Behalf Of Santarsiero, Bernard D.
Can I ask a dumb question? Just curious...
Why are we now limited to 80 columns? In the old days, that
was a limit with Fortran and punched cards. Can a record
(whatever it's called now) be as long as we wish? Instead of
compressing a lot on a
On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right ?
The real space refinement can be done either with the tools from
Chapman at
If you want to give it a try, I switched the
buttons to an alternate server. It is slower
than the one we were using, but it will
give you the idea. Try
http://biomol.dowling.edu/WPDB/
put in a PDB id code in the box near the top
of the page and click on CLICK HERE for WPDB version ...
The
That's easy: Backward compatibility, both in terms of old programs and
old data.
The idea is to maintain as much interoperability as possible.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Santarsiero, Bernard D.
Sent: Friday, August 10, 2007
Correction: Scratch what I wrote -- the PDB format does now support a
formal charge field in columns 79-80 (1+,2+,1- etc.). Hooray!
Thus, adoption of the CONECT valency convention is all it would take for
us to be able to convey chemically-defined structures using the PDB
format.
I'll
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Have a look at this very nice paper:
Acta Cryst. (1999). D55, 835-845
Critical initial real-space refinement in the structure determination of
arginine kinase
G.
Dear George,
I like your hybrid_ 36 scheme and will implement it and the two character
hain IDs PDB file columns 21 and 22, right justified) when I next update
HELXL. Of course I will need to do some programming because of the SHELX
zero dependency' philosophy, but it seems to me to be
On 10 Aug 2007, at 20:12, Pavel Afonine wrote:
Anastassis Perrakis wrote:
On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right ?
Actually, everything proposed with break some software.
The real question is one of how much value the
community gains from how much of a change. mmCIF
was one proposal that would solve the problem,
but which met a lot of resistance. The change
in atom serial numbers to strings is another
A couple of buccaneer releases have gone by since I last made an
announcement:
release 0.7.2:
- new 'correlation mode' gives better results after MR or when
completing an initial model.
- sequenced fragments are now renumbered to match the position in the
final sequence.
release
If I may expand on what Eleanor said.
The issue is not the atom labels, but that the atom labels are in the
right place (i.e. the refer to the right atoms).
There is an IUPAC convention on the torsion of CB-CG-CD-OE1 (for GLU).
The torsion should be between -90 and +90. Yours is not.
PROTEROS is a leading service-provider for the preparation and
three-dimensional structural analysis of proteins for structure-guided
drug discovery. Our work contributes to fast and rational development of
new therapeutic compounds. Since its foundation in 1998, PROTEROS is a
continuously
Quoting Anastassis Perrakis [EMAIL PROTECTED]:
On Aug 9, 2007, at 15:02, Tommi Kajander wrote:
so, a) WHAT IS GAMMA??
gamma is possibly the letter of the greek alphabet that has had most
abuse from scientists.
thats what i thought...
ping sun wrote:
Thanks for your answer.
I guess I did not make it clear. I used the data file for refinement
which is also used for phasing (peak_anomalous.hkl).
Traditionally, people will reprocess the same set of data for
refinement (rescale it in hkl2000 without using the option
Anastassis Perrakis wrote:
On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right ?
The real space refinement can be done either with
Dear Ralf,
I like your hybrid_ 36 scheme and will implement it and the two character
chain IDs PDB file columns 21 and 22, right justified) when I next update
SHELXL. Of course I will need to do some programming because of the SHELX
'zero dependency' philosophy, but it seems to me to be
I support CCP4 adopting the hybrid36 and 2 char chain id extensions too.
If no-one else steps up to do it, I'll try and patch mmdb to support it
when I get time.
Kevin
George M. Sheldrick wrote:
I like your hybrid_ 36 scheme and will implement it and the two character
chain IDs PDB file
Research Technician (Fixed-term)
Protein expression for Structural Biology
Applications are invited for the above post from highly motivated individuals
with a strong interest in eukaryotic protein expression, protein biochemistry
and protein purification. The research project is funded by
Hello there
How do I tell Refmac that I have an inhibitor covalently bound to a Ser
residue? I am using the ccp4i interface and this is what I've came up
with (looking through the archives) but it does not seem to work
1) I made the inhibitor mon_lib.cif
2) I made the following
Folks,
Don't take this as an argument with software people - I have a side note about
structures.
Back in the day when I used to solve Structural Genomics structures, we almost
always knew substitution rate from masspec and Se always refined to lesser
occupancy. Could it be the decay instead?
20 matches
Mail list logo
