Hi Kenneth,
...1.2A resolution... refinement of individual parameters for a hydrogen
atom... Hm.. Are you refining against neutron diffraction data?
Anyways, to answer your question: technically yes, you can refine individual
parameters of any selected atom(s) against X-ray or neutron data (or bo
Not sure if all the sirs will concur (and it might be a good idea to ask
madams also), but the answer is probably no. As far as protonation
state goes (guess that is what you are after, not oxidation), a better
strategy may be to look into the bond lengths between the appropriate
heavy atoms that
Sirs:
We are attempting to refine hydrogens on a ligand (which is 100 % occupied) and
has ~ 40 heavy atoms (CNO). The data is 1.2 A, 325 AA, 83335 data points in C2.
We have refined aniso and with H riding along (Rf= 17, R = 15) in CCP4. Can we
individually
refine the protons on the ligand? Let t
[ scala 3.3.16 ]
in scala's "final table", there's "Mean((I)/sd(I))". i could be wrong,
but the error of this measurement seems to me to exist, considering
the uncertainty of sigma = 1 / sqrt( 2 (N-1) ) ... but its not clear
where the logfile has the values of I or sigma and N that correspond
to
Reminder: deadline to register approaching
Dear Colleagues,
Announcing an intensive 2-day School in Biological and Chemical Crystallography,
to be held at the University of Manchester on the 11th and 12th January 2011.
The Course is sponsored by Bruker (a PhD student Bursary) and the
Course is
I'm all in favor of (rational) length limits for the text - almost everybody's
prose is easier to read when they've been forced to cut 10-20%.
However, some journals include references in the character limit, and that just
encourages unscholarly behavoir.
Phoebe
For info, Dennis Sherwood's book 'Crystals, X-rays and Proteins' is now firmly
back in print (well, as Sherwood and Cooper, this time)... and it has quite a
few citations of Acta Cryst papers, with titles ;-)
A couple of tiny errata can be found at the following link...
http://www.ucl.ac.uk/~rm
A non-ccp4 related question. Does anyone know if the 2D and 3D stereo-imaging
on Insight II will work on a Linux client computer and an LCD monitor? We still
use old SGI computers but need to upgrade to Linux. We still have an Insight
license and we use the program quite frequently. Any feedback
Maybe article submissions could just contain the pubmed ID for
references, then everything would be pretty simple, no? The journal
could format it as it sees fit, and there would only be errors if
there were errors in pubmed. I guess books are trickier, but most
references are articles anyway.
JPK
Hi Bert,
rReferences in Science do NOT contain article titles, like in quite a number
of other journals (e.g. JBC, just to mention one of them) .
and I agree that it's a pain to find out whether a reference is really of
interest to you - but I also agree that it's so much more convenient
for the
OK I get it, its about the supplements...apologies.
Bert
On 11/22/10 9:35 AM, "John R Helliwell" wrote:
Dear Jacob,
Additional content, like article titles, whether print or online, need
to be checked properly for accuracy.
Article titles (if supplied by authors) can often need heavy checking,
?? I don't know if I understand the question, but don't most journals have
references that do include the article titles?
Science, Nature, Cell, NSMB, PNAS, JMB, Structure all have references
titlesas they should.
Bert
On 11/22/10 9:35 AM, "John R Helliwell" wrote:
Dear Jacob,
Additional
Dear Jacob,
Additional content, like article titles, whether print or online, need
to be checked properly for accuracy.
Article titles (if supplied by authors) can often need heavy checking,
and online systems to check
bibliographic information are not always reliable or comprehensive.
This I think
Dear Francois,
To my knowledge there are very few Journals that have article
references with titles. In crystallography I know of Crystallgraphy Reviews.
Best Wishes,
John
On Mon, Nov 22, 2010 at 2:07 AM, Francois Berenger wrote:
> Hello,
>
> For me the citation format is also a major problem.
>
It seems to me that this problem is really a hold-over from compromise
with the exigencies of hard-copy publishing, i.e. a way to save
physical space. Further, there seem to be many aspects of
e-publication that have not adapted to the strengths/weaknesses of the
new medium, which could and should
It makes an intelligent guess based on chain ID and proximity what is a
contiguous unit in the file, and moves on that basis. Separate chains
are always moved separately. Monomers within a chain which do not have
close contiguity to their neighbours - eg waters, broken chains - are
also moved s
Thanks, I should try it before I criticise ...
Regards
-- Ian
On Mon, Nov 22, 2010 at 10:01 AM, Eleanor Dodson wrote:
> It is a program Kevin Cowtan wrote - here is the info you get when you try
> to run it..
> E
>
>
> [c...@roo mariaH]$ csymmatch
>
>
>
>
>
> #
SSM - see superpose task under Coordinate utilities.
This matches secondary structure and gives RMSD for CAs - inceredibly
useful program..
Eleanor
On 11/19/2010 10:55 PM, Srivastava, Dhiraj (MU-Student) wrote:
Hi All
does anyone know any software that can calculate and print out RMSD
It is a program Kevin Cowtan wrote - here is the info you get when you
try to run it..
E
[c...@roo mariaH]$ csymmatch
###
###
I agree that refining a single occupancy parameter for the ligand is
a good approach. Because of the correlation with the B-values, it is
essential to refine occupancy and isotropic or anisotropic B-values
together, not in separate steps. SHELX has been able to do this
correctly for the last 40
Although Bfactors and occupancies are correlated, occupancy refinement is quite
feasible for the following reasons:
1) Modern maximum likelyhood programs like Buster do a decent job in separating
occupancies and Bfactors. It shows up as shells of negative difference density
e.g. around partiall
21 matches
Mail list logo
