ove all of the
delocalized bonds.
I hope 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 unsubs
r locations 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
clusion
of riding hydrogen atom 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.
oblem.
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
ld that change if this peak is "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
&g
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 en
and, the average B of 157 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
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 ne
of this solution 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 seem
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 sur
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
> op
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?
s is 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
inced of the 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
In addition, Fo-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.
Da
rience with a new technique should never be with your
current project'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
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
en
"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&#x
k to those 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&#x
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"
l database. 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
of that increase 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
map should 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
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 refineme
model is the same.
Dale Tronrud
On 11/21/11 14:47, Michael Thompson wrote:
> - Forwarded Message -
> From: "Michael Thompson"
> To: "e dodson"
> Sent: Monday, November 21, 2011 11:30:17 AM GMT -08:00 US/Canada Pacific
> Subject: Re: [ccp4bb] LESS
is sort 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 i
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 t
tern.
For a noncrystalline object the highest frequency 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
>
;t
as many long 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
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?
>
> Fo
phase
problem. The paper I referred to earlier gives the details.
Dale Tronrud
Regards,
ARKO
On Sat, Jan 14, 2012 at 12:42 AM, Dale Tronrud 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&
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
ile-config... /usr/bin/guile-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.
to not use the decayed data in the merge. I would
expect 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
>
>> -
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 i
something bad 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 2.5
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
amline. The
images would still 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
that map alone, of deciding which
is which. Because of this observation I don't believe it is supportable
to say "I don't see density for these atoms therefore they must be
disordered." Additional evidence is required.
Dale Tronrud
On 04/10/12 08:38, Tim Gruene wrote:
>
ade them no longer be absent in the maps. So it is a
> question 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 effec
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
p with any 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/?
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 a
ordered parts, or, say, the Wilson B.
Dale Tronrud
On 05/11/12 02:32, wrote:
> Hi,
>
> I would like to make the comparative study of different mutant structures.
> There
> is a region which is flexible and missing in some cases. Is there any direct
> method of calculating th
p. Not everything can be
identified
in a 1 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 tu
would be
sigma(2mFo-DFc). This would be estimated from a complex calculation of
sigma(sigmaA), sigma(Fo), sigma(Fc) and sigma(Phic). I expect that the
contribution of sigma(Fo) would be one of the smallest contributors to this
calculation, as long as Fo is "observed". I wouldn't expect the loss 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
>
>
s means 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"
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
reset 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
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
Personally I find it disturbing to have 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 co
ion and if they are close enough to
their symmetry image 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
say
> 10*rounding error of an axis as distinct from being on the axis, then
> a) there's no way that can be proved, and b) it would be
> indistinguishable from being on the s.p. and the difference in terms
> of structure factors and maps would be insignificant anyway, so it may
tom in the vicinity of that point and it might be exactly on
the axis but it might be a little off. All structural models are fuzzy.
Dale Tronrud
that
level 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 hand
and what great
science was done on them!
Dale Tronrud
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
pile even more 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 cr
e user of structural models wouldn't know
to check this tag - they aren't going to know about 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
We *should* go out of our way to make a solution to this common problem.
The solution we choose should be one that actually 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 :-)
g our models we
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 rema
o see
them before our precious 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 b>cutoff ("
be built for every surface lysine the
IMGATM keyword and the program WASNIAHC would allow 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
uations where this is a problem 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
nly change your
Wilson B but it is quite inappropriate.
Dale Tronrud
On 05/20/11 09:43, fulvio.saccoc...@uniroma1.it wrote:
> Thanks Ian,
> but your reply confused me a little.
> I hope you can explain me where I was wrong.
>
> I know that
>
> I(twin)=tf*I(h1)+(1-tf)*I(h
cause 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 solve
alone and reproduced this problem.
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 fo
Since this is a change in cell convention from an acute monoclinic to an
obtuse monoclinic indexing, I suspect that more than a change in the mtz
header is required. The reciprocal lattice needs to be reindexed. Will
pointless perform this task?
Dale Tronrud
On 06/08/11 08:10, Vellieux
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 th
tliers.
The tools proposed 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
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 th
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:
>
> Pro
#x27;t be sure, but I suspect that that model 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".
looks like. 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
on user-friendly software is not good
enough. This is the question facing the crystallographic
community 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 lea
on to reject it.
Dale Tronrud
On 08/11/11 14:42, Jacob Keller wrote:
> Do reviewers ever get taken to task for these things? Don't they share
> at least some of the responsibility? Maybe they should have to give
> their explicit imprimatur, perhaps only after the fact, if published?
n 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,
>
> Althoug
in that definition. The
basic definition would start with the deviation of scattering
points from the Miller planes and those deviations are probably
defined in cycle or radian and later converted to Angstrom so
there are conversion factors present from the beginning.
I'm sure that if the M
the answer will be something like B in A^2 radian^2
and in A^2 cycle^2. It would be much clearer it someone
figured out exactly what 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
method worked in this case. Kudos 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
>
>
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 tr
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 cr
ange 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 th
inement to remove "vacuum bias", just leave it
alone while you fix everything you can figure out.
Dale Tronrud
> Mark
>
> Quoting Katja Schleider :
>
>> Dear all,
>>
>> I found some fairly substantial density in the active site of my
>> protein
e residuals not only 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
to
use additional labels 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...@
t;your own program, but equations have to obey the rules of algebra. I don't
>know what was the context that gave rise to the original question but I think
>it's quite likely to have been the equation f = f0 + f' + if", in which case
>one needs to be careful to avoid ambig
nd I should get 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 -
uot;electron
scattering equivalents"/A^3 (OMG we're 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 v
u find it hard to
understand or it doesn't work. Certainly the Phenix solution looks
simpler.
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 differen
ould be more popular 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
> wrote:
>> The greater the difference in cell constants the greater the "no
f is way out 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
> reve
without
making it less stable when approached "from the right".
Dale Tronrud
On 05/18/10 12:34, Maia Cherney wrote:
> If you change the reaction rate in one direction 1000 times slower than
> in the other direction, then the reaction becomes practically
> irreversible. And the
iginal poster could clarify
the question.
Dale Tronrud
On 05/21/10 13:53, Lijun Liu wrote:
>> If I understand what you are saying, I think it is too.
>>
>> You imply that asymmetry in the enzyme results in two isomerase
>> pathways. This may be true, but it has no consequ
ts 3A data very well.
Dale Tronrud
Paul Lindblom wrote:
Hi everybody,
once more I need your help. I solved the structure of an enzyme at
resolution of 1.9 A. Now I was trying to get a complex and soaked some
ligand to my crystals. I could solve the structure (and see poor density
for my liga
he absence 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
> wrote:
>> One of the great mysteries of refinement is that a model created using
>> high resolution data will f
between the domains.
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 12:1
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 c
codes and residues 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 turne
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