Dear all,
Sorry for the off-topic Question.
I just tried to extract files *.* from EDS server for a PDB entry.
The page tells us that
There is no map available for this entry (),
because our automatic script failed to produce an electron density map
with an R-value (0.309) within 5 percentage
Dear Jai,
you can find lots of possible explanations in that very same website:
http://eds.bmc.uu.se/eds/eds_help.html#PROB_RFAC
On 4 April 2014 09:07, jai mohan jaimoha...@yahoo.co.in wrote:
Dear all,
Sorry for the off-topic Question.
I just tried to extract files *.* from EDS server for a
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear S. M. Jaimohan,
one reason such a discrepancy is often the presence of TLS, which may
be present in the PDB-header but is not found in the PDB coordinates.
Another reason might be that during deposition |F| and I got confused
- - this is not too
Hi,
I was wondering if anyone can help me with the installation of xds on iMac?
regardsSaleem
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Hash: SHA1
Dear Saleem,
the file you download from Wolfgang Kabsch's page is a gzipped
tar-Archive.
You can look into its content with the command
tar tfz XDS-OSX10.5.8_Darwin9.8.0.tar.gz
This tells you that upon extraction (see below) you will have a
Hi Ingo,
I tried replacing the loggraph script and also running the old ccp4 in its
entirety on the same machine
Both of them popup the blank graph window and then promptly crash with the
message we had posted.
Can anyone confirm if they are using Redhat 6.5 and blt with loggraph
Thanks for your
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On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
A more up-to-date reason is that programs calculate R values very
differently. If you take a PDB file refined with program X and put it
into program Y you easily get discrepancies greater than 5%.
This is actually
Here you can find a list of reasons for R-factor discrepancy and how much
each of them affects the R-factor:
http://phenix-online.org/papers/he5476_reprint.pdf
Pavel
On Fri, Apr 4, 2014 at 8:18 AM, Nat Echols nathaniel.ech...@gmail.comwrote:
On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene
Dear Nat and Tim,
On Fri, Apr 04, 2014 at 08:18:06AM -0700, Nat Echols wrote:
On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
A more up-to-date reason is that programs calculate R values very
differently. If you take a PDB file refined with program X and put it
Hi,
Did you look at the same structure in the PDB_REDO databank
(www.cmbi.ru.nl/pdb_redo)? If the problem can be solved, the structure and maps
should be there. If it cannot, you might get a slightly more informative error
message from the WHY_NOT server.
Cheers,
Robbie
Sent from my Windows
It sounds very interesting: experimental and computational dance biology. Any
type of computational dance or there are style limitations?
Regards,
Vaheh Oganesyan
www.medimmune.com
[MedI Logo Sig]
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Sebastiano Pasqualato
I replied in too great a rush - it is the Rfree, or the Rfree-Rwork gap,
that would go up a lot if a structure originally refined at low resolution
with targeting to an external high-resolution one was re-refined without
that targeting.
Gerard.
--
On Fri, Apr 04, 2014 at 04:55:03PM +0100, Gerard
Ooopsss!!!
Of course it should read experimental and computational cancer biology but
with this invasive automatic correctors, one typo can lead to very interesting
fields of study, I guess…
Ciao,
S
On Apr 4, 2014, at 6:10 PM, Oganesyan, Vaheh oganesy...@medimmune.com wrote:
It sounds very
All - This crystal gave a hexagonal space group when the single reflections
are auto processed by xds. The streaks are very prevalent - can I get
suggestions what they are caused by? Thanks Laurie
https://drive.google.com/file/d/0Bx8-qQA_HKegUmliSkUxQ3JtYU1qci1LXzNnWlpxalJHaDBj/edit?usp=sharing
Hi Jai,
I had the same thing happen when I pulled up one of my lab's structures. It was
twinned, and at least in the past the EDS did not handle twinning.
Best regards,
Z
***
Zachary A. Wood, Ph.D.
Assistant Professor
The topic brings up a question that I've been wondering about for some
time, perhaps someone can enlighten me. Why is it not standard practice
to deposit map coefficients along with structure factors ? Unlike image
deposition there are no significant storage or file format issues. This
would
On Fri, Apr 4, 2014 at 9:36 AM, Alastair Fyfe af...@ucsc.edu wrote:
The topic brings up a question that I've been wondering about for some
time, perhaps someone can enlighten me. Why is it not standard practice to
deposit map coefficients along with structure factors ? Unlike image
Reconstructing the refinement may be necessary in some cases but there
are other applications (pdb-wide map statistics, development of map
analysis tools, quick model vs map checks) where access to the
depositor's final map would be sufficient. Perhaps the coefficients are
in fact included in
On Fri, Apr 4, 2014 at 10:39 AM, Alastair Fyfe af...@ucsc.edu wrote:
Reconstructing the refinement may be necessary in some cases but there
are other applications (pdb-wide map statistics, development of map
analysis tools, quick model vs map checks) where access to the depositor's
final map
On Friday, 04 April, 2014 10:44:18 Nat Echols wrote:
On Fri, Apr 4, 2014 at 10:39 AM, Alastair Fyfe af...@ucsc.edu wrote:
Reconstructing the refinement may be necessary in some cases but there
are other applications (pdb-wide map statistics, development of map
analysis tools, quick model
Thanks for the clarification. I thought at first this position might be
related to Dance Your PhD.
http://news.sciencemag.org/scientific-community/2013/11/dance-your-ph.d.-and-winner-…
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Hi all,
I need help creating links between units of sugar (ligands) in the PDB file
before refining so that CCP4 recognizes the sugars are attached.
I tried the one suggestion I got before Extension Make a Link, but I get
discontinued bonds instead of full bonds.
Thanks so much for all
Dear Alastair,
I really like the feature of shelxl which writes the cif-file (required
for deposition to the CCSD) including all restraints, constraints, the
data, and the coordinates. The program shredcif extracts the ins-file
and the hkl-file, which are checksum protected against manual
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