with Refmac5 (version 5.5.0109),
including refinement of isotropic temperature factors, and I am seeing some
very unusual behavior by the program. In the output pdb file, nearly all of
the individual atomic B factors have a value of 2.0! My data is o
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