Hi,
Does anyone have experience (or scripts!) to extract ligand SMILES from
macromolecular PDB records using the PDB data API or from a library of PDB or
mmCIF files? We would greatly appreciate any pointers to get us started.
Thank you,
Doeke
=
Doeke Hekstra
Assistant Professor of Molecu
Hi Arpita,
H and D have the same number of electrons (1). The D nucleus has an extra
neutron, changing its mass and therefore its vibrational energy levels. That
can affect hydrogen bonding patterns, although I would expect the effect to be
relatively minor (see e.g. Fisher and Helliwell, Acta
We got an aliquot of SG13009 once from
https://labs.utsouthwestern.edu/jiang-youxing-lab back when I was a postdoc at
UT Southwestern. I don't have any now.
Doeke
=
Doeke Hekstra
Assistant Professor of Molecular & Cellular Biology, and of Applied Physics
(SEAS),
Director of Undergraduate
data.
So, nothing fancy (aniostropy etc), there is just a lot of data that needs to
be adjusted and I am trying to avoid reprocessing all the frames again.
Matt
On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke
mailto:doeke_heks...@harvard.edu>> wrote:
Hi Matt,
It would be helpful i
Hi Matt,
It would be helpful if you could describe your case in more detail. Do you want
to change the resolution cutoff after scaling? Do you want to keep more data?
Fewer? Or do you mean something different such as truncation to generate
amplitudes, application of anisotropic resolution cutof
Hi Murpholino,
You could go the route of comparing refined models, as described by Dr. Yorke.
As Dr. Dodson describes, isomorphous difference maps are another way to compare
datasets. A benefit is that they do not require separate refinement of models
for both states, which can render the compa
To clarify, the simulations would be money-intensive. The interpretation would
(at first!) be people-intensive.
-Original Message-
From: CCP4 bulletin board On Behalf Of Hekstra, Doeke
Romke
Sent: Tuesday, April 2, 2024 9:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] request
Hi James,
With a budget of $1e12, I would like to ask for a database of fully ab initio
QM simulations of proteins and systems of interest. I'd love to see equilibrium
and non-equilibrium simulation, e.g. for photosystems I/II actually absorbing
photons and responding thereto. I'd like to see a
Hi,
I would like to be sure about which symmetry operation the M/ISYM column in an
MTZ file is referring to. Is it correct that this matches the order in CCP4's
/lib/data/syminfo.lib (at least when this order is unique-it is not always so)?
Would anyone know why the order in one of my favorite
7;
> structures when > it comes to phasing. You can repeat this for each side of
> the triangle > (each in two directions) in order to label the semantic
> triangle. > > Merry Christmas, more peace on earth and sanity for the
> elections in > 2024! > > Tim
Dear colleagues,
Something to muse over during the holidays:
Let's say we have three crystal forms of the same protein, for example
crystallized with different ligands. Crystal forms A and B have the same
crystal packing, except that one unit cell dimension differs by, for example,
3%. Crystal
Hi everyone,
When I was looking for faculty positions, I completely misunderstood this
language too. I didn't apply to some places because of this odd "9-month"
language, only to realize I was getting a 9-month salary after all!
Mark is, of course, right that this practice is nearly universal,
Dear Gyuhyeok,
Please feel free to describe any challenges with settings for Careless at
https://github.com/rs-station/careless/issues
We will be happy to help and improve our online documentation accordingly.
I assume some of the statistics you report below are simply duplicated from
Aimless?
Hi Gyuhyeok and everyone,
Thank you. We developed Careless to support scaling and merging of data from a
wide range of diffraction experiments, including Laue, XFEL,
time-resolved/serial, etc. Nice to hear that your electron density maps look
promising. This is new software and we will continu
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