Hi
I wanted to check is it possible that there could
be errors in the library cif files associated with CCP4 and coot ?
I have noticed a couple of potential errors in a ligand cif file from the CCP4
library.
Perhaps it is my error - I shall need to triple check it again but, if it
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Dear Jodie,
except for the matter if there is 'right' and 'wrong' in science or
rather 'good' and 'bad' models, Garib Murshudov maintains the
cif-library and if you send him a compilation of possible fixes he
would surely appreciate your input.
There are errors in every branch of human endeavour I am sure!
Please if you find something wrong. send your suggested correction to
Garib Paul, and once there is a fix notify us all via the BB.
CCP4 has always depended heavily on the users noticing the bugs
Thank you for your observation.
Thanks Everyone for your input
I shall triple check my reasoning tomorrow and
email Garib if I do think there is an issue.
Thanks
Jodie
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson
[eleanor.dod...@york.ac.uk]
Sent:
If you are interested in finding other interactions that look like one
particular one, rather than just classifying things (e.g., is this
cyan, sea-foam, turquoise or teal?), then I'd recommend the
substructure searching capabilities of the DrugSite server
You can specify any arbitrary
Hi Andre,
a very effective method is the use of a humidity control device. It has
the great advantage that you can characterize changes that occur and
also move straight to data collection. There are several HC1 devices in
Europe (developed here at the EMBL and available at Diamond, BESSY and
Dear Andre,
66% solvent is on the high side but not a good reason for poor resolution.
Other with similaa solvent content have achieved resolutions of 1.5 Ang.
and even better.
I would screen at a lower protein concentration. It will require more
precipitant
and you should end up with less
Dear Andre,
We had a similar case where the crystals were bigger and diffraction was lousy.
Our standard dehydration approaches were not very successful.
I suggest reading this -
Post-crystallization treatments for improving diffraction quality of protein
crystals.
Heras
I wonder if there is a big difference between dehydrating in a drop, where the amount of
mother liquor is essentially unlimited, and dehydrating a mounted crystal in something
like the FMS, where there is only a thin film of ML on the surface. In the latter case,
once the surface fluid is gone,
Dear Andre,
you could try with the protocol described in the following paper
Acta Crystallogr D Biol Crystallogr. 2013 69,920-3.
Using high-throughput in situ plate screening to evaluate the effect of
dehydration on protein crystals.
Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J,
On 29/10/13 06:54, Jodie Johnston wrote:
Thanks Everyone for your input
I shall triple check my reasoning tomorrow and
email Garib if I do think there is an issue.
Make suer that you are using the latest dictionary (of course)
UNIVERSITY OF CALIFORNIA, IRVINE
DEPARTMENT OF PHYSIOLOGY BIOPHYSICS
POSTDOCTORAL SCHOLAR
One postdoctoral position is available immediately in Dr. Rongsheng Jin’s
laboratory at the Department of Physiology and Biophysics, UC Irvine, and will
remain open until filled. The new postdoctoral
Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD
monitor. I would like to have a wall mounted monitor that one could easily
connect laptops and imacs to for structure display, doing tutorials on building
into maps, etc.
thanks
-tom
Tom J. Brett, PhD
IMHO Bluetooth is way too slow for a monitor connection.
On 10/29/2013 01:05 PM, Brett, Thomas wrote:
Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD
monitor. I would like to have a wall mounted monitor that one could easily
connect laptops and imacs to
The biggest I could find is a 7inches monitor for car media centers.
I'm not sure it will be a great deal for a wall monitor.
Gian
On 10/29/13 6:10 PM, David Schuller wrote:
IMHO Bluetooth is way too slow for a monitor connection.
On 10/29/2013 01:05 PM, Brett, Thomas wrote:
Hi all:
I was
The best technology would be Wigig, but I don't think it's on the
market yet.
Some wireless monitor connection solutions appear to be available using
Intel WiDi and Miracast. Check your favourite vendor for availability
and requirements.
On 10/29/2013 01:05 PM, Brett, Thomas wrote:
Hi
Can the fixes in the CCP4 dictionary be rolled out through the update system
of CCP4? That way we can avoid (at least to some extent) that people keep
working with erroneous restraint files. Some of these errors can really mess
up your structure.
Cheers,
Robbie
-Original Message-
From:
Hi, you could try dehydration in microdialysis buttons - this allows for slow
gradual increase in PEG over few days and full control of other parameters,
including lowering salt concentration.
It was the only dehydration method that worked well for our large membrane
protein:
Hi Andre,
Are you sure that the cryoprotectant has been optimized?..I am sure you
must have already done it but just in case..sometimes the cryo protectant
which makes the ice rings disappear is not the best one and playing around
that concentration as well as different alternatives can have a
Hello,
I am working on a project with several (separate) structures of the same
protein. I would like to be able to compare the solvent molecules between
the structures, and it would be best if the waters that exist in roughly
the same position in each PDB share the same residue number.
Downloading structures of the same homologous family with blast. Then
superimpose them on a reference structure. You may then try to look at over
lapping water molecules
On 30 Oct 2013 02:23, Elise B ek...@case.edu wrote:
Hello,
I am working on a project with several (separate) structures of
Hi Elise,
How about taking the homologue structure with highest number of waters and use
it to run molecular replacement on all other datasets? Then you could keep only
the good waters (manually unfortunately) which will ensure they will all have
the same numbers.
Probably not the fastest
Dear Colleagues,
A three year Wellcome Trust funded PhD studentship has recently become
available at the Wellcome Trust Centre for Cell Biology (www.wcb.ed.ac.uk). The
successful candidate will join students in the second year of the Wellcome
Trust Four Year PhD Programme in Cell Biology.
Hi Elise,
Not exactly what you are asking for, but
lsqman will compare waters between structures with a
cut-off. (However, it will not renumber the
waters as you wanted)
http://xray.bmc.uu.se/usf/lsqman_man.html#S71
If you want to look at waters related by NCS in a
single PDB file with
http://www.ccp4.ac.uk/html/watertidy.html
On 10/29/2013 04:43 PM, Elise B wrote:
Hello,
I am working on a project with several (separate) structures of the
same protein. I would like to be able to compare the solvent molecules
between the structures, and it would be best if the waters that
Hello experts,
I am currently working on a structure of a protein-peptide complex. The peptide
was synthesized with a C-terminal amide group. What is the best way to add this
in Coot and refine in Refmac? I did a search on the web but only found a
protocol for CNS not for Coot/Refmac.
Thanks
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