Hi,
I doubt you have a TaBr cluster bound in your soaks.
You'd expect a strong anomalous signal from cluster compounds (that's what they
are made for) and you can easily get a low resolution anomalous signal from a
few dislocated HA in the solvent channels, especially if you don't counter soak
Hi All,
I am looking for some advices on experimental phasing at low resolution,
any advices will be highly appreciated.
I have 3 data sets, with similar but not identical cell parameters,
Redundancy of each dataset is larger than 6 for overall and 2.5 for
anomalous signal, completeness >95% for
SSRL Bluice opens the image in adxv upon double click in the diffraction
window.
HTH,
Jens
On Mon, 2015-04-27 at 16:57 -0700, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> Thanks - particularly great if we had these images/option available to look
> at
> in real time during data collection, w/o f
Thanks - particularly great if we had these images/option available to look
at
in real time during data collection, w/o first having to download the raw
data (not
really feasible during remote data collection). I don't think the ESRF
online data base has the option, but other beam lines may?
Thx
In the ADXV viewer:
http://www.scripps.edu/tainer/arvai/adxv.html
Go to Edit:Settings and click on the "Small Spots" radio button. This
solves most of the "I can't interpret the spots" problems you describe.
-James Holton
MAD Scientist
On 4/27/2015 3:31 PM, Bernhard Rupp (Hofkristallrat a.D.)
Hi Fellows,
I wonder whether it's just me and my eyesight failing (or excessive internal
lubrication)
It seems that the art of looking at diffraction patterns and being able to
tell
a lot about modulation, superstructures, extinctions, etc. becomes kind of
useless
old fart stuff when dealing
Dear all,
Picking up from the earlier thread about Ramachandran outliers, how would
these outliers (Ramachandran as well as rotamer) affect the surface
electrostatic calculations e.g by APBS, especially when the number of such
outliers is very large.
Sincerely,
Asma
The Richardson's have another tool for RNA backbone rebuilding which *may*
help called RNABC - RNA Backbone Correction.
http://kinemage.biochem.duke.edu/software/rnabc.php
On Thu, Apr 16, 2015 at 8:22 AM, Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:
> Dear all,
>
> Despite molprobit
Once more to those who feel offended by the structures in discussion:
I’d be very careful at judging low resolution structures. This is a tricky
business
requiring a lot more info than just the PDB validation report. The 3+ to 4 A
resolution range is a particularly deceptive one: The crystal
Dear Misbah,
Please don't give up on Crystallography for the poor attitude of one senior
PI. Not
all of us have the same way of helping beginners.
Michael James
Sorry can't help it. The aggressive replies are mainly from senior PIs from
US - friend in need is friend indeed.
On Thu, Apr 23, 2015 at 2:20 PM, Bernhard Rupp (Hofkristallrat a.D.) <
hofkristall...@gmail.com> wrote:
> Well, with full respect to your sensitivities as far as your own person is
>
Hey Veera,
you have missed to assign all labels which were required as input parameters.
DM is trying to use your HLA labels for density modification. Either you assign
them if present or you choose to omit these and just use FHI and FOM labels.
This can be done in the header of the DM GUI.
B
Ramachandran outliers aside, amount of other outliers seem a bit worrying
to me, especially given that it may not be all that trivial to justify them
against 3.5A resolution map:
all-atom clashscore : 29.19
ramachandran plot:
outliers : 0.51 %
allowed : 5.44 %
favored : 94.05 %
rot
Hi,
I was trying to do density modification using DM,CPP4 suit, but not
able to run as I am getting an error msg:
FP = DELFWT SIGFP = SIGF_l5l6_009_p4212 PHIO = PHIC FOMO = Unassigned HLA =
Unassigned HLB = Unassigned HLC = Unassi
Data line--- LABOUT
FDM=FDM
PHIDM=PHIDM FOMDM=FOMDM HLADM
Hi Robbie:
Sorry, I just saw your email now.
To make that figure, I just downloaded the automated refinement results
manually from the server, loaded into coot, and took a screenshot. A couple of
days later, after Gert mentioned you had since fixed it, I checked with the
built-in coot interfa
Hi, Such kind of discussion are really great and fruitful.
thanks
Pankaj
On Mon, Apr 27, 2015 at 12:25 PM, Dale Tronrud
wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
>
>This particular model was deposited in early December of 2014, so
> the authors had the validation report in
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
This particular model was deposited in early December of 2014, so
the authors had the validation report in hand before publication and,
I presume could (should) have passed it on to the reviewers. The
release date of the entry has nothing to do wi
Dear Monica,
We can also, perhaps, most helpfully quote from our forthcoming article in J
Appl Cryst, Volume 48, Part 3 (June 2015):-
"An online computing server, Online_DPI, is created and maintained to calculate
the ‘Cruickshank DPI’ value for a given three-dimensional protein or
macromolecu
7 out of 1361 Ramachandran outliers (all prolines) doesn't seem high to me.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Oganesyan, Vaheh
[oganesy...@medimmune.com]
Sent: Monday, April 27, 2015 9:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [cc
Dear Monica:
To calculate Diffraction Precision Index (DPI) and individual atomic coordinate
errors:
You could either go through the IUCrJ article entitled "Do we see what we
should see? Describing non-covalent interactions in protein structures
including precision"
(http://journals.iucr.org/
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 at validation report. In my opinion,
whatever it is worth, every journal dealing with crys
Dear Appu,
Did you try to run phaser in C222 as well? Your space group is most likely
C2221 as pointless and xtriage suggest, but the space group might be different,
especially if the 2 molecules in the a.u. are related via some pseudo
crystallographic symmetry. Also, some additional runs of Ph
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Weifei,
choosing a longer wavelength for data collection should also lead to
better spot separation. You may collect different data sets at various
wavelengths to get the optimum.
Best,
Tim
On 04/27/2015 03:28 PM, herman.schreu...@sanofi.com wr
Hej,
In thread to my previous mail, i calculated the minimum and maximum errors
as well as DPI for the structure. But want to ask what are the allowed
limits for the above values to decide for the correctness of the positional
movements within the structure ?
Thanks
On Mon, Apr 27, 2015 at 10:54
Hi everyone,
Can anyone guide me to calculate the diffraction component precision index
(DPI) for validating the positional error of certain critical residues in
my structure ?
Thanks in advance
Monica
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