Dear All,
What are reasonable values of Rmerge in the outermost resolution
shell?
Some of the recent discussions suggest going to those sheels where
~2 and CC1/2 = 0.5. But I am getting Rmerge & Rmeas > 1 in the outermost shell
for those values of and CC1/2, and I don't think
That looks good to me Mean(I/sigma) = 2.0, CC1/2 0.74
See endless discussions on this BB about the uselessness of Rmerge as a
resolution criterion
Phil
On 2 Jun 2014, at 09:27, sreetama das wrote:
> Dear All,
> What are reasonable values of Rmerge in the outermost
> resolution
Can you send more details? the log file? the pdb
On 30 May 2014 22:54, Carter, Charlie wrote:
> This is a bizarre problem. I'm trying to superimpose multiple
> conformations of the same protein using segments I expect not to change.
> LSQKAB bails with this error each time:
>
> *** RWBROOK err
Try refining without disulfide bond - from the way density looks it might work.
Whether this is what happens in vivo is a different question entirely.
Sent on a Sprint Samsung Galaxy S® III
Original message From: Eze Chivi
Date:06/02/2014 1:08 AM (GMT-05:00)
To: CCP4BB@J
I have seen similar features fairly often when the data collection has been
pushed to the limit.
The theory is that it is due to radiation damage - you could check by only
merging say the first 50% of your data, then seeing if the di-sulphide is
intact in those maps. ( wouldnt re-refine much - jus
My suggestion is to ignore Rmerge when making decisions about resolution
cutoff. While cc1/2 may still perhaps qualify for the "recent discussion" tag
(is two years recent?), deeply flawed nature of the Rmerge concept is over a
decade old.
Sent on a Sprint Samsung Galaxy S® III
Orig
Charlie,
Most probably this indicates a problem with your PDB file, either a format or
things like misplaced or absent residue name etc. If you can send me your files
and exact command that you run, I can have a look into this.
In future, if you see a message like "report to developer" please s
Dear all,
I am using Phaser for Molecular replacement. After Phaser places part of
the structure, I would like to run it again, giving this time as search
ensembles new pieces of structure. I thought what I had to do was simply to
put in "know solution" the ".sol" file coming out from the previous
A new position is available in Boston at Harvard Medical School:
Senior Structural Biology Computing Scientist
Enviroment: The Center for Molecular and Cellular Dynamics Structural Biology Computing Center provides research computing support to 25 structural biolo
Dear Crystallographers,
I have a feeling that Moire finges are the real-space equivalent of the Laue
zones in reciprocal-space, and this seems like a very basic idea that must have
been explored--anyone know of a source connecting the mathematico-physical
dots? Or do the dots not connect?
JPK
Jacob
I included a demo using Moire fringes in a crystallography course some
years ago. The diagram I used looks just like the second Moire pattern
(the annotated one) at this site: http://spie.org/x8449.xml . This is a
static Moire pattern; in my demo the two gratings could be translated &
rota
Ezequiel,
since you mentioned you tried Phenix too:
in Phenix you can remove a particular disulfide bond by using a parameter,
for example:
disulfide_bond_exclusions_selection_string="(chain A and resseq 1 and name
SG) or (chain B and resseq 10 and name SG)"
This works in the command line and G
What does an omit map look like, if you omit both cysteines?
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY 10031
Tel. (212) 650-6070
www.khayatlab.org
Original message
>Date: Mon, 2
Hi CCP4,
Recently when I input my pdb file and run the baverage in the ccp4 suit to
check the temperature factor, it always tell me "No tables were fund in this
file." Could you tell me how to fix this problem? Or is there another software
instead of baverage I could use to check the temperatu
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