rgy 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=1
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MS 357742, University of Washington, Seattle 98195-7742
###
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for it.
> Please let me know if you need more information. Thank you in ahead.
>
>
> Regards,
>
> Lande Fu
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Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
##
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> lis
>
> 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: http://kato
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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
> > > apocalypse?
> >
cheers,
Ethan
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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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&
r 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
--
Ethan A Merritt
Biomolecular Structure Center
link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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>
>
>
>
ct 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
> Goethe University
hat'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
Biomolecular Struc
hat 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 Structure Center, K-428
iformly 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
>
>
>
> _
>
> ############
>
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Biomolecular Structure Center, K-428 Health Scienc
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 that
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
>
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
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, 27 February 20
tering 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,
> Alex
>
&
amp; 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
Biomolecular Structure Cente
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
stake, 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, click the f
; >
> > possibly relevant:
> >
> > https://mail.ncmir.ucsd.edu/pipermail/3dem/2019-February/006519.html
> >
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > htt
#####
>
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Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Was
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
corrupted? Assuming native format.
> >>>>>>>>>> CCP4 library signal library_file:End of File (Error)
> >>>>
> >>>>
> >>>> To unsubscribe from the CCP4BB list, click the following link:
> >>>> https://w
rom the CCP4BB list, click the following link:
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>
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.u
S.
> >
> >
> > *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 for
he 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.shtml
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
>
e 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
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.
> -- / Lao Tse /
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
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
ndle 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 -> Highlig
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 otherw
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
n 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 something?
>
> Cheers
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
copy over time
to multiple copies in a frozen crystal is the basis for TLSMD
analysis. In the special case of a single molecule per unit cell
I suppose a one-group TLS treatment reduces to what you originally
asked about - vibration of whole unit cells - but in general
it does not.
cheers,
this) but assume that the driving
> force, amplitude of oscillation and damping all balance out to give a steady
> state. As you imply, more frequency points would be useful.
>
> Colin
>
>
> From: Ethan Merritt [mailto:merr...@u.washington.edu]
> Sent: 05 November 2015 1
r 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
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
, 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 A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington
!
Sincerely,
Chen
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
the Rmeas is horrible.
Ethan
Thanks a lot,
Chen
On May 13, 2015, at 6:07 PM, Ethan A Merritt merr...@u.washington.edu
wrote:
On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
Hi all,
I am sorry about this question which I should have figured out earlier. For
point
, not the NSF's.
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
me how
reliable this structure of Lambda repressor bound to DNA is?
Thanks
Misbha
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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
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, K-428 Health Sciences Bldg
MS 357742, University
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 press the right pedal the harmonics
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
in all 3 copies?
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
, 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
MS 357742, University
Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle
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 Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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
/
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
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
*a !
**
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
(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
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
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
for the less informed users. At least that will
give users some warning in the case of particularly worrisome
structures. The authors of course could still reply to defend their
structure, and it may encourage some people to even correct their
errors.
--
Ethan A Merritt
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 af...@ucsc.edu 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
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 after
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 running
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
search
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
are
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 I/sigI (and
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 MA*
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 structure
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 after
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
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
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 Center
University of Washington, Seattle 98195-7742
program that indeed
does not run.
Sorry, I didn't see the rest of your post.
I had sc running and producing meaningful results back in 2006-2007,
I can check which version etc.
Ed
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
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 way F is a structure.
--
Ethan A Merritt
Program.
This message was sent using IMP, the Internet Messaging Program.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
? What criteria would I use to
argue that it is a crystal artifact? Yes, of course ideally one would
go back to the lab and survey for solution measurements that are
consistent with tetramerization, but that is not always practical,
and may lead right back to your original question.
--
Ethan
-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
intuitive feel for the answer.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
are applied to residual B-factors too
(although I didn't test it systematically).
Applyinig NCS restraints to B factors is a whole separate area
for discussion. Let's not go there just now :-)
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
91125
626-395-2453
[EMAIL PROTECTED]
http://www.br.caltech.edu/cmclab
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
.
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.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington
Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [EMAIL PROTECTED]
***
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
.
This is not a big structure with no more than 1000 residues in 2
molecules. I wonder why the R values keep so high.
Do I need to run anisotropic refinement for such resolutions? Or any
other reasons?
Thanks!
--
Ethan A Merritt
Biomolecular Structure Center
University
of scattering factors. If you have refined a SAS data set,
e.g. a Se-edge dataset of a SeMet metallo-protein, then the R factors may
vary by 1% just because of incorrectly reproduced f' terms for the
Se and metal atoms.
Ethan Merritt
I loaded this into Refmac and asked for zero cycles
!
Sun Tang
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
such a discussion on BB before, leads welcome.
Probably addressed in some Rf-ree paper?
Thx, br
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Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
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