Dear users, I was using Refmac 5.5.0102 (ccp4- 6.1.2) for refining the structures, I was supposed to do one more roundof refinement with final model but unfortunately system crashed and i had to install the new version of ccp4 (6.2.0) which has refmac-5.6.0117. So my doubt here is - can I do the
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Dear Kavya,
I would trust the authors of such programs (ccp4-, phenix-,
shelx-collection et al.) to only release new versions of their programs
if they believe that version is an improvement over the previous version
;-) and generally use the latest
Dear Kavya
In principle you should be able to use newer version for old pdb file unless
you have pdb v2 namings for DNA/RNA etc.
New version of ccp4 has more dicitionary elements (1 or so). Older version
was compiled for 3000. That is the reason why old version does not work with
new
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hello everyone,
I am new in this bulletin board. I would like to know on how to cut my
resolution in my datasets that have been processed/produced in diamond light
source. In my processed directory, I found there are 3 files (free.mtz,
scaled.sca and unmerged.sca). May I know which one can be
Qs
1) Why do you want to limit your data?
Most applications allow you to only use a specified sub-set - see GUI tasks
for resolution limits.
In general you may want to run moleculer replacement or exptl phasing at a
limited resolution, but for refinenement or phase extension it is good to
... presuming of course the automated software got this resolution limit right.
If for whatever reason you would like to cut the limit mtzutils will
do this nicely:
mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof
resolution 1.8
eof
(say) - I am sure there are other ways within the suite
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Dear Abd Ghani,
The method described by Graeme is how the resolution can be delimited
artificially.
If you want to get the best from your data, determine the resolution
limit of your data e.g. with pointless (I/sigI 2.0 is a good marker)
and
Hi Tim,
That's interesting. When I looked at this (and I would say I looked
reasonably carefully) I found it only made a difference in the scaling
- integrating across the whole area was fine. However, I would expect
to see a difference, and likely an improvement, in scaling only the
data you
Dear Crystallographers,
it occurred to me that most datasets, at least certainly since the advent
of synchrotrons, have probably some degree of radiation damage, if not some
huge degree thereof. Therefore, I was thinking an exposure-dependent
parameter might be introduced into the atomic models,
Hi all,
I was using SHELXL for the refinement of a small peptide molecule (6-7
residues), and it was working for the first round. But then it gave me an
error message. I don't know what's going on and have you had the same
problems? Can you give me some suggestions?
*For more information*:
I was
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Dear Lu Yu,
your wR2 in the first log-extract seems very high (43%) - it might
simply be that you model is still not good enough to refine the data
anisotropically.
Does it work if you refine the model isotropically? If so, improve the
model as much
Dear Lu Yu,
SHELXL is usually very stable so there must be an error in your .ins
file, but it is difficult fo us to guess what it is without seeing the
full file. A common error that can cause such instability is caused by a
long-standing bug in Coot, which sets some occupancies in the .ins
As you observe, radiation damage is local, but the effect is - to different
extent - on all Fs i.e. global (all atoms and their damage contribute to
each hkl).
So one would need additional local parameters (reducing N/P) if you want to
address it as such, your use of occupancy is an example (even
I was thinking actually the dose-dependent-occupancy would really be a tau
in an exponential decay function for each atom, and they could be fitted by
how well they account for the changes in intensities (these should actually
not always be decreases, which is the problem for correcting radiation
Dear all,
The generation of reliable restraints for novel small-molecule
ligands in macromolecular complexes is of great importance for both ligand
placement into density maps and subsequent refinement. This has led us to
develop Grade, a ligand restraint generator whose main source of
On Tue, 10 Jan 2012, Stephen Graham wrote:
On 10 January 2012 09:50, John Liebeschuetz j...@ccdc.cam.ac.uk wrote:
...available to anyone who has access to the Cambridge Structural
Database System
How many academic labs will bother / can afford to buy a CCSD license
just to check the geometry
On Mon, 9 Jan 2012, Soisson, Stephen M wrote:
I will second Ian's recommendation for GRADE from the Global Phasing
group. GRADE overcomes nearly all of the shortcomings we have
encountered with other approaches for ligand dictionary generation.
Steve,
Thanks to you and to Ian Tickle for
Dear All,
I have few papers in hand which explain me about microseeding, matrix
microseeding, and cross seeding.I have also read few earlier threads and some
more literature in google.Using Phoenix robot, I did a matrix micro-seeding and
matrix cross seeding. I have few hits with this.In 96
Scaling up 100nl drops is problematic. What I understand is that it is
not only the different equilibration conditions, but primarily the
amount of protein that gets absorbed on the surface is relatively higher
for small drops. There were some empirical formula for scaling up (i.e.
how much you
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Hi Graeme,
That's interesting. When I looked at this (and I would say I looked
reasonably carefully) I found it only made a difference in the scaling
- integrating across the whole area was fine. However, I would expect
to see a difference, and likely an improvement, in scaling only the
data
Rajesh
If you set up the volumes you suggest you will probably get precipitation.
This is counterintuitive until you realize that (as Ed says) you will be
losing a lot of protein with those small drops. When you scale up the
surface area to volume ratio is lower, so a smaller proportion of the
Dear All,
Do you need some help for structure refinement or structure analysis?
I will be very happy to work for you, while I am looking for next
position.
To me, solving structure is a puzzle game and for fun.
Regards,
Kevin Jin
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