Similar to distang, one can also do it with the gemmi contact program
and some
simple filtering with awk (or other tool). It will also look for
symmetry related
contacts and can read mmcif or pdb format. (One can adjust distance
thresholds etc with
parameters to gemmi
https://gemmi.readt
Hi Pedro,
Back when we were developing the Stanford Automouting robot,
I ran several tests with thermocouples mounted in Hampton Cu Pins
and loaded into SSRL cassettes. These were placed in a shipping
dewar and the temperature at the bottom and top of two stacked cassettes
was monitored over ti
Another good way to test the dry shipping dewar is to its dry/empty weight.
If you don't know your "as new" mass, you can weigh it, then
purge with dry air/nitrogen for 24 hours and check the weight again,
if it is unchanged, then you can use that as your dry/empty weight.
Next you can charge the
The Baker group has also reported substantial progress in all atom predictions
Krishna et al.,
Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
bioRxiv 2023.10.09.561603
doi: 10.1101/2023.10.09.561603
https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1.full
Regards,
PDBj has a nice web-based mmCIF editor that
can help you edit mmCIF an validate the
data entered.
See https://pdbj.org/cif-editor/
Regards,
Mitch
Quoting Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>:
Hi
There is no particular special editor from PDB (or from anywhere
else
Dear all,
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Dear all,
On Tuesday, January 10, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC)
Ken Duncan, Deputy Director, The Bill & Melinda Gates Foundation
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You can also look at your anomalous maps. For most
energies/wavelengths used to
collect protein data, f" for K will be just under 2x the f" for S
while for Na f"
will be much less (0.2-0.25 of S). So you can use S atom anomalous as
an internal reference.
If you see anomalous peaks at your S a
On behalf of The U.S. National Committee for Crystallography (USNC/Cr)
of the National Academies of Sciences, Engineering, and Medicine, I am
happy to announce that registration is now open for "EXPLORING
STRUCTURAL DATABASE USE IN CRYSTALLOGRAPHY: WORKSHOP SERIES". The
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Hi,
I just noticed that there is a page --
https://www.ccp4.ac.uk/?page_id=2593
that allows downloading various versions.
It notes there is an issue with the
Package Managers for Mac and Linux
due to a server error. It sounds
like this page was added as a workaround
until things are back to n
You can also use phaser.famos to compare MR solutions to see if
they are related --
https://www.phaser.cimr.cam.ac.uk/index.php/Famos
phaser.famos moving.pdb=pdbfile1 fixed.pdb=pdbfile2
(from the it looks like there is also a phenix
GUI to access this functionality as well --
https://phenix-online
What about coot? Have a look at
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/coot-may-2017-ligands-madrid-mcs2017-csic.pdf
pp28-40
and
Emsley P. (2017). Tools for ligand validation in Coot.
Acta Crystallogr. D73, 203–210.
https://doi.org/10.1107/S2059798317003382
https://www.ncbi.n
You can also use the ccp4 legacy program crossec ---
http://legacy.ccp4.ac.uk/html/crossec.html
for your case --
echo -e "NWAV 1 1.2782\nATOM Sr\nEND\n" | crossec | grep SR
Atom symbol and number SR 38
$TABLE:Wave length v F' and F"- SR :
$GRAPHS:Lambda v F' and F" SR :A:2,3,4: $
I am not sure about in the PDB format or mmCIF format.
However, other refinement programs have this ability too, e.g. the
occupancy groups of refmac
http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy
buster refine has a tool pdb2occ to help generate appropriate
groupings in
When the JCSG was in production, we would routinely collect X-ray emission
spectra from our samples to look for metals. We also saved all crystals
after data collection and if we saw extra anomalous peaks in the maps
during refinement, we would put the crystal up again and collect
quick low resolu
You can also do a reverse image search with tineye
https://www.tineye.com/search/153d902d2e4567ccb3299daefa3cef8d207d197a/
or google image search
https://www.google.com/search?tbs=sbi:AMhZZiua3avdA9z9KnzBOe4pBpsmp-1LJjdEXd13gP1bdXWtunUl2CB6caY5wjn56t8GA8l9KNMqKZdLYHBYPpAuwanPvVp6nJImULD5vgQ9FtisQ
We used to use dichlorodimethylsilane in toluene to siliconize both
coverslips and the special glass capillaries for crystal mounting.
I don't have the protocol we used anymore, but the one listed on
protocolpedia sounds familiar.
https://www.protocolpedia.com/blog/2017/05/11/siliconized-coverslip
As Ditlev points out, measuring the channels ignores the flexibility /
dynamic nature of proteins in crystals. Also, if you have any disordered
tag residues or loops, they also occupy space in the solvent channels. That
said, I have found the Doug Juers' lab's program map_channels very useful
for
The power supply on the Zebra brand bar code printer we have for
labeling plates is part of a recall. I thought I would pass on the
details in case others are affected.
The recall was expanded to include 1.3 million units manufactured
between 2006 and 2012 for the North American market.
The
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