Success! Thank you to everyone who replied :)
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harman,
Christine
Sent: Friday, December 07, 2012 1:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Reading CCP4 maps into PyMol
Hi,
Can anyone
Hi Christine,
I used this tutorial: http://pymolwiki.org/index.php/Display_CCP4_Maps
~Sean
On Fri, Dec 7, 2012 at 12:52 PM, Harman, Christine <
christine.har...@fda.hhs.gov> wrote:
> Hi,
> Can anyone tell me how to open a CCP4 map in Pymol.
>
> Thanks,
>
> Christine
>
>
>
>
Hi Christine,
This link may help... http://pymolwiki.org/index.php/Display_CCP4_Maps
Hüsnü
Am 07.12.2012 19:52, schrieb Harman, Christine:
Hi,
Can anyone tell me how to open a CCP4 map in Pymol.
Thanks,
Christine
--
Hüsnü Topal, Dr. rer. nat.
University of Zürich,
Department of Biochemistr
Give it the suffix .ccp4
On Dec 7, 2012, at 10:52 AM, "Harman, Christine"
wrote:
> Hi,
> Can anyone tell me how to open a CCP4 map in Pymol.
>
> Thanks,
>
> Christine
>
>
>
Hi,
Can anyone tell me how to open a CCP4 map in Pymol.
Thanks,
Christine
Dear Zbyszek,
That is a useful point. Another way of making it is to notice that the
correlation coefficient between two random variables is the cosine of the
angle between two vectors of paired values for these, with the proviso that
the sums of the component values for each vector add up to
I was confused because it seemed like CC1/2 wasn't very informative at
lower resolution since (in my datasets) they were all 99.9-100. So if
i've understood this correctly (and i'm honestly not sure that i have)
could CC1/2 be useful to show the quality of low resolution data, given
more preci
I too like the idea of reporting the table 1 stats vs resolution
rather than just the overall values and highest resolution shell.
I also wanted to point out an earlier thread from April about the
limitations of the PDB's defining the resolution as being that of
the highest resolution reflect
The difference between one and the correlation coefficient is a square
function of differences between the datapoints. So rather large 6%
relative error with 8-fold data multiplicity (redundancy) can lead to
CC1/2 values about 99.9%.
It is just the nature of correlation coefficients.
Zbyszek Otwin
A good way to think about it is that if CC1/2=100%, that means you can split
the data in half, and use one half to perfectly predict the corresponding
values of the other half. So yes, perfect internal consistency.
On Dec 7, 2012, at 11:41 AM, Phil Evans wrote:
> It is internally consistent,
Yes, well, actually i'm only a middle author on that paper for a good
reason, but I did encourage Rebecca and Stephan to use all the data.
But on a later, much more modest submission, where the outer shell
was not only weak but very incomplete (edges of the detector),
the reviewers found it diffic
It is internally consistent, though not necessarily correct
On 7 Dec 2012, at 16:23, Alan Cheung wrote:
> Related to this, I've always wondered what CC1/2 values mean for low
> resolution. Not being mathematically inclined, I'm sure this is a naive
> question, but i'll ask anyway - what does C
Related to this, I've always wondered what CC1/2 values mean for low
resolution. Not being mathematically inclined, I'm sure this is a naive
question, but i'll ask anyway - what does CC1/2=100 (or 99.9) mean?
Does it mean the data is as good as it gets?
Alan
On 07/12/2012 17:15, Douglas The
Hi Boaz,
I read the K&K paper as primarily a justification for including extremely weak
data in refinement (and of course introducing a new single statistic that can
judge data *and* model quality comparably). Using CC1/2 to gauge resolution
seems like a good option, but I never got from the p
Does this mean that, when placing the first (or only) copy of a model,
the score will not be elevated by presence of tNCS (Unless the model contains
domains separated by more or less exactly the distance of the tNCS vector)?
(In general, using a generic MR program that does not correct for TNS.)
S
Hi Ed,
Thanks for the comments. So what do you recommend? Refine against weak data,
and report all stats in a single Table I?
Looking at your latest V-ATPase structure paper, it appears you favor something
like that, since you report a high res shell with I/sigI=1.34 and Rsym=1.65.
On Dec
Roger,
Very low values of Kd (nM) may mean that you have a good chance of finding both
the proteins (or protein-nucleic acid) together if you get crystals of the
mixture. I therefore think that the measurements are useful in that sense.
However, low Kd does not necessarily mean that you get th
Dear Roger,
I disagree with Ganesh. Knowing the stoichiometry is not necessary.
Stoichiometry
may need adjusting to reflect the relative solubility of the interacting
partners
under the various crystallization conditions.
See also:
Stura, E.A., Graille, M., Taussig, M.J., Sutton, B.J. Gore,
Dear Roger,
In my humble opinion, the qualitative knowledge that the complex
actually forms (established through pull down assays, gel filtration
etc) is probably far more important than the Kd values in solution. In
any case, the crystallization is done at very high concentrations, far
abov
Dear all - is there a rule of thumb for favourable values of Kd, kon and
koff of protein-protein or protein-dna complexes for protein
crystallisation? Are these measurements useful in crystallisation, or
should one just put it down a gel filtration column, hope for a complex and
not worry? If an
Registration is now open for the second annual meeting of CCP-BioSim "Frontiers
of Biomolecular Simulation" at the University of Nottingham, Monday 25th to
Wednesday 27th March 2013. The meeting is open to all - registration provides
free membership of CCP-BioSim.
* Invited Speakers: Alessio Ci
Dear professor George Sheldrick,
Thank you very much for your prompt and patient reply.
I think I can solve my problem now.
Thanks again!
Best regard!
Ding wei
At 2012-12-07 19:14:46,"George Sheldrick" wrote:
Dear Ding Wei,
The Patterson function is discussed in most crystallographic text b
Ok - problem resolved. Would appear to be a problem with X11 on our current
system image.
Installing Xquartz 2.7.4 (http://xquartz.macosforge.org) and replacing the
default X11 from Apple - seems to have cured all ills.
Many thanks to Bill Scott, Nat Echols and Charles Ballard for their off-l
perhaps a second table in which certain statistics (Rsym, I/sigma,
CC0.5) are given as a function of, say, 10 bins of resolution would be
more useful than the same table twice at different resolution cutoffs.
then editors, reviewers and ultimately readers can decide for
themselves what resolu
Hi Douglas,
Using two Table Is is a good way to show the difference between the two
cut-offs, but I assume you will only discuss one of the models in your
paper. IMO you only need to deposit the high res model, so there should be
no problems with resolution conflicts in the PDB file. The annotator
Hi,
I'm sure Kay will have something to say about this but I think the idea of the
K & K paper was to introduce new (more objective) standards for deciding on the
resolution, so I don't see why another table is needed.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben
Dear Ding Wei,
The Patterson function is discussed in most crystallographic text books.
I recommend the IUCr text by Giacovazzo et al., "Fundamentals of
Crystallography" starting about page 423 in the third edition for a
detailed discussion. If you just require a sorted peak list, shelxd is
a
On 07/12/2012 10:43, Appu kumar wrote:
Dear Users,
I am refining a enzyme structure with ligand.
I want to make the simulated annealing omit map of ligand including
with 4 Angestron radius around the ligand. I am seeking your valuable
advice to help me out. I know how
Dear Users,
I am refining a enzyme structure with ligand. I
want to make the simulated annealing omit map of ligand including with 4
Angestron radius around the ligand. I am seeking your valuable advice to
help me out. I know how to make omit map but i have not come accross
Dear Yurong,
I just wanted to check that you're using an up-to-date version of Phaser, which
will account for the presence of translational NCS (tNCS). With older versions
of Phaser, you could get apparent solutions that were incorrect but would give
a high LLG just because they satisfied the
Dear all,
Can everyone tell me the patterson peaks outputted by shelxd (see below) are
calculated by which formula and software?
Thank you very much!
Ding wei
shelxc_fa.lst:
Patterson (* indicates vector selected for search)
X Y ZHeight Mult Length
0. 0. 0.00
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