Hello All,
I noticed some things different about the PDB today causing me to rub
my eyes vigorously and to put my nose right on my monitor in disbelief:
* -> ' for nucleic acid sugars
O#P -> OP# for the phosphate oxygens
C5A -> C7 for thymidine exocyclic methyl (didn't it used to be C
If you want to be 'by the book' on it, you should follow IUPAC rules for
atomic numbering of chemical compounds. Unless you're an organic chemist,
these rules are pretty hard to follow, so most people number at will.
If you're dealing with a 'known' series of compounds, such as analogous
inhibi
Dear Joe,
Atom labels are, in principle, arbitrary. The molecule doesn't case
what we call its atoms. To make the PDB more useful, it is handy if
all the people working with a particular compound use the same names for
their atoms. If you find that someone has already deposited a structure
Dear SLS users,
Reminder, Call for Proposals: SLS PX Beamlines
==
Call is open for proposals for the following
beamlines of the Swiss Light Source, SLS:
PX (X06SA and X10SA), Protein Crystallography
Periods:
===
Dear developers and users,
This is just a reminder for anyone who wishes to contribute to the next
issue of the web-based CCP4 newsletter. The current deadline is 1st week
of December, so more or less in two months.
Articles may cover any topic of interest to macromolecular
crystallographers, on
Hi,
I would like to invite you to submit articles for a special issue of
IEEE Software on
"Developing Scientific Software". The call for articles is below, and
also at:
http://www.computer.org/portal/site/software/menuitem.538c87f5131e262449
55a4108bcd45f3/index.jsp?&pName=software_level1&path=sof
Hi, all
I am a rookie in crystallography. I know this may be a little bit off topic.
I have cocrystallized several compounds with my favorite protein. I found
crystal structures for some of these chemicals. But the numbering systems
are different in those original papers for the small molecules. S
It is actually possible to calculate R(free) with SHELXL for the outer
most resolution shell. Gabor Bunkoczi indicated the solution and I
forward it here to the public:
- Rename the .res file of the last refinement run to .ins
- adjust the CGLS parameter in the .ins file to 0 -1 (Zero refinement
Dear Colleagues,
So far there have been over 30 letters of support
for CCP4. There is a further 14 days for you to send your letter of support.
I know many labs do not use CCP4BB or at least many lab heads do not.
Perhaps you can ask them to read the message below? This is
Dear All
the ccp4 website and ftp site will be "off air" from 4pm BST on
Friday 12 October until Monday 15 October. This is to allow
necessary maintenance on the server room.
Happily, the ccp4bb mailing list and ccp4 e-mail address will not be
affected
Charles Ballard
CCP4
Boaz,
If you had used the U option in SHELXPRO to update from .res to .ins the
free R should have been included in the deposition PDB file by the B
option!
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel
SHELX is much older than the free R so this was added as an afterthought,
and unfortunately I did not think of calculating R-free for just the outer
resolution shell. There isn't an easy way of doing this without some
programmeing effort. I also think that it is NOT a good idea, in the outer
re
Dear all,
I used SHELXL for anisotropic structure refinement of high-resolution
data (1.3 Angstroem) and a reviewer asked me to include refinement
statistics for the outer most resolution shell in the crystallographic
table. While R-factors for the outer most resolution shell belong to the
st
Postdoctoral Scientist in Protein Crystallography
A postdoctoral staff position is available at the Institute of
Biological Chemistry of the Technical University Munich starting as
soon as possible for initially three years, with the option for
prolongation.
Projects are focused at aspects o
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