Dear all
During PDB deposition the annotator me to verify and review the sigma value
in the structure file which in my case was -0.03. I have some basic queries
and request you all to please answer them. My first question is, what
actually is a sigma value of a structure file. 2nd) where the
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The only thing that seems to make sense is bonds rmsd - but you should
ask the annotator for specifics directly. If it is bonds rmsd, this has
been discussed many times - just google rmsd bonds ccp4bb and look for
most recent entries.
On Mon, 2013-06-17 at 12:11 +0530, Faisal Tarique wrote:
Dear Faisal,
I might be missing something, but why not ask the annotator instead of the
bulletin board? He should know which value is meant. For me, a sigma belongs to
a set of observations or parameters and without any further information one can
only guess (as Ed just did) which set. My
At the risk of (more) people pointing at me and laughing...
I used to use SHELXPRO to get my .ins files sorted for SHELX, but that
seems to have gone.
How is it done now?
I want to do a full-matrix refinement to get ESUs on some (specific) atoms
and as far as I can remember SHELXL is the best
Dear group
I have a crystal data diffracted around 2.9 A*,
during the data reduction HKL2000 not convincingly showed the space group
(indexed in lower symmetry p1), while the mosflm given C-centered
Orthorhombic, and again with little play around HKL2000 given CO, now the
model for molecular
Hi Pramod,
1. You should try to identify the correct space group first. Did you
integrate in p1 and run pointless?
2. A template with 31% identity is not a great model. The number of
molecules in ASU will affect your chances of success. Hopefully it's not
large. wrfac of 0.6 and Rfree of 0.5
Dear Peter,
i am planning to produce a new pdb2ins containing several improvements,
but until this is ready please continue to use the old shelxpro.
Best wishes, George
On 17.06.2013 16:57, Peter Moody wrote:
At the risk of (more) people pointing at me and laughing...
I used to use
*Dear Abhinav Kumar
*
*thanks for kind suggestions
*
*
I have tried as follow.
1. You should try to identify the correct space group first.
*integration in p21 given the following statics in pointless
*
* Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation*
*
I noticed something strange when processing a dataset with imosflm. The
final output ctruncate_etc.mtz, contains IMEAN and F columns, which
should be the conversion according to FrenchWilson. Problem is that
IMEAN has no missing values (100% complete) while F has about 1500
missing (~97%
Hi Ed,
I'm not directly familiar with the ctruncate implementation of French and
Wilson, but from the implementation that I put into Phenix (based on the
original FW paper) I can tell you that any reflection where (I/sigI) -
(sigI/mean_intensity) is less than a defined cutoff (in our case -4.0),
Jeff,
thanks - I can see the same equation and cutoff applied in ctruncate
source.Here is the relevant part of the code
// Bayesian statistics tells us to modify I/sigma by
subtracting off sigma/S
// where S is the mean intensity in the resolution shell
h =
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