it to be generated
and represented in an unambiguous and minimally confusing fashion. I
wouldn't be happy having to add imaginary atoms to my models, but the
representation meets my criteria, and I think it meets yours too.
Dale Tronrud
JPK
On Mon, Apr 4, 2011 at 1:55 AM, Dale Tronruddet
are:
Calculating structure factors (Fcalc) from a model electron density map.
Calculating gradients using the Agarwal method.
Phase extension via ncs map averaging (including cross-crystal averaging).
Phase extension via solvent flattening (depending on how you do it).
Thank you for your time,
Dale
the overall rms to be low even if the rms calculated over the
protein is the same.
Dale Tronrud
course, crystals with a high solvent content tend to diffract poorly and
if the solvent is not featureless, this will not work either.
If you get high Rfree values for a structure with high solvent content,
I
.
If you have refined a model with space group P1 in Refmac I suggest
you download the new version and see if your stats improve.
Dale Tronrud
On 5/27/2011 3:29 AM, Petr Kolenko wrote:
Dear colleagues,
Q2 is solved by new installation of Refmac. Many thanks for your time
and effort. I
If you have atomic resolution data you could use shelxl to invert
the least-squares matrix and calculate standard uncertainties for all
the bond lengths and angles.
Dale Tronrud
On 06/15/11 07:57, Tian-Min Fu wrote:
Dear friends,
A zinc atom is located in the active center of my
by the Validation Task Force should cause a
model like this to pop out clearly. Even the old tools show this
model is quite unreliable. We just have to use them.
Dale Tronrud
On 08/10/11 14:35, Jacob Keller wrote:
On the surface it doesn't seem as bad as others, i.e., it does not
seem
Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable
but not quite as bad.
Sorry,
Dale Tronrud
On 08/10/11 15:45, Dale Tronrud wrote:
I've made a quick look at the model and the paper - and it doesn't
need more than a quick look. The description of the model
where the average B factor of the
solvent wasn't higher than the protein.
Dale Tronrud
On 08/11/11 07:10, David Schuller wrote:
At the request of reviewers, I worked up the average B factor for some
structures using CCP4 programme BAVERAGE. Here's one example:
Protein33.1
Solvent53.9
would be an
apo form and probably of little interest. This is a good case for an
obsolete without replacement.
I should note that, while the paper has been retracted, I see no
indication that the entry 2QNS has been obsoleted. Perhaps that update
is still in the pipeline.
Dale Tronrud
On 08/11
. Apparently some
people don't
know what features to look for to distinguish between signal and noise.
Dale Tronrud
On 08/11/11 09:40, Diana Tomchick wrote:
A quick glance at the header of the PDB file shows that there is one glaring
discrepancy between it and the table in the paper that hasn't been
that desperately needs an answer.
Dale Tronrud
On 08/11/11 13:33, Maia Cherney wrote:
As the macromolecular crystallography becomes more automated and
user-friendly many biologists learn to solve structures and they can
make mistakes. Besides, new data become available that can give new
ideas
on the vial. In
addition I've had cases where bits were cleaved from the compound
at some point before binding. Sometimes you can't see it because
it simply isn't there.
Dale Tronrud
On 08/24/11 01:02, herman.schreu...@sanofi-aventis.com wrote:
Dear Francis,
Although I am a member of the never
have been very convincing
to have convinced even you.
If the density in that map bleeds a little into the protein density, so
be it. That is not important.
Dale Tronrud
On 08/26/11 07:44, RONG hui Rong wrote:
Dear all,
Do you know how to generate some closed density map (mesh) that can
On 10/11/11 12:58, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even
for 2mFo-DFc maps. In refinement we
is the same.
Dale Tronrud
On 11/21/11 14:47, Michael Thompson wrote:
- Forwarded Message -
From: Michael Thompson mi...@chem.ucla.edu
To: e dodson e.dod...@ysbl.york.ac.uk
Sent: Monday, November 21, 2011 11:30:17 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] LESS MR pleae
of motion.
Dale Tronrud
On 11/21/11 14:52, Filip Van Petegem wrote:
Hello Jacob,
that's correct, I'm only looking at the mathematical significance, not
the biological one. I follow the same reasoning - it is highly
improbably for all atoms to be skewed in the same direction.
In a case I'm
James Holton has software for calculating molecule transform images.
Check out http://bl831.als.lbl.gov/~jamesh/nearBragg/. The program
doesn't read PDB format coordinates, just lists of three numbers.
Dale Tronrud
On 01/06/12 09:44, Jacob Keller wrote:
Actually, as a way to make this type
component corresponds
to the longest Patterson vector or, in other words, the diameter of
the object! The bigger the object, the higher the highest frequency
of the scattergram, and the smaller its features.
Dale Tronrud
JPK
On Fri, Jan 13, 2012 at 11:41 AM, Yuri Pompeu yuri.pom...@ufl.edu
vectors as short ones, but the distribution depends on
the exact shape of your object. Once you have a Patterson map that
has an isolated edge (no cross-vectors) back calculating the original
object is pretty easy. (Miao, et al, Annu. Rev. Phys. Chem. 2008,
59:387-410)
Dale Tronrud
On 01/13/12 10:54
It's not the strength of the electron density it's the shape that is
important.
Dale Tronrud
On 01/13/12 14:21, Dialing Pretty wrote:
Dear All,
For the electronic density of LEU and Pro in the electronic density map,
which is much stronger?
For the electronic density of LEU and Lys
the details.
Dale Tronrud
Regards,
ARKO
On Sat, Jan 14, 2012 at 12:42 AM, Dale Tronrud det...@uoxray.uoregon.edu
mailto:det...@uoxray.uoregon.edu wrote:
I think you have to be a little more clear as to what you mean
by an electron density map. If you mean our usual maps that we
How many names do you propose to use to describe SIRAS?
If someone wrote in their paper the Rossmann method was used to
solve this structure what method would come to mind?
Dale Tronrud
On 1/19/2012 12:51 PM, Petr Leiman wrote:
It would be so much more convenient to call
-config
checking for guile-tools... /usr/bin/guile-tools
and during the compile an option is -lssm, which seems to be linking
to libssm.
Where is the need for libmmdbssm checked for and how to I get one?
Thanks,
Dale Tronrud
Is this observation about redundancies a general rule that I missed?
It seems rather surprising to me. What have results have others seen?
Dale Tronrud
On 01/24/12 07:23, Greg Costakes wrote:
snip...
Higher redundancies (7 or so) do tend to increase overall R/Rfree.
snip
that decayed data would only be merged with the early data if
the redundancy was so low that you had to just to get a full data set.
Dale Tronrud
-- Miguel
---
Greg Costakes
PhD Candidate
Department of Structural
around
1920 that even Germans have great trouble reading today.
The paper is holding up quite well though. ;-)
Dale Tronrud
On 01/26/12 08:30, Phoebe Rice wrote:
As the proud owner of a carefully organized, highly annotated VMS backup tape
(reel-to-reel, of course), my main concern
there is a problem with the regularizer not the structure.
Does you model have any ligands that might have horrible angles but not
be reported by MolProbity?
Dale Tronrud
On 02/16/12 09:00, Greg Costakes wrote:
Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees
(not bond length
It could be that your partial model has a loop, not present
in the true solution, that is causing a clash. You could run
Phaser again with the anti-bumping restraint weakened or disabled,
or more carefully edit your partial model.
Dale Tronrud
On 3/10/2012 11:33 PM, xiaoyazi2008 wrote:
Hi
be more useful than spending time staring at blobs.
Dale Tronrud
Drew Waight wrote:
Hello all,
I'm just finishing up my first structure, a membrane protein with 5
fold NCS. The native dataset is good to about 2.1A. The R factors are good,
around .22/.26 without waters. The only problem
the fit to your data.) Your best hope would be that the new difference
map will show you the water molecules that occupy this site when your compound
does not. Failing that you will have an occupancy for your group but no error
bars for that value.
Dale Tronrud
Ian Tickle wrote:
Hi Pat
I concur
should be fine at this resolution
too.
Dale Tronrud
Jian Wu wrote:
Dear all,
Recently we have collected one set of data which is processed to 2.9A
and 3.0A and the Wilson-B values are 50.1 and 59.1, respectively. As for
the completeness of the highest shell is only 66% in 2.9A (80% in 3.0A
Dear Jin,
As a conceptional issue, I don't see the different between disorder
and alternating configuration. Disorder is present, at a site, when
several alternative conformations have nearly equal energies resulting
in some molecules adopting one conformation while others adopt others.
Each
. With 1.1A data the calculation might be
stable.
Dale Tronrud
Ivan Shabalin wrote:
Dear all,
I have an atomic resolution (1.1#197;) structure of enzyme with the bound
cofactor NAD. During the analysis of the refined structure I found that
important double C=O bond of the cofactor in the active
I think if you are reading a file format which is defined to
be fixed fields, you should read it as fixed fields. For better
or for worst, the PDB format is defined so that each field has
a particular column that it begins on and a column that it ends
on.
I've looked in the PDB format
Yes
Dale Tronrud
Mike England wrote:
Hi all,
I will appreciate your comments on the following case:
I have two datasets from the same or identical crystals. Initially, I
refine a structure against the first data set and later on switch to
another dataset for further refinements.
Do you
to optimal, but cannot be expected to be
optimal. Since we haven't seen an optimal model yet it's hard
to say how far we are off.
If you have the ability to choose a test set that is unbiased
you might as well do so.
Dale Tronrud
Ian Tickle wrote:
-Original Message-
From: owner-ccp
of anisotropy correction in your refinement.
Dale Tronrud
Ben Spiller wrote:
I refrained from entering the fray during last month’s discussion of
anisotropic data in refinement, but I wonder if there is any consensus
regarding treatment.
It seems to me that during refinement scaling to calcs
down
the sequence a search of your organism's genome would be very
informative.
Dale Tronrud
Fabien Bergeret wrote:
Hello
We’re resolving a structure of a soluble protein and in the electronic
density map (maximum resolution at 2.2Å), we observe a supplementary
density that does not belong
the beginning.
I'm sure that if the MS sits down with the OPDXr and follows
all these units through he will uncover the units of B, 8 Pi^2,
and u_x^2 and the mystery will be solved. If he doesn't do
it, I'll have to sit down with the book myself, and that will
make my head hurt.
Dale Tronrud
James
those units are and we started properly
stating the units of each. I'm sorry that I don't have the time
myself for this project.
Dale Tronrud
P.S. As for your distinction between the convenience units used to
measure angles and the absolutely required units of length and mass:
all units are part
to the University
of Alabama at Birmingham for facing this problem and following
through with their investigation of earlier allegations.
Dale Tronrud
=
Dr Paula Salgado
Division of Molecular Biosciences
Department of Life Sciences
using rms's.
Dale Tronrud
Charlie Bond wrote:
Hi Gerard,
Interesting - isn't it the case that for Arg, the the NH1 and NH2 atoms
are chemically distinguishable and the convention is unambiguous (NH1
cis to CD and NH2 trans, if I recall correctly).
The truly symmetric sidechains of Asp, Glu
was reported.
With today's data collection techniques I can't for the life
of me figure out a reason for having both Rsym and Rmerge.
Dale Tronrud
Bart Hazes wrote:
For what it's worth, I've been told that Rmerge was used originally, in
the pre-cryo few images per crystal age, to indicate the R
these keywords and see if that
helps.
On the other hand, I can't imagine what Coot could do to
improve on the fantastic Val-Lys model in 8TLN. Surly that
model is without flaw! ;-)
Dale Tronrud
Tim Gruene wrote:
Dear all,
we would like to ask coot to fit the Val-Lys dipeptide of a thermolysin
while you fix everything you can figure out.
Dale Tronrud
Mark
Quoting Katja Schleider katjaschlei...@yahoo.de:
Dear all,
I found some fairly substantial density in the active site of my
protein structure. But I don´t know what it should be. My
crystallisation condition consists
possible but inevitable?
Dale Tronrud
Eleanor Dodson wrote:
Two possible points. Could there be a problem with twinning, or
spacegroup? The Rfactors seem rather high..
You dont say whether you have a non-crystallographic translation, but it
is faintly possible with 2 molecules that the SG
when certain quantities arise in my work. It
isn't a matter of you being right and me being wrong or the other
way around. The only logically consistent solution is to have
no units at all, and that would be terribly confusing to everyone.
Dale Tronrud
marc.schi...@epfl.ch wrote:
I fully agree
to avoid ambiguous definitions.
Which is exactly what I've been advocating. I'm glad we have reached
agreement.
Dale Tronrud
P.S. to respond out-of-band to Dr. Schiltz: On the US flag I see 7 red
stripes,
6 white stripes, and 50 stars. If I state I see 7 I have conveyed no
useful
together
in a bar somewhere and hash this out.
Dale Tronrud
Gerard Bricogne wrote:
Dear all,
Two slight confusions seem to have popped up intermittently in this
thread, in messages other than those included here. The first one was
related to the charge of the electron - even the colour
not back to that again ;-) )
and avoid this whole sliding scale problem.
Dale Tronrud
On 04/21/10 17:21, James Holton wrote:
Like so many rules of thumb, the 3-sigma fofc and 1-sigma 2fofc is a
reasonable guideline that works very well in most cases despite being
based on a flawed assumption
.
Dale Tronrud
On 05/03/10 15:27, Yi-Liang Liu wrote:
Hi Everyone,
I've checked the previous posts about how to generate the difference map
from two crystals with different cell constants. I tried MAPMAN to
generate this map but I never got luck on this. It turned out to show
Maps have different
if they weren't so cumbersome
to calculate in the CCP4 world.
Dale Tronrud
On 05/04/10 04:48, Ian Tickle wrote:
Dale,
On Tue, May 4, 2010 at 12:19 AM, Dale Tronrud det...@uoxray.uoregon.edu
wrote:
The greater the difference in cell constants the greater the noise
in the map. I think
and display,
separately, contours for the real and imaginary components of the
density. Then, even if you didn't notice the presence of anomalous
scattering in your diffraction, you would still see the anomalous
peaks on your display.
Dale Tronrud
On 8/29/2014 11:43 AM, Alexander Aleshin wrote:
Could
(of course) and the maps look
fine. I'm guessing that PDB_REDO junks these reflections before its
Refmac refinement and avoids the issue.
Dale Tronrud
On 9/1/2014 2:00 AM, Magali Mathieu wrote:
Please consider the environment before printing this email!
-Message d'origine- De
on its own,
but you have to keep in mind the library's limitations.
Dale Tronrud
On 9/15/2014 8:42 AM, C wrote:
Isn't Molprobity too tight anyway for _high resolution_ structures?
I have often (for proteins) found it highlighting outliers when
in fact that is what the density shows
before I suggest you check out other models in the PDB with good, strong
density and see what a full power ligand looks like in a map. Only
settle for weak density if there is no alternative and never settle for
ambiguous density.
Dale Tronrud
On 19 September 2014 22:06, ansuman biswas bubai_
would have three space-like
and three time-like dimensions. I have enough problems with the
on-rush of one dimension of time.
Dale Tronrud.
On 9/22/2014 10:40 AM, Chen Zhao wrote:
Hi Dale,
Thank you for your reply! Yes, the real term of all eigenvalues are
very close to 1, and as I said
to describe TLS in the PDB format. Don't tell me it's stuffed in
REMARK! What kind of a file format is that?
I believe that 100% of the models that we should be building can't
be described in the PDB file format, and that has been true for a
great many years.
Dale Tronrud
I greatly appreciate Nat's
reflections in the test set which, while giving you a more reliable
free R, cause a larger degradation in the model itself.
Dale Tronrud
On 11/20/2014 2:43 PM, Keller, Jacob wrote:
Dear Crystallographers,
I thought that for reliable values for Rfree, one needs only to
satisfy counting statistics
resolution data are scrambled?
Dale Tronrud
Xavier
On 20/11/14 11:43 PM, Keller, Jacob wrote:
Dear Crystallographers,
I thought that for reliable values for Rfree, one needs only to
satisfy counting statistics, and therefore using at most a couple
thousand reflections should always
and refine the occupancy.
Dale Tronrud
On 2/12/2015 9:07 AM, Kimberly Stanek wrote:
Hello all,
I am in some of the final stages of refinement of a 1.5 A
resolution oligomeric protein and I'm noticing what appears to be
extra density corresponding to a carbonyl peptide flip near the
N-terminus
row having more than three decimal places.
Dale Tronrud
On 4/1/2015 2:52 PM, Shane Caldwell wrote:
Hi ccp4bb,
I'm trying to solve a problem I never quite figured out in the past. I'd
like to use the *sortwater* utility to send my picked waters to various
protein chains, and to give them
one out in the not too distant future.
All the best,
Randy
On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com
wrote:
We are having a problem with AMPLE and hope someone can help.
The protein is about 70 amino acids long and we suspect it forms a
coiled-coil. Our
-frags_9mers
/user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
- -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_shelxe
True -shelx_cycles 15 -use_arpwarp False
Any help is appreciated,
Dale Tronrud
Sarah Clark
-BEGIN PGP SIGNATURE-
Version: GnuPG v2.0.22
and judge for themselves.
Dale Tronrud
On 4/27/2015 7:04 AM, Oganesyan, Vaheh wrote:
Hi Robbie and Co,
These things are happening now too. Look at the entry 4x4m. The
paper got published in January, PDB released coordinates in April.
That means reviewers did not have a chance to look even
In addition to the other excellent suggestions you have received, you
can download the map for a re-refined version of a PDB entry at
PDB-Redo. The latest Coot has a button for that.
It appears that the EDS is down. I'll notify the authorities.
Dale Tronrud
On 6/9/2015 1:11 PM, Xiao Lei
.
Dale Tronrud
On 6/22/2015 7:48 AM, ansuman biswas wrote:
Dear CCP4 users,
I am working on a protein from a hyperthermophilic archaeon.
I have collected mutliple X-Ray datasets, both from home source and
synchrotron and always found a clear density for tetrahedral geometry,
co-ordinated
description in a REMARK 800
statement. This option would allow you to acknowledge that something
is binding at this location but leave the difference peak for others
to view and puzzle over on their own.
Dale Tronrud
Cheers, Robbie
-Original Message- From: CCP4 bulletin board
of the image will not depend on the region of
space covered by your map nor the percentage of solvent in the crystal.
Dale Tronrud
On 6/1/2015 9:16 AM, Thomas Holder wrote:
Hi Emilia et al.,
I tried to figure out the PyMOL vs. Coot normalization discrepancy
a while ago. As far as I remember, PyMOL
normalize you should use Coot's e/A^3 level. It is
quite possible that they could differ by a factor of two.
Dale Tronrud
On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote:
Hello. I am struggling with an old question--old because I've found
several discussions and wiki bits on this topic, e.g
Dear Kay,
You are right. I had forgotten the normalization part of the CC
calculation.
Dale
On 7/3/2015 12:01 AM, Kay Diederichs wrote:
Hi Dale,
On Thu, 2 Jul 2015 10:45:45 -0700, Dale Tronrud de...@daletronrud.com wrote:
While I was puzzling over an entry in the PDB some years ago
refinement can't be fooled in this way.
Dale Tronrud
On 7/2/2015 10:25 AM, Edward A. Berry wrote:
My take on this-
No one has been willing to specify a cutoff (and probably there is no
rigorous way to
mathematically define the cutoff) and say If CC* (or CCfree or
whatever) is below X
the server.)
Dale Tronrud
On 7/1/2015 3:40 PM, Chen Zhao wrote:
Hi all,
Sorry to bother you, but I am trying to fix a long-standing problem
that I cannot run Coot and Pymol through Xming/PUTTY by SSH
connection on a windows client. The error messages are pretty
similar for both: Coot: PuTTY X11
resolution data I would expect the geometry
stats to get worst.
Dale Tronrud
On 7/7/2015 11:17 AM, Shane Caldwell wrote:
Chiming in late with a follow-up question:
On the other hand in paired refinement, if adding the data improves the
structure
as measured by Rfree in a zone excluding the added
It is confusing, but "high" is meant to indicate the quality of the
final electron density map based on the data. Your 1.8 A data set will
give the better map, and is the high resolution data set.
Dale Tronrud
On 2/5/2017 4:09 AM, wrote:
> Dear All,
>
> For one p
is if there is a mistake either in the calculation of the R value
or the map.
I think you need to double-check your work.
Dale Tronrud
P.S. Are you contouring your difference map at a reasonable level?
Think e/A^3 not "sigma"s. When I look at a difference map I start at a
level of
. Why would you expect otherwise?
Dale Tronrud
On 10/14/2016 12:28 AM, Carlos CONTRERAS MARTEL wrote:
> Sunanda,
>
> As "common people", ... "agreement" don't means for me "equals" ...
>
> So I hope I'm not so "incorrect" if I keep on
analysis.
Of course, if you trick a validation statistic like this you haven't
accomplished anything. All you are saying is that one should rank RSRZ
scores with and without hydrogen atoms separately. Perhaps you should
suggest that to the PDB validation people.
Dale Tronrud
>
>
ctly
> you mean by "is there any way to better the B factors".
> Pavel
>
>
> On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud
> <de...@daletronrud.com <mailto:de...@daletronrud.com>> wrote:
>
>I'm sorry but I don't unde
I'm sorry but I don't understand what your problem is. Do you think
the B factors are too small for a 3A data set? A range of 70 to 75 is a
little smaller than usual but probably not out of bounds.
Dale Tronrud
On 10/12/2016 7:59 PM, sunanda williams wrote:
> Hi all,
> I have a str
Your first step is to look at your images and see what is going on in
that shell. Since you are looking at merged stats the first guess is
that there is something wrong with all of the images, but only by
looking at them can you tell.
Dale Tronrud
On 8/15/2017 9:39 AM, rohit kumar wrote
a requirement of the
wwPDB rules but it makes the situation much clearer the someone wanting
to understand this protein. Having a second model in the PDB w/o a
publication would not leave many clues to decide which model to use.
Dale Tronrud
On 6/27/2017 12:15 AM, Trevor Sewell wrote
ded clashes when everything is in one plane. Some restraint
libraries inappropriately restrain this group to be co-planar with the
six-membered ring. As always, check you CIF!
Dale Tronrud
On 5/17/2017 12:46 PM, Jorge Iulek wrote:
> Dear all,
>
> I came across some difficulty to
I'm sorry but I'm a little confused by your question. If your map
already has four-fold symmetry why can't you simply build your model
once in one quarter of the map? What do you hope to change by
specifying that the space group is P4?
Dale Tronrud
On 5/18/2017 10:06 PM, Qingfeng Chen wrote
ot used to seeing. Selecting a contour level
based on the e/A^3 is much less sensitive to the amount of solvent in
the crystal is gives much more consistent results.
Dale Tronrud
>
> Could these observations be linked to the high solvent content? (1) A
> high solvent content structure
. I know that James is not recommending this, but
that is what some people in that bad period in the 1990's were doing.
Most of us were not!
Dale Tronrud
On 10/16/2017 8:02 AM, James Holton wrote:
>
> If you suspect that weak data (such as all the spot-free hkls beyond
> your an
of the model of a
bound ligand.
In my opinion the most likely explanation is that multiple
conformations of the peptide are binding. Without seeing the density or
being able to examine the data it is hard to generate possibilities.
Dale Tronrud
On 10/1/2017 2:20 AM, Meytal Galilee wrote:
> Hi
uncertainty.
Dale Tronrud
On 12/1/2017 10:02 AM, chemocev marker wrote:
> Hi
>
> I am calculating the Electrostatic Potential of my protein. But there
> were few flexible region with high B-factor and I deleted that part of
> the protein and then recalculated it. But there
ope tends to be of very high quality and you
don't have precise models of the object to calculate phases so there is
no advantage of going to "diffraction mode"..
Dale Tronrud
>
> JPK
>
> -Original Message-
> From: herman.schreu...@sanofi.com [mailto:herman.sch
ctron density we are used to look at. Alternatively, you could
>> display an bona fide electron density map as voxel blocks and I am
>> sure it will look similar to the voxel map you showed in your first
>> email.
>>
>> Best,
>> Herman
>>
>> -Ursp
come up with programs that would perform Fourier summations of
square waves to calculate electron density. Our instrument is an analog
computer for calculating the Sin wave Fourier transform of the electron
density of our crystal because we designed it to do exactly that.
Dale Tronrud
>
>
>
On 11/12/2017 6:48 AM, Kay Diederichs wrote:
> On Fri, 10 Nov 2017 14:04:26 -0800, Dale Tronrud <de...@daletronrud.com>
> wrote:
> ...
>>
>> My belief is that the fact that our spot intensities represent the
>> amplitude (squared) of a series of Sin waves
I agree with Phil. A P2 crystal with nearly perfect
noncrystallographic translational symmetry (~1/2,~1/2,0) will look like
a C2 cell with twice the length along a and b and weak spots between the
indexed spots. Look for those spots on your "C2" images.
Dale Tronrud
On 11/9/20
p
will have many more voxels but no more information because the density
values are correlated.
Dale Tronrud
On 11/9/2017 4:10 PM, Keller, Jacob wrote:
> Dear Crystallographers,
>
>
>
> I have been considering a thought-experiment of sorts for a while, and
> wonder what y
d see what their properties are. I'm not aware
that anyone has done this, but my literature search has been very limited.
Dale Tronrud
On 12/2/2017 5:51 AM, Sam Tang wrote:
> To add to the discussion, could I raise a relevant question about
> generating ESP (Apologies to Jiri if this distrac
ne quantum of
negative charge for each electron, then calculate the charge density due
to the proton density, using knowledge of the charge of a proton, and
then sum the two charge densities, which are not only commensurate but
identical. My code would then be ready should I run into a Xi baryon
wi
omplains about your model. Your model is
fine and the validation software needs better validation itself.
Dale Tronrud
On 2/9/2018 10:18 AM, Oganesyan, Vaheh wrote:
> Dear crystallographers,
>
>
>
> Lately when refining a structure (at 2.8A) with Refmac5 I’ve found that
> n
be
willing to accept that you may never figure it out. Don't build a model
you don't believe.
I once spent about twenty years trying to figure out a blob (not full
time!). I got a nice paper about it in the end.
Dale Tronrud
On 8/5/2018 7:00 AM, Preeti Preeti wrote:
> Dear CCP4 member
>
, of
your model should be considered less reliable. Tricking people into
placing too much trust in your model is not a good idea.
Dale Tronrud.
On 7/5/2018 1:11 AM, zheng zhou wrote:
> Hi all
>
> Just finishing up a new structure at 2.4A. Buster refine gives RMS bond
> 0.008 and angle
I will leave some known atoms out of the model and
see how the heights of their difference peaks compare to the heights of
the mysterious peaks. This method is fairly insensitive to the
systematic problems that affect both rms and electrons/A^2.
Dale Tronrud
On 4/19/2018 8:30 AM, Ian Tickle wrote:
>
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