the helix, all your maps
will be omit maps.)
It is quite common to submit models to the PDB that do not
contain all of the amino acids expected based on the sequence.
If you can't see where the chain goes you certainly can't be
expected to build it.
Dale Tronrud
On 05/13/2013 04:23 AM, atul
based R values are lower
when you refine against F's, that means nothing.
If we could get the PDB to report both the F and I based R values
for all models maybe we could get a start toward moving to intensity
refinement.
Dale Tronrud
On 06/20/2013 09:06 AM, Douglas Theobald wrote:
Just trying
back through your Fcalc's and
Fobs's.
Dale Tronrud
On 06/23/2013 09:57 PM, Peter Randolph wrote:
Short version:
Hi, I'm working on what should be a straightforward molecular
replacement problem (already solved protein in new space group), but my
Fo-Fc map contains a peculiar series
exist
that displays for the user whatever representation they want. Then the
representation stored in the master repository would not be very
important.
Dale Tronrud
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
the presence
or absence of hydrogen bonds will distinguish between these two compounds
before you go to the trouble to build a model of either.
Dale Tronrud
On 7/17/2013 6:35 AM, Wei Feng wrote:
Dear all,
Thank you for your advices.
I had tried to use MPD and pyrophosphate etc to fix the density
Since Phil is no doubt in bed, I'll answer the easier part. Your
second matrix is nearly the equivalent position (x,-y,-z). This
is a two-fold rotation about the x axis. You also have a translation
of about 31 A along x so if your A cell edge is about 62 A you have
a 2_1 screw.
Dale Tronrud
for yourself.
Everything you have said points to your crystal being P212121
(or very nearly P212121).
Dale Tronrud
On 10/15/2013 02:31 PM, Yarrow Madrona wrote:
Thank you Dale,
I will hit-the-books to better the rotation matrices. I am concluding
from all of this that the space group
loops. If I recall, my model has about 10 more amino acids
than the PDB model.
In all of these cases the majority of the resides in each model are
fine. 3SQK has been replaced with a corrected model (4F4J).
Dale Tronrud
On 10/17/2013 06:51 AM, Lucas wrote:
Dear all,
I've been lecturing
It doesn't look like you left a CN on your gold atom. These things
are pretty much covalently bound.
Dale Tronrud
On 12/10/2013 08:13 AM, PriyankMaindola wrote:
dear all:
I. i am not able to fit trp,
since
1. trp doesnt fit well
2. positive density comes in fo-fc map after refinement
I would write back to the annotator who send the processed files
to you and ask if you can restart the deposition. The worst they
can say is no and you're back to ADIT. On the other hand they
will probably be as happy as you to save the work that has already
been done.
Dale Tronrud
On 01/31
(Pacific) Northwest Crystallography Workshop
http://oregonstate.edu/conferences/event/nwcw2014/
June 20-22, 2014
Registration is now open for this year's edition of the Northwest
Crystallography Workshop. It is being hosted at Oregon State University
in
When you don't normalize the map you have to specify your contour
level in whatever units the map came in. Your output says the stdev
is 0.075 so I guess you need to contour at 0.225 to see the equivalent
image.
Dale Tronrud
P.S. I feel compelled to note that what the program is reporting
can give it a pass
for not fitting the model. The model has to fit the density, and
fit it better than any other model.
You must also make clear to your readers what the occupancy of your
ligand is and the quality of the maps that lead you to this conclusion.
Dale Tronrud
P.S. I have had great
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Second announcement for the
(Pacific) Northwest Crystallography Workshop
http://oregonstate.edu/conferences/event/nwcw2014/
June 20-22, 2014
Registration is continuing for this year's
based on the traditional criteria.
This solution allows for the best possible model to be constructed and
the buyer is still allowed to make quality judgements the same way
as always.
Dale Tronrud
On 4/18/2014 5:22 PM, Lavie, Arnon wrote:
Dear Kay.
Arguably, the resolution of a structure
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Northwest Crystallography Workshop
http://oregonstate.edu/conferences/event/nwcw2014/
June 20-22, 2014
The (Pacific) Northwest Crystallography Workshop is a regional
gathering of people who are
structure does
have 2 fold symmetry (see below) and as Dale Tronrud pointed out,
there is always tNCS in a P21 space group with two monomers
related by a 2-fold axis.
I calculated the translation to be unit cell fractions of 0.36
0.35, 0.32.
rota_matrix -0.9860 -0.1636 -0.0309 rota_matrix
of the crappy Matrix movies.
Dale Tronrud
On 5/14/2014 6:47 PM, James Holton wrote:
A little loophole that might make everyone happy can be found
here: http://www.wwpdb.org/policy.html search for A re-refined
structure based on the data from a different research group
Apparently, anyone can
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
(Pacific) Northwest Crystallography Workshop
http://oregonstate.edu/conferences/event/nwcw2014/
June 20-22, 2014
Summer is fast approaching and so is the Northwest Crystal-
lography Workshop to be held here
,
eventually becoming darker than the surrounding liquid.
The speed of binding is controlling the kinetics not diffusion.
Dale Tronrud
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Keller, Jacob
Sent: Friday, June 27, 2014 3:07 PM
To: CCP4BB
.
Dale Tronrud P. Andrew Karplus
Department of Biochemistry and Biophysics
Oregon State University
-BEGIN PGP SIGNATURE-
Version: GnuPG v2.0.22 (MingW32)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
iEYEARECAAYFAlOt044ACgkQU5C0gGfAG12aZACdG68Vyjw7JJimw0ofMZrJQLu8
it.
Hope that helps,
Dale Tronrud
On 6/27/2014 1:49 PM, Keller, Jacob wrote:
I have wanted for some time to search for catalytic-triad-like
configurations by defining three Ca-Cb bonds from known catalytic
triads, then searching the pdb for matches, but have not thought of
a quick and/or easy
have to be deposited, however. (And this provides
no protection against forgeries of home source data sets.)
Dale Tronrud
On 04/03/12 13:19, Bryan Lepore wrote:
On the topic of MX fraud : could not an encryption algorithm be
applied to answer the question of truth or falsity of a pdb/wwpdb
of the quality of the phase information.
With best wishes,
Gerard.
--
On Tue, Apr 10, 2012 at 12:00:28PM -0700, Dale Tronrud wrote:
The phases do have effects all over the unit cell but that does not
prevent them from constructively and destructively interfering
On 4/10/2012 10:44 PM, Kay Diederichs wrote:
Hi Dale,
my experience is that high-B regions may become visible in maps only late in
refinement. So my answer to the original poster would be - both global reciprocal-space
(phase quality) and local real-space (high mobility) features contribute
other reasonable model.
Saying that my map is consistent with my model is a very weak statement in the
absence of exclusivity.
A recent example of this sort of problem can be read about at (warning:
tooting
my own horn)
http://www.springerlink.com/content/b8h6lg138635380v/?MUD=MP
Dale Tronrud
there to
begin with.
Dale Tronrud
On 4/28/2012 12:06 AM, Zhijie Li wrote:
Hi,
My first thought was same with David: the truncation won't change the crystal's
space group. The symmetry of the crystal is
reflected by the symmetry of the amplitudes of many many reflections across all
resolutions
A map. Your job is to say these parts I understand and these parts I
don't.
Dale Tronrud
On 05/15/12 07:51, RHYS GRINTER wrote:
Dear Community,
As I'm a relatively new to protein crystallography this might turn out to be
an obvious question, however.
I'm working on the structure
of
sigma(Fo) to be catastrophic.
Wouldn't sigma(sigmaA) be the largest component since sigmaA is a function
of resolution and based only on the test set?
Dale Tronrud
All the best,
Nicholas
they want and not be guilty of overstating the quality of
their model.
Dale Tronrud
JPK
On Thu, May 31, 2012 at 1:59 PM, Edward A. Berry ber...@upstate.edu wrote:
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL(I) : 1.21700
I noticed structure 3RKO reported
, and then adjust the averaged map so that it mostly
matches those contours. If your ncs is less perfect this will not work as
well for you.
Dale Tronrud
On 6/6/2012 2:20 PM, Paul Emsley wrote:
On 06/06/12 21:47, Ursula Schulze-Gahmen wrote:
I calculated threefold averaged omit maps in coot. These maps look
overlay two models and have a logical solution without
a rotation matrix with a determinate of -1.
Besides, you will continue to be bitten by this problem as you use other
programs, until you actually swap some labels.
Dale Tronrud
On 07/12/12 15:00, Joel Tyndall wrote:
Hi all,
Thanks very
defining the labeling for a number
of the groups we use, I think it is up to you to justify why this group
should be treated differently.
Dale Tronrud
P.S. On a only slightly off topic note - I'm quite afraid of using both
as the definition for chirality. I've noticed that this keyword is used
'
conformation of your mixed model, leaving the 'g' conformation unrestrained
by ncs.
Dale Tronrud
P.S. I'm avoiding the use of 'A' and 'B' alt locs because these are
routinely used when splitting side chains but are almost never intended
to imply that all 'A's are coordinated with each other and all 'B's
into the space above. Was your protein exposed to that compound somewhere
along the way?
Dale Tronrud
On 08/08/12 04:56, Mario Sniady wrote:
While building our crystal structure model we encountered density which
we weren't able to assign. The unknown molecule/molecules seems
that
they can calculate as many maps as they do.
Dale Tronrud
On 08/08/12 13:39, Shya Biswas wrote:
Hi all,
I was trying to get maps using the *fetch PDB and Map using EDS option*
in coot, however the map would not open I am using coot version 0.6.2
was wondering if anybody else had similar
you could download the map even if it existed.
Dale Tronrud
If you're not in a super rush I know the person who refined that
specific PDB and I may be able to get you a copy of her final maps to
send you off-board once she gets back from vacation.
Cheers,
Katherine
On Wed, Aug 8
objects.
Remember, a lysine on the surface can probably be built in twenty
different conformations and the difference map flat in every case while
a couple atoms elsewhere could have a shift of 0.1 A that lights up the
map. There are no generic cut-offs or thresholds that work.
Dale Tronrud
On 9
with some long chelating molecule around the equator. In
the extreme it could be some sort of porphyrin, although the density
would be very poor if it was.
Dale Tronrud
On 11/28/2012 7:48 AM, Read, Jon wrote:
Anyone see anything like this before? The data is 1.7Angstrom data with good
statistics
will be surrounded
by a huge number of other features when you contour at 0.18 e/A^3
and by very few in the last map, but isn't that as it should be?
The map is supposed to be flatter at the end.
Dale Tronrud
On 11/28/12 12:30, Pavel Afonine wrote:
For map in e-/A^3 units to make sense one needs
to be nonsense. If the molecule
you are building will refine to an occupancy of 0.1 you could spend
you time better by doing something else.
Dale Tronrud
On 11/28/12 15:13, Lijun Liu wrote:
F000 contributes to the whole map as a level (F000/V). If calculated
with a only difference of with or w/o F000
Good luck on your search in 100 years for a computer with a
USB port. You will also need software that can read a FAT32
file system.
Dale Glad I didn't buy a lot of disk drives with Firewire Tronrud
On 12/12/2012 1:02 PM, Richard Gillilan wrote:
SanDisk advertises a Memory Vault disk for
Holton has pointed out.
I suppose there might be a cloud solution where you rely upon data just
floating around out there in cyberspace with a life of its own.
Richard
On Dec 12, 2012, at 4:41 PM, Dale Tronrud wrote:
Good luck on your search in 100 years for a computer with a
USB port. You
and it is still going strong so I have high hopes for solid-state
memory. It will be several years before 1 TB SSD's drop in price
enough for the next move of my little archive. The SanDisk Memory
Vault that started this thread maxes out at 16 GB.
Dale Tronrud
By the way if anybody has
conformational variability being some changes with
cis-peptide bonds. Shelxl still uses EH 1991.
Dale Tronrud
On 01/14/13 09:54, Ed Pozharski wrote:
To what extent modern geometric restraints have been upgraded over
original EnghHuber? And where I can find a consensus set of values
(with variances
the
things you know with confidence as your guide.
Dale Tronrud
On 01/16/13 11:15, ruisher hu wrote:
Hi, Dear All,
I recently got a dataset about 2.3 A resolution, however, I got some
trouble assigning the metal sites. It suppose to have multiple binding
site(possibly four) around those four
. I'll have to experiment a bit.
Dale Tronrud
On 04/11/2013 05:17 AM, eugene.krissi...@stfc.ac.uk wrote:
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing changed (and why it should be used from command line at
all ?:)). The name was changed because
0.3% test set is as precise as a 10% test set
in HEWL. (Even though the affect of leaving these reflections out of
the refinement will be quite different, of course.)
Dale Tronrud
Andreas Forster wrote:
Hey all,
let me give this discussion a little kick and see if it spins into outer
space
/import.script: can't read fo: no such
variable
#CCP4I TERMINATION TIME 08 Feb 2007 22:59:11
#CCP4I MESSAGE Task failed
I'm afraid I'm not fluent in TCL/TK. Can anyone tell me what
I should do to get this working?
Thanks,
Dale Tronrud
model should be
no more or no less than what you can justifiably claim is a reflection
of the true state of the molecule in your crystal.
Dale Tronrud
solution.
Dale Tronrud
Peter Adrian Meyer wrote:
I add a fake sigma column for each data column because so many
programs require one.
This is slightly tangential, but does anyone know of a good way to
generate semi-realistic sigma values for calculated/simulated data?
The best I've been able
U Sam wrote:
Hi
I would like to know following issue for a ligand.
A ligand of a long alkyl chain can have multiple conformation.
In coot in order to fit any protein residues into difference Density, we can select a
specific rotamer conformation and refine.
For fitting ligand of above kind, how
work.
Dale Tronrud
Edwin Pozharski wrote:
Mischa,
I don't think that the field of nanotechnology crumbled when allegations
against Jan Hendrik Schon (21 papers withdrawn, 15 in Science/Nature)
turned out to be true. I don't think that nobody trusts biologists
anymore because of Eric
is spreading out into space and so entropy increases.
Dale Tronrud
at the experiment either way.
Dale Tronrud
. The
refinement program will attempt to overestimate the amplitudes of the
high resolution Fc's to match the overestimated low resolution Fc's.
Check you log files to ensure you bulk solvent correction is operating
correctly.
Dale Tronrud
Jorge Iulek wrote:
Dear all,
Please, maybe you could give some
compound is in the
PDB, using atom names based on it would simplify comparisons.
Dale Tronrud
Zheng Zhou wrote:
Hi, all
I am a rookie in crystallography. I know this may be a little bit off
topic. I have cocrystallized several compounds with my favorite protein.
I found crystal structures
averaging a map that is only
sampled at twice the rate you are interested in will not be a useful
way to spend your time.
Dale Tronrud
whittle wrote:
Hi:
I am trying to generate structure factors from a mask/map that I made
with NCSMASK. I get the following error message in SFALL:
The program run
is much harder than building
a model to fit the density. What is harder than identifying a bit
of density, is coming up with an experiment to prove it.
Dale Tronrud
Ronaldo Alves Pinto Nagem wrote:
Dear CCP4bb users,
As suggested by some users, I am attaching to this email the electron
density
if this is not what you would
otherwise do.
Dale Tronrud
Charlie Bond wrote:
Hi Jie,
Depending on your resolution, you may be forced use to use S(0.5) and
4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement.
Cheers,
Charlie
Jie Liu wrote:
Dear all
I have a sulfate ion sitting
binding of
a compound, for example, than a bias reduced map after refinement.
Dale Tronrud
michael nelson wrote:
In my understanding, unbiased electron density map usually refers to the
Fo-Fc map.But I have seen in some papers sentences like that The
initial, unbiased 2F_o -F_c map is contoured
Dirk Kostrewa wrote:
Am 10.01.2008 um 01:53 schrieb Dale Tronrud:
...
Your quote bring up another matter. An initial map, i.e. before
refinement, is unbiased if it is an omit map. If you have done no
refinement and you leave the interesting part out of the calculation
of Fc there can
of the problems we have with ncs in refinement and
structure solution.
Dale Tronrud
Dirk Kostrewa wrote:
Dear Dean and others,
Peter Zwart gave me a similar reply. This is very interesting
discussion, and I would like to have a somewhat closer look to this to
maybe make things a little bit
justify breaking your ncs. A drop in Rfree when you break ncs does
not necessarily mean that breaking ncs is a good idea. You always
have to perform the proper null hypothesis test.
Dale Tronrud
At 01:05 PM 2/8/2008, Axel Brunger wrote:
In such cases, we always define the test set first
Bart Hazes wrote:
Dale Tronrud wrote:
[EMAIL PROTECTED] wrote:
Rotational near-crystallographic ncs is easy to handle this way, but
what about translational pseudo-symmetry (or should that be
pseudo-translational symmetry)? In such cases one whole set of
spots is
systematically weaker
winded post, but sometimes I get these
things stuck in my head and I can't get any work done until I get
it out. I hope it helps, or at least is not complete nonsense.
Dale Tronrud
in are not present in the
Electron Density Server, so I suspect I'm not alone in fighting
this battle.
Any advice would be appreciated,
Dale Tronrud
is going on here.
Dale Tronrud
Dale Tronrud wrote:
Hi,
I am looking over a number of models from the PDB but have been
unable to reproduce the R-factors for any model that was refined
with Refmac and contains TLS parameters. I usually can't get within
5% of the reported value
(with the limiting case of only F000).
Dale Tronrud
Bernhard Rupp wrote:
Let's try this again, with definitions, and pls scream if I am wrong:
a) Any reflection pair hR = h forms a symmetry related pair.
R is any one of G point group operators of the SG.
This is a set of reflections (S
not the original reflection.
Dale Tronrud
Sounds more like centric or perhaps simply symmetry related to me.
A few lines below:
A Bijvoet difference refers to the difference in measured
amplitude for a Bijvoet pair
I don't think you can have it both ways ??
BR
the result, drag the CA to the side you want. You may have over-drag
to get it to stay. It only takes a moment.
But don't assume that your refinement program is just doing something
stupid. Look for the primal cause.
Dale Tronrud
Yusuf Akhter wrote:
Hi Everybody,
I am refining structure
for deposition, since you will not
have to worry about enforcing the superposition of atoms any longer.
That may be clearer to people who use the model at a later date.
Dale Tronrud
Andy Millston wrote:
I am currently trying to refine a structure where a 5 residue stretch of
a chain is in 2
.
Dale Tronrud
Peter Schmidtke wrote:
Dear CCP4BB List Members,
first of all I am not a crystallographer, but I would like to get some
things clear, things I did not find in Crystallography Made Crystal Clear
and on the internet for now.
I am trying to read electron density maps
deposited only to find out that
the investigator's wedding photos were accidentally deposited instead.
Validating that the images correspond to the claimed structure
will be an enormous task; probably more difficult than coming up
with enough hard drives to store them all.
Dale Tronrud
Frank
of equilibrium (such as
ATP hydrolysis in the cell) but I don't think that's a simple mutation of
your enzyme. ;-)
Dale Tronrud
On 05/18/10 00:31, Vinson LIANG wrote:
Dear all,
Sorry for this silly biochemistory question. Thing is that I have a
reversible epimerase and I want to mutate
...@gmail.com/
//
On May 18, 2010, at 11:54 AM, Dale Tronrud wrote:
Hi,
I'm more of a Fourier coefficient kind of guy, but I thought that a
#916G of zero simply corresponded to an equilibrium constant of
one. You
can certainly
of high resolution data as they are in its presence.
Dale Tronrud
On 06/01/10 04:51, Ian Tickle wrote:
On Mon, May 31, 2010 at 9:15 PM, Dale Tronrud det...@uoxray.uoregon.edu
wrote:
One of the great mysteries of refinement is that a model created using
high resolution data will fit a low
.
Don't worry about the ligand until you solve the protein
structure. Whether you see it in the end will depend on how
big it is and how good your 4 A data are. Of course, it's
possible that it doesn't bind at all.
Dale Tronrud
On 06/07/10 12:17, yang li wrote:
Dear colleagues
A new version of the Protein Geometry Database (PGD) has just been released.
This version includes
- The ability to compose queries and analyze the behavior of side chain
chi angles.
- Structures released in the wwPDB up to April 8, 2010 consisting of
roughly 18,000 nonredundant protein
of any matches found.
If you need any detailed assistance using this server, I'd be
happy to help.
Dale Tronrud
On 07/02/10 05:44, Domen Zafred wrote:
Dear all,
There is an odd loop on the surface of my structure. Three back-bone
oxygen atoms are turned in the same direction the structure
idea of offsetting the minimum
to zero may be more satisfactory.
Ed
Ed is right, of course. Just remember to include ALL the electrons
in the unit cell - both those of the protein and those of the solvent,
ordered and disordered.
Dale Tronrud
Cyclized DTT can look similar to this blob. Of course the sulfur
atoms would make one end of the blob more dense than the other.
Dale Tronrud
On 07/09/10 05:12, Nick Quade wrote:
Dear CCP4 community,
I have solved the structure of a protein in complex with DNA. But,
inside the protein
. Otherwise it's the same as saying that
I've refined TLS ADP's but not saying what the TLS parameters were
nor listing the atoms in each TLS group.
Dale Tronrud
P.S. George: Do you think hydrogen atoms generated by the HFIX 137
command should be deposited? They are placed based on the electron
out a
water molecule. That way you can see what a good water molecule
looks like in your current difference map and can compare other
potential water molecules to it.
Dale Tronrud
On 09/16/10 10:13, Nathaniel Clark wrote:
Hi,
It can, just do
fm-mode
select rmsd
I am curious though, I have
that in the
presence of anomalous scattering the phase of F(000) is not zero.
It is also the only reflection who's phase is not affected by
the choice of origin.
Dale Tronrud
On 10/13/10 22:38, James Holton wrote:
An interesting guide to doing phasing by hand is to look at direct
methods (I recommend
On 10/15/10 12:38, Bart Hazes wrote:
The photon moves through the crystal in finite time and most of the time
it keeps going without interacting with the crystal, i.e. no
diffraction. However, if diffraction occurs it is instantaneous, or at
least so fast as to consider it instantaneous. In
the waters in each cluster to
the average location.
Has someone already written something along these lines?
If so, I would rather not duplicate their effort.
Thanks in advance,
Dale Tronrud
.
With the assumption of C centering these weak reflections are
discarded and the R values will go down. Your goal is not to
reduce the R values, but to fit the data. If these reflections
have non-zero intensities you must integrate them and add them
to your refinement.
Dale Tronrud
On 12/01/10 08:31, Xiaopeng
the occupancy of B 31
set to 0.33 and that of D 31 set to 1.00 simply because of an
insignificant shift in the position of the atom.
Dale Tronrud
On 12/10/10 13:53, Ian Tickle wrote:
Good point Colin! 2-Zn insulin is of course a classic example of
this, where the two independent Zn2+ ions both sit
to forbid coexistence the occupancy should
be 1/n. I think either assumption is reasonable but, of course,
prefer mine for what I consider practical reasons. It helps that
I have to code to make mine work.
Dale Tronrud
On 12/15/10 08:54, Ian Tickle wrote:
Hi Herman
What makes an atom
and maps would be insignificant anyway, so it may
as well be on-axis.
If the difference is insignificant, it may as well be off-axis. I
guess if the difference is insignificant it just comes down to personal
preferences.
Dale Tronrud
I think this is how the Oxford CRYSTALS software
be a little off. All structural models are fuzzy.
Dale Tronrud
are errors as significant as the one you created.
Dale Tronrud
On 01/28/11 12:29, Todd Geders wrote:
Greetings CCP4bb,
*Short version:
Very noisy difference maps from a crystal with extremely high solvent
content, seeking advice on how best to handle such high solvent content
to eliminate
!
Dale Tronrud
on ATOM/HETATM records are already defined with great specificity, if
you want the model to contain additional information you will have to
define new parameters, or some way to specify the information you want
to include using other, existing, records more adequate to the task
(e.g. SIGATM).
Dale
factors into
this field in the PDB file.
Dale Tronrud
On 3/31/2011 9:06 AM, Zbyszek Otwinowski wrote:
The B-factor in crystallography represents the convolution (sum) of two
types of uncertainties about the atom (electron cloud) position:
1) dispersion of atom positions in crystal lattice
2
your magic B factor
either. You can't out-think someone who's not paying attention. At
some point you have to assume that people being paid to perform research
will learn the basics of the data they are using, even if you know that
assumption is not 100% true.
Dale Tronrud
solves the problem
and not simply creates more confusion.
Dale Tronrud
P.S. I just Googled occupancy zero. The top hit is a letter from
Bernhard Rupp recommending that occupancies not be set to zero :-)
will continue to return to this argument again and again with no
possibility of coming to a solution.
Dale Tronrud
P.S. I've even thought about using the model of the REMARK statement,
where all sorts of information have been added by the hack of
standardized remarks. I thought that one could create
works of art are unleashed on the world.
Seems like a win-win solution to me.
Dale Tronrud
On 4/3/2011 9:17 PM, Jacob Keller wrote:
Well, what about getting the default settings on the major molecular
viewers to hide atoms with either occ=0 or bcutoff (novice mode?)?
While the b cutoff
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