Hi, Ian Tickle has asked the most pertinent question - there are many
reasons for highish FreeR factors. Only some are due to errors or missing
molecules or other problems. How many Free reflections are there? When
the sample is very small ( 500 say) you can get different results from a
different
You may also want to try 0.5 - 2% (w/v) glucose in your plates alongside
transformation into the NEB T7 Express strains:
http://www.neb.com/nebecomm/products/productC3013.asp
http://www.neb.com/nebecomm/products/faqproductC3013.asp
LysY gives you higher final ODs [no lysozyme activity] than
I know, in PyMOL using 'symexp' possible to generate symmetry related
molecules for a given crystal structure. But I'm looking for some
program/software (for batch) by which I can find out the number
of symmetry related molecules (distance cutoff = 5A) interacting with
a given chain in a crystal
Dear Careina,
As other have mentioned, my feeling is that something is suspicious.
However the problem might be very difficult or impossible to catch and
other structures have been deposited with similar R/Rfrees...
What I would check in addition to what has been mentioned, is if some
twinning
hi ,
in CCP 4 package u can run CONTACT program use NCONT to find symmetry
contacts only. u can Fix contact distance minimum and maximum also .
On Thu, Jul 14, 2011 at 5:18 PM, sukanta mondal sukanta.mon...@gmail.comwrote:
I know, in PyMOL using 'symexp' possible to generate symmetry
On Thu, 14 Jul 2011, Wonjin Bae wrote:
Hi, all
Recently, some bactrial source enzyme(sialidase) was subcloned pET20b and
pGEX4T3 vector.
Then, these two construct were transformed to BL21(DE3) expression host.
DNA sequencing results were accurate.
In case of pGEX, many colony was formed and
oops - I just caught that the empty pET20 did transform well so the other
suggestions about toxicity are probably more accurate.
On Thu, 14 Jul 2011, Eric Larson wrote:
On Thu, 14 Jul 2011, Wonjin Bae wrote:
Hi, all
Recently, some bactrial source enzyme(sialidase) was subcloned pET20b and
Hi all
Walking through multi xtal averaging with RAVE. I finally got a good
mask and optimized NCS for my xtal forms. However, in the CRAVE manual
I see this
- the reflections in the input MTZ files *MUST* have been put on the
same temperature factor scale prior to cross-crystal
If I recall correctly DATAMAN does Wilson scaling in which the scale
and B-factor are adjusted so the average reflection intensity in
resolution bins are the same. I suspect it may not be required if
all the data have been put on an approximately absolute scale by
e.g. truncate (although that
Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) continues to improve
its services to the scientific community. As part of our recent website
update, we have reorganised and simplified the way information about NMR
entries is shown. We have also released Vivaldi (Visualisation
This is correct - see http://xray.bmc.uu.se/usf/dataman_man.html#S27
At the time I wrote this (1993...), I was a recovering NMRtist and The Other
Gerard was doing a sabbatical in Uppsala and in fact in the office next to
mine. He pointed out that I had to do this and also provided code.
I am looking for a way to output redundancy per individual reflection,
preferably for scala but if that is not possible then maybe for
scalepack.
From my (admittedly quick) look at the scala manual it seems that I can
use something like UNMERGED output option to exclude outliers and then
would
On Thursday, July 14, 2011 02:55:26 pm Ed Pozharski wrote:
I am looking for a way to output redundancy per individual reflection,
preferably for scala but if that is not possible then maybe for
scalepack.
If you read the unmerged file from scalepack into ccp4 using
combat, it creates a data
You are right that refining occupancy and B value at the same time cant
be done with REFMAC, and probably wouldnt work anyway at 2.9A
However, if you set the ligand occupancy to 0.7 say, and refine the
residue B factors, the occupancy should not be set back to 1.0. It
certainly isnt in the
They must represent a different packing - the volume of Shape 1 is 10%
than 2*Vol-Shape2
But it isnt uncommon to get different forms - check your symmetry contacts
(PISA will do that) and see how the two forms pack.
eleanor
On Mon, 11 Jul 2011 18:09:52 +0800, ferrol shariff
This seems somewhat weird - your Rmerge values increase with more frames
as explained by Tim, but I cant see why the I/SigI should increase sharply
for the 180 degree set then fall off again.
if you have run Scala look at the scaling plots v batch, and resolution to
see if there are any weird
Roberto steiner has told you how to use these new REFMAC5.6 features,
Rob Nicholls has suggested how to generate secondary structure restraints,
and Martyn Winn given a page to install a new interface to make it easier
to use them..
But with such limited data it isnt surprising that the FreeR
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