From the idea you described, HET codes in the last pages of this article may be
useful.
http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1000&context=chemistrypowers
Best wishes,
Duangrudee
Postdoctoral Research Fellows
Department of Biochemistry and Molecular
Biology, Faculty of Medicine, Nursing and Health Sciences
http://research.med.monash.edu.au/rossjohn/
Prof. Jamie Rossjohn, ARC Federation Fellow, seeks talented
post-doctoral scientists to join his research group. The selec
Dear All,
Thanks to all that sent comments/suggestions during the webcast that allows
us to keep sound and video in the best conditions.
We would like to have a few answers if you watched talks online (privately
to me, not to the list). This will allow us to report to HEANET (
http://www.heanet.i
On Thursday 16 September 2010 10:34:14 am Dr. Mark Mayer wrote:
> >Huh? That's not a cif fragment. What file are you looking at?
> >In my experience the PDB feeds back to you a cif format structure factor
> >file with a name like rcsb054058-sf.cif
> >Near the top of that file you should find a d
Thanks!
> According to the really good documentation of O, e.g. at
> http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html
> you have to use the command "fm_mode" to change this (and while doing so
> might
> read Alwyns "FM_Overview" in the same documentation which I just did and
> found
> very in
Huh? That's not a cif fragment. What file are you looking at?
In my experience the PDB feeds back to you a cif format structure factor
file with a name like rcsb054058-sf.cif
Near the top of that file you should find a description of the data
columns. The columns present depend on what you fed
The main advantage of contouring in absolute units is consistency.
The density for a water molecule with a B factor of 20 A^2 will look
about the same even if the "noise" level of one map is higher than
another. (Within limits, of course) This means that the actual value
you contour at isn't a
On Thu, Sep 16, 2010 at 10:19:14AM -0700, Ethan Merritt wrote:
> [...]
> > What's a structural biologist to do?
>
> The empiricist's approach.
> Experiment till you find a procedure that works, then stick to it :-)
... or the social approach: communicate with the person at the PDB responsible
fo
Dear Colleagues,
We are pleased to let you know about the upcoming International Conference
on Structural Genomics 2011, to be held in Toronto, Canada on May 10-14,
2011.
This meeting is the 6th in this series of biennial meetings of the
International Structural Genomics Organization.
The meet
According to the really good documentation of O, e.g. at
http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html
you have to use the command "fm_mode" to change this (and while doing so might
read Alwyns "FM_Overview" in the same documentation which I just did and found
very interesting!).
Cheers,
On Thursday 16 September 2010 09:56:14 am Dr. Mark Mayer wrote:
> Ethan wrote
>
> >I believe that deposition of Fc Phic FOM should be required.
> >Certainly it should be the recommended practice.
> >
>
> For the same series of structures I just deposited, which started the
> the riding H discuss
Hi Mark,
I assume you deposited the mtz? This is what Ethan was referring to - the pdb
does not do well with maintaining all the relevant columns when submitting the
mtz file. However, if you convert your mtz to cif yourself and make sure it
has all the columns you would like to include and
Hi,
It can, just do
fm-mode
select rmsd
I am curious though, I have heard that it is 'better' to build in
units of absolute density, but I couldn't find any values. Does any
one have a suggestion as to what absolute electron density setting is
'correct' for an Fo-Fc difference map? Or do you jus
Hi,
I generated a map using FFT, and tried to display it in O. By comparing
with coot, I found that the "level" in O seems to be the absolute electron
density instead of the sigma level. I am sorry I ask a question more
related to O: can O draw the map by a given sigma level instead of the
absolut
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the
the riding H discussion, my mtz file had Fc Phic FOM + other data put
out by Phenix - pavel can ela
Try both and look at the maps. Both are easy to run.
(Which works best seems to vary a lot from case to case.)
Yamei Yu wrote:
Hi all,
To decrease model bias from molecular replacement we can either use
Parrot or prime-and-switch-phasing. What's the difference between these
two programs? Whi
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote:
>
> > so, wouldn't be the deposition of the final model's Fcalc, Phic (and
> > their weights) along with the final coordinates be the best solution?
> > The final Fcalc are our best model and can be used to reproduce the
> > final s
Hi all,
To decrease model bias from molecular replacement we can either use Parrot
or prime-and-switch-phasing. What's the difference between these two
programs? Which one is better?
Thank you very much!
Yamei Yu
Hi Dirk,
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (which would remove the sfcheck annoyance) and to
reproduce
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote:
> so, wouldn't be the deposition of the final model's Fcalc, Phic (and
> their weights) along with the final coordinates be the best solution?
> The final Fcalc are our best model and can be used to reproduce the
> final statistics
SARChI POSTDOCTORAL FELLOWSHIPS IN PROTEIN BIOCHEMISTRY AND STRUCTURAL
BIOLOGY AT THE UNIVERSITY OF THE WITWATERSRAND SOUTH AFRICA
Postdoctoral positions in protein biochemistry and structural biology
are available for suitably qualified PhD graduates to pursue research
into improving our u
Hi Nukri,
Note that in the ultra-high resolution structure of aldose reductase
http://www.ncbi.nlm.nih.gov/pubmed/15146478
we didn't see all (or most) hydrogens. So, the converse question one could ask
is why we didn't see all of them? Was it only because of higher B-factors or
because some
Well , maybe they are there (hydrogens), maybe they are not (also depends on
location). They, or something else also boils sometimes.
I also understand from some other publications such as
doi:10.1107/S090904509002192 (cyclosporine) that hydrogen abstraction is
irreversible. Is it supported my
Hi Pavel,
Note that in the ultra-high resolution structure of aldose reductase
http://www.ncbi.nlm.nih.gov/pubmed/15146478
we didn't see all (or most) hydrogens. So, the converse question one could ask
is why we didn't see all of them? Was it only because of higher B-factors or
because some o
Dear CCP4 users
The Shelx lst file includes the entry:
Most Disagreeable Reflections (* if suppressed or used for Rfree)
and includes 50 hkl's with
h k lFo^2 Fc^2 Delta(F^2)/esd Fc/Fc(max) Resolution(A)
Is there a corresponding or similar facility in CCP4?
Rex Palmer
B
Dear Ian and contributors to this interesting thread,
(please, scroll down a little bit)
Am 15.09.10 23:34, schrieb Ian Tickle:
I should just like to point out that the main source of the
disagreement here seems to be that people have very different ideas
about what a 'model' is or should be.
Dear All
there will be a CCP4 school at Osaka University from 8 - 12 November 2010.
The aim of this school will be to cover all aspects of the structure solution
process in macromolecular crystallography, starting from data processing,
through phasing and refinement, and ending with validation
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