l energy which raises the b-factors and this trend is universal when
> comparing datasets from different temperatures.
>
> Thank you and happy to supply more information if that is helpful,
> Matt
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742
B list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
###
>
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>
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tion for it.
> Please let me know if you need more information. Thank you in ahead.
>
>
> Regards,
>
> Lande Fu
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
#
gt;
>
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shes,
>
> Gergely
>
>
> Gergely Katona, Professor, Chairman of the Chemistry Program Council
> Department of Chemistry and Molecular Biology, University of Gothenburg
> Box 462, 40530 Göteborg, Sweden
> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> Web: h
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rom the CCP4BB list, click the following link:
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> list hosted by www.jiscmail.ac.uk, terms & conditions are availabl
lems? Is there any reason, practically, why this approach would
> > > not be feasible?
> > >
> > > Maybe we don't really know enough to manipulate A, B, C yet?
> > >
> > > Or maybe it's too scary for primetime...nightmare bio-warfare
> > &g
cheers,
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
To unsubscribe from the CCP4BB list, click the following link:
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web site:
E.A. Merritt (2012). "To B or not to B: a question of resolution?"
Acta Cryst. D68, 468-477.
http://skuld.bmsc.washington.edu/~tlsmd/ActaD_68_468.pdf
cheers,
Ethan
>
> BRS
>
> Sam
--
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>
>
o be happy for product recommendations (optimally available at the
> German Amazon).
>
> Cheers
>
> Matthias
>
> https://www.amazon.de/dp/B00XNMXYBY/ref=cm_sw_r_cp_apa_i_5YsoFbFQXTBP9
>
> ___
> Buchmann Institute of Molecular Life Sciences
> G
am).
That's the "destroy" part of "diffract and destroy".
Since an XFEL pulse can be shorter than 10 fs,
that observation does not contradict the idea that the measured
diffraction occurs faster than the damage.
Ethan
> Cheers,
> José
--
Ethan A Merritt
Bio
would imagine that the same can happen for electron diffraction
but I can't point to any prior examples in the literature.
good luck!
Ethan
> Thanks in advance!
>
> Best,
> Jessica
>
>
--
Ethan A Merritt
Biomolecular Struc
are not
uniformly licensed or available for code inspection/modification.
I hope I have that right!
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
ular and Cell Biology, University of Leicester
> Henry Wellcome Building
> Lancaster Road, Leicester, LE1 7HB
> England, United Kingdom
>
> Skype: roversipietro
> Mobile phone +44 (0) 7927952047
> Tel. +44 (0)116 2297237
>
>
>
> _
37
>
>
>
> ############
>
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>
--
Ethan A Merritt
Biomolecular Structure Center,
(and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
>
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
>
> But maybe there are other ways th
lthough only after several rounds of discussion.
good luck,
Ethan
>
> Thanks
>
> Nick
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
#
On Sunday, 8 March 2020 01:08:32 PDT Rangana Warshamanage wrote:
> "The best estimate we have of the "true" B factor is the model B factors
> we get at the end of refinement, once everything is converged, after we
> have done all the building we can. It is this "true B factor" that is a
> property
Matthew:
I think your nice summary leaves out an important point that has not been
explicitly mentioned. That is the question of whether depositing hydrogens
actually adds information to the model. I submit that for a typical protein
refinement it does not. The model is adequately described by s
A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
> On Feb 28, 2020, at 12:51 PM, Ethan A Merritt
> mailto:merr...@uw.edu>> wrote:
> EXTERNAL MAIL
>
> On Thursday,
t does use scattering factors f' and f" from the mmcif coordinate file
- I have no idea what it does with twinning descriptions
As a result there is often a noticeable discrepancy between the R-factors
from "Depositor" and "DCC" in the validation reports.
> Regards,
nt of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
>
>
>
>
> To unsubscribe from the CCP4BB list, click the following link:
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--
Ethan A Merritt
Biom
ad two structures where incorrect diagnosis of tNCS prevented
Phaser from finding the correct solution. If you are not using Phaser, the
caveat still stands in principle.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences B
On Thursday, 28 November 2019 16:51:15 Jurgen Bosch wrote:
> Think of completeness with an analogy to turkey.
> Say you happen to find a one-legged turkey (incomplete by conventional
> standard) you could still stuff it and put it in the oven and enjoy 93% of
> the turkey. The 7% missing, who car
sage by mistake, please reply to this message and follow
> with its deletion, so that we can ensure such a mistake does not occur in the
> future.
>
>
>
>
> To unsubscribe from the CCP4BB list, cli
gt; server running scientific linux.
> >
> > possibly relevant:
> >
> > https://mail.ncmir.ucsd.edu/pipermail/3dem/2019-February/006519.html
> >
> > ############
> >
> > To unsubscribe from the CCP4BB list, c
#########
>
> To unsubscribe from the CCP4BB list, click the following link:
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Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of
cribe from the CCP4BB list, click the following link:
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--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
###
> > On Nov 13, 2018, at 3:44 PM, Ethan A Merritt
> > wrote:
> >
> >> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote:
> >> If somebody is going to send these files by email, please send one to me
> >> too. Thanks in advance. I actual
t;> Warning: Machine stamp corrupted? Assuming native format.
> >>>>>>>>>> CCP4 library signal library_file:End of File (Error)
> >>>>
> >>>>
> >>>> To unsubscribe from the CCP4BB list, click the following link:
>
ubscribe from the CCP4BB list, click the following link:
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>
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jisc
and SAXS.
> >
> >
> > *So, my question is, has anyone encountered such situation,
> > where the As-purified Fe-S protein having a completely different oligomeric
> > state compared to the in vitro reconstitution protein? *
> >
> >
> > Looking forward to
itive to the order of secondary structure elements.
This is relevant if you are looking for evolutionary relatedness, but
not if you just want to ask "does it look like this".
For the latter question, I suggest the VAST server at NCBI.
https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.
this is only
a still image. In the paper you cite it was more than that, but still
very small compared to "normal" data sets.
Ethan
> Their data improved not only in resolution, but also in the statistics. The
> method seems impressive.
> Thanks!
>
> Charles
>
th the entire subdomain XX". This is not the same thing
as saying individual B factors are higher or lower.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
-
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> --
Do you want to compare B factors for different residues in the same structure,
or B factors for the same residue in different structures,
or something else entirely?
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
ess than 100% occupancy.
> Any suggestions?
Could it be that a cloning error introduced a Cys->Arg mutation?
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
P4 bundle also.
If render is not being found, you may have a PATH error.
Is your Coot finding other CCP4 programs?
Ethan
>
> Paul.
>
> p.s. Draw -> Additional Representation -> Ball & Stick makes things a
> bit nicer, as does Extensions -> Representation -> Hi
ould crystallographers learn from or
> appropriate the concept of local resolution to good benefit, or perhaps vice
> versa? Anyway, if there is a good reason for the discrepancy, fine, but
> otherwise, having these different measures prevents straightforward
> comparisons which would o
wants from
the output of SIGMAA run from the ccp4i interface?
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
bs and Fcalc can provide an
estimate of how good/bad wrong/right your current model is.
But that still doesn't tell you whether the current model is bad because
pieces are missing or bad because existing pieces are in the wrong place.
Ethan
> Or am I missing somethin
>
> It has been refusing connections for already two days?
>
> Perhaps a mirror exists somewhere ?
>
>
> Best
>
>
> Carlos
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
ers,
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
t; object
>
> were "in phase" or "out of phase" and the narrator pointed that out, but
> neither
>
> state is a general phenomenon. I think. But maybe I'm confused.
>
>
>
> Ethan
>
>
>
>
>
> > Of course this is trying
uch that many photons
> are in some sense in the crystal at once? Or maybe this is a red herring.
> But, to change topics a bit: part of the reason I am wondering about this is
> anomalous scattering. Since the resonance energy of an atom is a fixed
> amount, how can one photon provide that energy simultaneously to the
> requisite number (at least thousands, I would think) of resonant scatterers?
> Something's very funny here.
> Or, come to think of it, perhaps resonant scattering is no worse than normal
> scattering: if the energy is divided up between the all the
> normally-scattering electrons, you even have a problem with the one-photon
> picture, since the emerging radiation is still of the same energy. You want
> to have everything being scattered with a certain energy, but you also want
> all the scatterers to scatter. The concept of "energy" seems to get strange.
> Does one then need two terms, in which "energy" is just a characteristic of
> radiation, like a color, and then there is some other attribute like
> "probabilistic intensity," which describes how much "photon" is there?
> It is striking to me how much depth these everyday occurrences really have
> when one starts wondering about them.
> Jacob
>
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
en the two formats ? (I don't expect there to be a data
> field in the PDB header for everything in mmCIF but I do for the reverse
> case).
>
>
> Thanks
> Phil Jeffrey
> Princeton
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
e any suggestions of how to
> refine this twinned structure, such as softwares to use, tricky strategies
> to choose, etc. I really appreciate any recommendations you would come up
> with my situation!
>
> Thank you in advance!
>
> Best,
> Mengbin
>
>
--
Ethan
ood that the Laue
group is P2 even though the Rmeas is horrible.
Ethan
> Thanks a lot,
> Chen
>
>
> > On May 13, 2015, at 6:07 PM, Ethan A Merritt
> > wrote:
> >
> >> On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
> >> Hi all,
>
> IDXREF.
>
> You inputs are really appreciated!
>
> Sincerely,
> Chen
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
ample,
> >> you are expected to share and "make widely available and usable" software
> >> and inventions created under a grant (section VI.D.4. of the Award and
> >> administration guide). I don't know how enforceable that clause is,
> > however.
> >>
> >> The funding shouldn't matter. I suggest that a publication that has the
> > purpose
> >> of describing non-open source software should be summarily rejected by
> >> referees. In other words, the power is in our hands, not the NSF's.
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
oot and
> > checked for Ramachandran outliers, the results are:
> > In preffered region: 58.04%
> > In allowed regions: 19.78%
> > Outliers: 22.17% !
> >
> > With an R-free of 37.4% at 3.9 A resolution, could you please tell me how
> > rel
; > Driver "nvidia"
> > VendorName "NVIDIA Corporation"
> > EndSection
> >
> > Section "Screen"
> > Identifier "Screen0"
> > Device "Device0"
> > Monitor"Monitor0"
> > DefaultDepth24
> > Option "UBB" "1"
> > Option "Stereo" "10"
> > Option "AllowDFPStereo" "1"
> > SubSection "Display"
> > Depth 24
> > EndSubSection
> > EndSection
> >
> > Section "Extensions"
> > Option "Composite" "Disable"
> > EndSection
> > --
> >
> >
> > cheers,
> > lukasz
> >
> >
> >
> >
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
used other MR programs, but
> still it still continues to be in the same range.
>
> I will look forward to any suggestions. Thank you.
What was the Wilson B factor reported by Aimless or Truncate?
What is the resolution of the data?
--
Ethan A Merritt
Biomolecular Structure Center,
On Thursday, 12 March, 2015 10:41:46 Ethan A Merritt wrote:
> On Thursday, 12 March, 2015 13:11:10 Keller, Jacob wrote:
> > >If projects a middle-C-tone into a piano, do all of the lower notes
> > >resonate as well, according to the Kramers-Kronig relation?
> > If you
it may actually happen in the mammalian cochlea's travelling wave, but
> is it completely general to resonance phenomena?
>
> Just interested, and have wondered these things for a long time in the
> background of my mind...
>
> Jacob Keller
>
>
>
h
> >>>>
> >>>
> >>> - --
> >>> - --
> >>> Dr Tim Gruene
> >>> Institut fuer anorganische Chemie
> >>> Tammannstr. 4
> >>> D-37077 Goettingen
> >>>
> >>> GPG Key ID = A46BEE1A
> >>>
> >>> -BEGIN PGP SIGNATURE-
> >>> Version: GnuPG v1.4.12 (GNU/Linux)
> >>>
> >>> iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
> >>> j0JFZac4kAh8twpov71MG84=
> >>> =XN57
> >>> -END PGP SIGNATURE-
> >
> > Mark J van Raaij
> > Lab 20B
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > c/Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://www.cnb.csic.es/~mjvanraaij <http://www.cnb.csic.es/%7Emjvanraaij>
> >
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
not tried this.
Yes, but that doesn't actually help.
It restrains the ligand copies to look like each other internally,
but does not restrain their binding pose relative to the surrounding
protein.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
M
e the same in all 3 copies"?
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
multiple sampling?
>
> This general math/science concept must have been discussed somewhere--can
> anyone point to where?
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr,
t gone back
to look again at the published example structures since the advent of
jellybody refinement. But note that jellybody is primarily useful when
you already have a high-qualityl, good geometry, starting model.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health S
relative to changes in the model
> and I've been unable to determine which restraints/weights are responsible.
> Thanks for any pointers,
> Alastair Fyfe
> UCSC
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
Earlier this year for the first time I got back a validation report from the
PDB for a deposited structure that included wwPDB validation of a ligand.
This is great stuff. I approve. I am happy.
Unfortunately the validation check reported problems with my ligand.
This is bad. I am unhappy. What w
0:27 AM, Tim Gruene
> > wrote:
> >
> >
> >
> > I hope that the contents of this section is obvious to most readers of
> > the ccp4 bulletin board.
> >
> > Cheer,
> > Tim
> >
> >
> > On 06/10/2014 03:40 PM, Jeffrey Bell wrot
astromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
> of that pizza is equal to pi*z*z*a !
> **
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
agment that has been
> >>> extracted and then modified (changed the Phi and Psi) from the native.
> >>>
> >>>
> >>> I have the original MTZ and MAP.
> >>>
> >>>
> >>> Is it even possible to calculate these values without inserting the
> >>> extracted fragment back into the rest of the PDB (the unmodified part)?
> >>>
> >>>
> >>> I am reluctant to do that since I have many such fragments I have
> >>> extracted and modified and wish to compare with the native.
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> George
> >>>
> >>
> >>
> >
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
grams use it. Math, charts, and
example demonstrations of the too-large Beq are reported in
"Some Beq are more equivalent than others". Acta Cryst. A67, 512-516.
E. A. Merritt (2011).
Ethan
>
>
> Thanks in advance,
>
> Carles Palanca.
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
ee:
"To B or not to B: a question of resolution?" Acta Cryst. D68, 468-477.
http://scripts.iucr.org/cgi-bin/paper?S0907444911028320
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
till reply to defend their
> > structure, and it may encourage some people to even correct their
> > errors.
> >
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
uld.bmsc.washington.edu/parvati/
Among other things, it will create a nice picture of your 3 chains colored by
B factor.
Ethan
>
> Best Regards,
>
> Oarabile Kgosisejo
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
On Friday, 04 April, 2014 10:44:18 Nat Echols wrote:
> On Fri, Apr 4, 2014 at 10:39 AM, Alastair Fyfe wrote:
>
> > Reconstructing the refinement may be necessary in some cases but there
> > are other applications (pdb-wide map statistics, development of map
> > analysis tools, quick model vs map
On Monday, 31 March, 2014 19:01:33 Oganesyan, Vaheh wrote:
> Colleagues,
>
> Sorry to bother for something really minor. The Refmac usually always
> recognizes tetrahedral SO4 groups and there were no problems related to its
> geometry. Two attached files demonstrate SO4 geometry before and afte
On Friday, 28 March, 2014 12:35:57 mesters wrote:
> The OpenGL performance is rather poor on intel HD chips up to and
> including the HD 4600
My experience differs.
I have not seen dramatically different performance in practice between coot
running on nvidia and the same program version runnin
On Thursday, 14 November, 2013 18:58:27 Niu Tou wrote:
> Dear Phil,
>
> I used PHASER to do the task. I have double checked and both files have
> the same prefix, so they are from the same output. I have also checked the
> headers again, they have the same spacegroup. Actually I was trying to
> s
On Thursday, 17 October, 2013 10:51:08 Lucas wrote:
> Dear all,
>
> I've been lecturing in a structural bioinformatics course where graduate
> students (always consisting of people without crystallography background to
> that point) are expected to understand the basics on how x-ray structures
> a
On Thursday, 10 October, 2013 22:44:34 Jim Pflugrath wrote:
> Please tell me why Rpim should be looked at. Cannot one have meaningless
> data and have lots of multiplicity to drive Rpim lower without any real
> benefit? Under what conditions is Rpim useful?
> And suppose one looks at (and no
On Wednesday, 02 October, 2013 17:31:06 wtempel wrote:
> Tim,
> I agree with your statement.
> Consider this situation:
> Macromolecular sample MA produces crystal CA. Data scale well in C2221 and
> refinement proceeds smoothly to give stuctural model SA.
> Slightly modified macromolecular sample M
On Monday, 23 September, 2013 22:01:32 RHYS GRINTER wrote:
> Hi all,
>
> I have been attempting to find a MR solution for a low resolution data set
> (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel
> I'm working on.
>
> I've created a trimmed poly-alanine from a struc
ingle clipping value along Z.
That is, you cannot rotate the sliced object to view the same slice from
some other angle.
Ethan
>
> 2013/9/5 Ethan A Merritt
>
> > On Thursday, 05 September, 2013 13:30:21 Arthur Glasfeld wrote:
> > > I am hoping to create som
On Thursday, 05 September, 2013 13:30:21 Arthur Glasfeld wrote:
> I am hoping to create some images of protein cross-sections where the atoms
> are depicted as spheres, and the spheres that are "cut" by the slab are shown
> as solids with the same color as the surface. An example of what I'm aft
On Mon, 15 Apr 2013, Raji Edayathumangalam wrote:
Hi Folks,
Does anyone know of an accurate way to mine the PDB for what percent of total
X-ray structures deposited as on date were done using molecular replacement? I
got hold of a pie chart for the same from my Google search for 2006 but I'd
l
On Wed, 27 Oct 2010, Frank von Delft wrote:
So, since the experimental error is only a minor contribution to the total
error, it is arguably inappropriate to use it as a weight for each hkl.
I think your logic has run off the track. The experimental error is an
appropriate weight for the Fobs(
mallish number of mouse clicks in
Coot or PyMol or ccp4mg that feed the information to Raster3D for rendering.
But nothing is currently in place that would allow a label
"no actual brains were consumed in producing this figure".
Ethan
--
Ethan A Merritt
Biomolecular Structure Cen
calculations - oops!
>
>
>
> Oganesyan, Vaheh wrote:
>
> > Among non-runnable programs in CCP4 there is the sc program that indeed
> > does not run.
> >
>
> Sorry, I didn't see the rest of your post.
> I had sc running and producing meanin
a, and feed the
unmerged intensities from both datasets into the SAD phasing program.
Let it do the scaling jointly.
Better yet would have been to collect the data in smaller wedges using
"inverse beam mode".
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
On Saturday 10 January 2009, Bernhard Rupp wrote:
> Dear All,
>
> I am getting conflicting comments on the use of
> 'structure factor amplitude'
> vs. just
> 'structure amplitude'
> for |F|.
???
That's just... odd.
|F| is the amplitude of F.
But no
0.0, 16th October 2008 (requiring Mosflm 7.0.4)
> >>
> >> iMosflm cannot run "usr/local/xtal/ccp4/ccp4-6.1.0/bin/ipmosflm":
> >>
> >> /usr/local/xtal/ccp4/ccp4-6.1.0/bin/ipmosflm: error while loading
> >> shared libraries: libtermcap.so.2: cannot open shared object file:
> >> No such file or directory
> >>
> >> Please configure iMosflm with the correct executable.
> >>
> >> I searched for libtermcap.so.2 and couldn't find it in my computer.
> >>
> >> Help please and thank you
> >>
> >> Victor Alves
> >>
> >>
> >>
> >>
> >> This message was sent using IMP, the Internet Messaging Program.
>
>
>
>
> This message was sent using IMP, the Internet Messaging Program.
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
program.
Perhaps there should be a registry of the parameters associated with
each version of each refinement program, and the PDB file could refer
to the appropriate parameter set by name rather than including it
in-line in each individual PDB entry.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
ight back to your original question.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
On Friday 28 November 2008, Donnie Berkholz wrote:
> On 16:04 Fri 28 Nov , Ethan A Merritt wrote:
> > On Friday 28 November 2008, Ben Akiyama wrote:
> > > I am measuring and comparing torsion angles in several solved
> > > crystal structures of RNA helices using
y
an interesting question, but I don't have any intuitive feel for the answer.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
Uniform distribution of neighbor-neighbor distances?
Uniform fractional coodinates?
Must the placement conform to space group symmetry?
It is probably impossible to satisfy all of the above jointly.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
e a
> decision, I systematically tried both possibilities, and the best result
> was to apply the restraints to residual B-factors.
I hesitate to suggest it, but...
might this be pointing to a coding error rather than to a flaw in the
rationale?
> The NCS restraints are applied to re
cular Crystallography Laboratory
> Howard Hughes Medical Institute
> California Institute of Technology
> Division of Biology
> 1200 E. California Blvd. MC 114-96
> Pasadena, CA 91125
> 626-395-2453
> [EMAIL PROTECTED]
> http://www.br.caltech.edu/cmclab
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
h
> temperature factor for further refinment?
By "fix", do you mean "correct" or do you mean "not refine"?
The high average value is quite possibly correct already,
but it is true that you should probably not be refining individual
B factors at that resolution.
-
in essence it's "déjà vu all over again".
Whether the cloud computing fad will extend to crystallography remains
to be seen. Note that distributed ("cloud") data storage has been
seriously proposed as a possible solution to the problem of archiving raw
diffraction images.
--
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