Pramod:
[1] Please refrain from posting excessively large (>1MB) attachments to the
ccp4bb. Either use a compression technique or use another means of transmitting
large files to your recipients without spamming the entire group.
[2] Your predictions are not overlaying well with the spots . W
Dear CCP4ers/REFMACers,
the C-terminal peptide bond of a modified lysyl, M3L, appears less planar
than other peptide bonds in the same structure. What is the currently
preferred method of restraining such planarity? I have currently not added
any link record in the header of my coordinates file. Wo
I hope I am not duplicating too much of this fascinating discussion with these
comments: perhaps the main reason there is confusion about what to do is that
neither F nor I is really the most suitable thing to use in refinement. As
pointed out several times in different ways, we don't measure
However you decide to argue the point, you must consider _all_ the observations
of a reflection (replicates and symmetry related) together when you infer Itrue
or F etc, otherwise you will bias the result even more. Thus you cannot
(easily) do it during integration
Phil
Sent from my iPad
On 2
On Jun 21, 2013, at 2:52 PM, James Holton wrote:
> Yes, but the DIFFERENCE between two Poisson-distributed values can be
> negative. This is, unfortunately, what you get when you subtract the
> background out from under a spot. Perhaps this is the source of confusion
> here?
Maybe, but if y
On Jun 21, 2013, at 2:48 PM, Ed Pozharski wrote:
> Douglas,
>>> Observed intensities are the best estimates that we can come up with in an
>>> experiment.
>> I also agree with this, and this is the clincher. You are arguing that
>> Ispot-Iback=Iobs is the best estimate we can come up with. I
Douglas,
Observed intensities are the best estimates that we can come up with in an
experiment.
I also agree with this, and this is the clincher. You are arguing that Ispot-Iback=Iobs is
the best estimate we can come up with. I claim that is absurd. How are you quantifying
"best"? Usually
On Jun 20, 2013, at 2:13 PM, Ian Tickle wrote:
> Douglas, I think you are missing the point that estimation of the parameters
> of the proper Bayesian statistical model (i.e. the Wilson prior) in order to
> perform the integration in the manner you are suggesting requires knowledge
> of the al
I kinda think we're saying the same thing, sort of.
You don't like the Gaussian assumption, and neither do I. If you make the
reasonable Poisson assumptions, then you don't get the Ispot-Iback=Iobs for the
best estimate of Itrue. Except as an approximation for large values, but we
are talking
On 06/21/2013 10:19 AM, Ian Tickle wrote:
If you observe the symptoms of translational NCS in the diffraction
pattern (i.e. systematically weak zones of reflections) you must take
it into account when calculating the averages, i.e. if you do it
properly parity groups should be normalised separa
On 21 June 2013 17:10, Douglas Theobald wrote:
> Yes there is. The only way you can get a negative estimate is to make
> unphysical assumptions. Namely, the estimate Ispot-Iback=Iobs assumes that
> both the true value of I and the background noise come from a Gaussian
> distribution that is all
On Jun 21, 2013, at 8:36 AM, Ed Pozharski wrote:
> On 06/20/2013 01:07 PM, Douglas Theobald wrote:
>> How can there be nothing "wrong" with something that is unphysical?
>> Intensities cannot be negative.
>
> I think you are confusing two things - the true intensities and observed
> intensiti
Dear Tim,
I normally do not use Refmac, so I have no idea what to expect and what would
be a good weight. I will do the molprobity test, but I do not expect major
problems. This is a MR structure with a high resolution search model with 100%
sequence identity. A few amino acids may have problem
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Dear Herman,
a large gap between R and Rfree might indicate a horrible geometry of
your structure, especially if R increased by lowering the matrix
weight in refmac. Or, to put it the other way round: it is easy to
achieve a low R-value by screwing up
Hi Robbie,
That is what I tried. The Rfactor got a lot worse (14%->18%) and the Rfree got
a little worse (by 0.1-0.2%). My feeling is that that is not the right
approach. Roger Rowlett suggested to give PDB_REDO a try. Maybe you have some
instructions available how to get a local version?
Best
Hi Michael,
Thank you very much for your suggestions. I will rerun with both buffer
conditions and report back later.
Thanks to everyone for your reply.
Zhen
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of R. M.
Garavito
Sent: Friday, June 21, 2013 9:28 AM
To: CCP4BB@JIS
Hi Herman,
Tighter restraints typically close the gap between R and R-free. This does
not mean one should just tighten the restraints to satisfy one's own (or a
referee's) idea of what the gap should be. I don't think there is a clear
target of how large or small the gap should be. If you optimiz
On 21 June 2013 13:36, Ed Pozharski wrote:
> Replacing Iobs with E(J) is not only unnecessary, it's ill-advised as it
> will distort intensity statistics. For example, let's say you have
> translational NCS aligned with crystallographic axes, and hence some set of
> reflections is systematically
Dear Zhen,
I should also point out that the statement Matt made ("Superdex is known to
have some ion-exchange characteristics, so that it can weakly interact with
some proteins.") is not completely correct. Superdex and all chromatographic
media made from carbohydrates (dextran, agarose, etc.)
At your resolution that seems to me a reasonable gap between R and Rfree?
Eleanor
On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote:
> Dear Bulletin Board,
>
> After some headbanging (Refmac5 had helpfully created gap records for all
> insertions and deletions present in the structur
On 06/20/2013 06:20 AM, Eleanor Dodson wrote:
But you say you took the Balbes model into phaser? and I think Balbes
automatically runs cycles of refinement so any comment on R factors
may not mean much.
I have seen a model coming out of Balbes pipeline hitting extremely high
marks when fed in
I have found PDB_REDO is an efficient way of tweaking structure solutions.
Among other things, it sorts through various MATRIX and BFAC weights and
tests effectiveness of TLS if not used already. It usually improves typical
"final" structure solutions for our group by about 1% or so Rfree and
reduc
On 06/20/2013 01:07 PM, Douglas Theobald wrote:
How can there be nothing "wrong" with something that is unphysical?
Intensities cannot be negative.
I think you are confusing two things - the true intensities and observed
intensities.
True intensities represent the number of photons that di
On 06/20/2013 06:56 PM, Monika Pathak wrote:
Hi
Please can I ask about how can I put NAG to asparagine in coot (I
think its 2NAG that I can put in density) and if possible to refine
it in refmac then.
Calculate -> Scripting -> Scheme:
(add-linked-residue imol chain-id res-no ins-code "N
Dear Bulletin Board,
After some headbanging (Refmac5 had helpfully created gap records for all
insertions and deletions present in the structure), I got refmac5 running with
the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other
possible domains because they were too small
The Helmholtz Zentrum Berlin für Materialien und Energie, the
Max-Delbrück-Center, the Freie Universität Berlin and the Humboldt Universität
zu Berlin jointly operate three experimental stations for bio-macromolecular
crystallography at BESSY II, one of the world’s most modern synchrotron
radia
Hello Everyone,
I'm looking for a group/person that has PIMS and Xtailpims installed which does
not throw Java errors while using the program.
I've been struggling to get the program to work without error trying different
versions of the below programs.
I believe PIMS and Xtalpims has potential
Hello, Monika,
1) Add NAGs
2) Remove their hydrogens and O1 atom and put them in density
3) In menu: Calculate->merge molecules, choose your pdb and both NAG
residues
4) save coordinate file
2013/6/20 Monika Pathak
> Hi
>
> Please can I ask about how can I put NAG to asparagine in coot (I think
Dear all,
thanks to all for your first responses; however, I probably wasn't precise
enough in my original message.
I DO have an XDS.INP for the mar345 image plate (and i also now where to
find the others).
What I would like to have is a modified version of Kay Diederichs
script, to ge
Dear all,
sorry for the slightly off-topic question:
Does anyone have a modified version of generate_XDS.INP for the mar345
image plate detector?
I know I could -relative easily- make it on my own, but why inventing the
wheel twice?
Regards,
Jan
--
Dr. Jan Gebauer
AG Prof. Baumann
Instit
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