eating a bad
contact or maybe something else. Maybe it is reality peeking through.
Simply increasing the weight only hides the issue and may actually
create its own error in your model. (The hardest errors to identify are
those that are inappropriately consistent with the validation criteria!)
Dale
nd in a specific way
after the crystals are placed on the grid. I'm not qualified to say if
this is actually novel and unobvious, but the application seems to me to
be very narrow and specific and NOT a blanket claim of performing
structural biology using electron scattering.
Dale Tronrud
O
Hi,
Just ask ChatGPT to write it for you!
Dale Tronrud
On 4/1/2023 5:06 AM, Subramanian, Ramaswamy wrote:
Dear All,
I am unsure if all other groups will get it - but I am sure this group
will understand the frustration.
My NIH grant did not get funded. A few genuine comments
I'm going to dive back in here again to expand this discussion.
Whether this diversion clarifies or obscures issues surrounding the
"crystallographers' dilemma" I'll leave for others to decide.
There is currently considerable discussion, among people who care
about cell phone cameras,
Hi
As a frequent contributor to prior discussions on this same topic I
would like to broaden the discussion a bit. I'm sorry to say that most
of the comments on this threat are exactly the same positions that have
been expressed many times over the years. I don't want to spent time,
And now it is time for an "old man story". Back in the early 1990's
the Brookhaven PDB started to worry about "validating" the models being
deposited. One of the things they implemented was to add to the header
of the PDB a complete list of all bond lengths and angles that deviated
from
The second part of your question has to do with assessing the
probability of correctness of a model by comparing the distribution of
the individual values of geometry items with the distribution observed
in large sets of high quality crystal structures. Certainly, if your
model has many
Let's say you have decided that you want to know if the CA-CB bond
of residue 123 in your favorite protein differs from the expected value
for that type of bond. You solve the structure and refine a model
against your crystallographic data, then look at residue's 123 CA-CB
bond and find
is smaller than the working R,
particularly when the overall R values are similar as in your refinement.
Dale Tronrud
On 9/19/2022 11:30 AM, Prasun Kumar wrote:
Hi All:
I have collected a dataset for a crystal of a 30 residues long helical
peptide that makes a trimer in the solution. I also solv
your refinement with a moderate starting value for
the B you will end up a more sensible result.
The only other way to end up with a parameter that directly
conflicts with the difference density is a bad restraint, but that
doesn't sound likely based on your description.
Dale Tronrud
On 8
es, but am never happy with that solution.
Perhaps someone should do a survey of ASN residues in the PDB and
see what the very high resolution/high quality models say?
Dale Tronrud
On 7/22/2022 4:37 AM, Eleanor Dodson wrote:
It is hard to see from a still but there couldn't be anoth
I don't see any reason to believe that software designed to validate
crystallographic or NMR models would have any utility validating
AlphaFold predicted models. Doesn't the prediction software already
ensure that all the indicators used by Molprobity are obeyed? I'm
afraid that the tools
ot; and I can
trust that the variability in the ensemble reflects the structural
variability.
Dale Tronrud
On 5/26/2021 2:38 PM, Mark J. van Raaij wrote:
Dear Dale,
Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the
lucky situation though that they should have
ple, the N-terminal region of a protein may have a
broad distribution in the ensemble model either because this region
experiences many conformations in solution, or because this peptide was
cleaved from the protein at some earlier time and its absence was not
recognized by the experimentalist.
Da
re many reasons
why these data are be absent and high mobility is only one.
Dale Tronrud
On 5/26/2021 8:45 AM, Cécile Breyton wrote:
Hello,
In my understanding of NMR, the loops and terminii that adopt very
different conformations in the structure ensemble rather reflect the
fact tha
Something to give context and scale would be helpful. Two views
would also be good.
Dale Tronrud
On 5/26/2021 6:08 AM, leo john wrote:
Hi Group
Can you please suggest what this unmodeled blob can be (see appended
picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals
, for the systems I use the big,
crystallographic, packages on I tend to follow the pack and use a Linux
that is widely used. I'll stick with 7 until the rest of you settle on
something. I'm in no hurry.
Dale Tronrud
On 2/19/2021 12:35 PM, Matthias Zeug wrote:
Hi all,
I just came across
used in the US for many years because the only cases of
polio in the country were due to the vaccine.
100: Your extremely contagious virus could never be recalled, and once
it mutates, could only be overcome by an even more contagious vaccine
virus. Goto 100
Dale Tronrud
On 2/17/2021 9:33 AM
the result of a special view of the same cubes you
are seeing elsewhere.
Dale Tronrud
https://filesender.renater.fr/?s=download=71d70da4-5ea2-4cf3-ae5f-5d89545574ce
May be all this is just an optical Fata Morgana.
We are waiting for our next synchrotron beam time to see whether, and
what
Remember, the program may be writing files to some partition other
than the one your current working directly is located. Maybe /tmp, for
example.
Dale Tronrud
On 2/2/2021 12:36 PM, Amit Singh wrote:
Dear Abhilasha, It seems that the partition where you are running your
simulation has
se in
ease of interpretation to be less than if you defined ahead of time the
map you planed to look at.
Yes, when your defined protocol fails, look around for alternatives.
Just ensure that your personal skepticism setting is cranked up when
doing so.
Dale Tronrud
My 2 cents,
Herman
. I don't recall anyone in this
long thread refuting this statement.
Dale Tronrud
On 12/5/2020 4:02 AM, Marcin Wojdyr wrote:
On Fri, 4 Dec 2020 at 22:36, Dale Tronrud wrote:
It is very important not to read more meaning into a data tag than
is actually defined in the mmCIF spec
On 12/4/2020 12:15 PM, Marcin Wojdyr wrote:
> On Fri, 4 Dec 2020 at 19:16, Dale Tronrud wrote:
>> learn the sequence you have to go to the mmCIF records that define the
>> connectivity between residues. It is entirely possible that "3" comes
>> before "1"
rules, and not
make unwarranted assumptions about the meaning of data items.
Dale Tronrud
On 12/4/2020 10:37 AM, Tristan Croll wrote:
OK, I understand your point more clearly now - but I'm not sure I fully
agree, for the simple reason that people aren't computers. You're right
n
"1" and "3" in the sequence. This is not necessarily true at all. To
learn the sequence you have to go to the mmCIF records that define the
connectivity between residues. It is entirely possible that "3" comes
before "1" because these indexes don't conta
and the, now separated, glycan chain?
If not, I think this is the principle failing of their new scheme.
Dale Tronrud
On 12/4/2020 12:06 AM, Tristan Croll wrote:
To go one step further: in large, heavily glycosylated multi-chain complexes
the assignment of a random new chain ID to each glycan
oject's data. You should work to add that technique to your
tool box, and then move back to your data. Practice, and more practice
will build that squishy neural network in your head.
Descending from soapbox,
Dale Tronrud
On 12/1/2020 8:31 AM, Robert Nicholls wrote:
Dear all,
I feel the ne
-Fo maps between the
crystals of varying occupancy, even very small changes in occupancy, are
surprisingly informative. They tend to be highly isomorphorus and
provide direct information for deconvoluting multiple conformations
which is vital in partial occupancy binding.
Dale Tronrud
P.S
he value of a FEM, or a Buster map, or a SA omit map, or
whatever, calculate that map instead and live with it.
If you have to calculate twenty different kinds of maps, with
varying parameters in each, before you find the one that shows the
density for your ligand; it probably didn't bind.
for your
second refinement to be working with a newly created test set. It is
possible that somehow you have reset your R free flags? In an MTZ the
full data set is divided into twenty subsets -- one is the test set
while the other nineteen are the working set. When you ran Refmac the
secon
Hi,
I'm seeking insight into some geometry outliers in my Refmac refined
model. It would be nice to have confidence in the target values used by
Refmac. Does Refmac use the library distributed by CCP4 in
lib/data/monomers, or do it have its own library squirreled away somewhere?
Dale
If there is a covalent link, maybe sending a sample off to mass spec
would be a good idea. That would remove some of the guesswork.
Dale Tronrud
On 7/20/2020 9:16 AM, samer halabi wrote:
> Hello all,
> I have few blobs in an MHC II structure I am working on, especially
>
been
"free", however. To get it one had to agree to the license from the
University of Oregon and, if a for-profit organization, pay money.
Dale Tronrud
On 5/7/2020 10:18 AM, Roversi, Pietro (Dr.) wrote:
> Thank you Ethan for taking the the time to answer and explain.
> Yes I am
olution we can only repeat the, conflicting,
arguments in favor or against the various less than optimal solutions.
You can go back to the archives to find those.
Dale Tronrud
On 4/28/2020 8:37 AM, Thomas, Leonard M. wrote:
> Hello all,
>
> This is one of those issues that seems to come
In addition, REFMAC has tightened your model's geometry which can
cause a slight increase in the working R. A one percent increase in
while in the upper thirties is slight.
Dale Tronrud
On 4/8/2020 7:30 AM, Schreuder, Herman /DE wrote:
> I guess the molecular replacement model has never b
A^2 seems quite reasonable
for a 3 A model (using modern resolution cutoff criteria). It is higher
than your Wilson B, but that is expected. In addition, as you note, the
uncertainty of a Wilson B is quite large in the absence of high
resolution data.
Yes, this is the short version. ;-)
Dale
Just a note: James Holton said "true B-factor" not "true B-factors".
I believe he was talking about the overall B not the individual B's.
Dale Tronrud
On 3/8/2020 3:25 PM, Rangana Warshamanage wrote:
> Sorry for not being clear enough.
> If B-factors at the end of
"noise" or not? All we have now is a
peak that we don't have a good way to interpret.
Dale Tronrud
>
> Jessica
>
> On Wed, 4 Mar 2020 at 12:45, Barone, Matthias <mailto:bar...@fmp-berlin.de>> wrote:
>
> hey Jessica
>
> a tip that might
.
Besides, as Glusker and Tureblood noted, a peak in a difference map
(the green blob in this discussion) cannot be caused by series
termination. If there is series termination the shape of a difference
map peak can be affected, but not the presence of the peak itself.
Dale Tronrud
On 3/5/2020 12:20
m positions vrs the confusion that results from
their absence. I think we agree strongly that all of the list items
above need to be tackled by the wwPDB and are of extreme importance. I
think we need a comprehensive solution, not a piecemeal, special case,
for each.
Dale Tronrud
> Moreover,
ations can
be inferred from the deposited atoms?
Dale Tronrud
P.S. I realize that I am open to charges of inconsistency since I have
advocated not depositing an atomic model for atoms that weren't placed
by the depositor (i.e. disordered side chains). I don't believe I'm
committing this sin.
this note makes it to acedrg's developers and they find it
useful. It may also be helpful to others attempting this task (at least
until the bugs are fixed).
Dale Tronrud
To unsubscribe from the CCP4BB list, click the following li
a valuable
contribution to humanity. ;-)
Dale Tronrud
On 9/19/2019 4:03 PM, Murpholino Peligro wrote:
> A quick glance at the entries of hen egg white lysozyme in the PDB show
> that it can be crystallized at different pH values, but the space group
> is not always the same. I still have to
he present? Nothing but speculation that the climate "might" be
driven by this or "might" be driven by that. Dr Akasofu brings nothing
to the table.
Dale Tronrud
On 8/20/2019 6:23 PM, Daniel M. Himmel, Ph. D. wrote:
> Dear colleagues,
>
>
>
> Since when does
ght of
the two peaks will give insight to the occupancy ratio.
Remember, if the PO4 has two orientations in the crystal, the water
molecules it (they?) is/are bound to will likely also have alternatives.
Dale Tronrud
On 8/5/2019 6:05 AM, Maria Håkansson wrote:
> Dear CCP4 bulletin board,
>
can actually see the population of atoms
contributing to each increasing resolution has a lower and lower average B.
Dale Tronrud
On 3/12/2019 2:24 PM, Edward A. Berry wrote:
> What if you have one domain with many B-factors aroun 70 and above, and
> another domain with B-factors aro
, it is simply a reflection of the Wilson B's insensitivity to
atoms with large B.
I do not believe comparing the average B to the Wilson B has any
utility at all.
Dale Tronrud
On 3/12/2019 11:34 AM, Eze Chivi wrote:
> Dear CCP4bb community,
>
>
> The average B-factor (calculated from
You are correct, other than your typo. The centric zone in a
monoclinic space group (B setting) is h0l.
This web site is a wiki so you should be able to correct it yourself.
Dale Tronrud
On 3/2/2019 2:00 PM, Edward A. Berry wrote:
> The wiki:
>
> https://strucbio.bio
alism so I can't be
confident of the m's and D's. I also assumed that Fridel's Law holds,
but that assumption was made with the traditional maps as well.
Dale Tronrud
On 12/6/2018 11:01 AM, James Holton wrote:
> Sorry for the confusion, I was going for brevity.
>
> Any time you do a tho
is model, like maybe not
being able to detect the image of the allegedly bound ligand, a great
number of details of the protein, data collection and the current model
would have to be shared. When asking such a question on this BB you
should never be concerned that your letter is too long.
Dale Tr
this structure was solved via molecular
replacement. No indication of high R factor or stuck refinement. No
details at all. Just a model with a fairly reasonable, if somewhat low,
average B factor.
Dale Tronrud
On 11/10/2018 6:31 PM, Daniel M. Himmel, Ph. D. wrote:
> Anandhi,
>
> Assuming
alculating this average? In any case, you certainly shouldn't be
worrying about your "high" B factors.
Dale Tronrud
On 11/8/2018 4:30 PM, Anandhi Anandan wrote:
> Hello everyone,
>
>
> I am trying to solve the structure of a protein with a bound ligand at
> 2.65 A resoluti
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
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
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:
>
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
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
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
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
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
>
>
>
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
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
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
. 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
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
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'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
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
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
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
>
>
. 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
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
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
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
.
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
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
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
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
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
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
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
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
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
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
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
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
(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
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
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