I don't know how many people still use it, but doesn't CNS give you that
capability? In the bgroup.inp script, I think you can easily specify which
atoms or residues to include in each overall B-factor.
Daniel
____
Daniel M. Himmel, Ph. D.
Principal, Himmel Sci Med Com, L
).
Daniel
____
Daniel M. Himmel, Ph. D.
Principal, Himmel Sci Med Com, LLC
E-mail: danielmhim...@gmail.com
URL : https://himmelscimedcom.com
Member, American Medical Writers Association
You can also find me at https://www.talusfreelance.com
On Tue, Jul 30, 2024 at 10:35 AM James Hol
20th and 21st centuries, not eons ago.
So, my humble request: Can we stick to crystallography and allied fields
of structure determination on this e-mail list, and not digress into
divisive politics, please?
Respectfully submitted,
Daniel
Daniel M. Himmel, Ph. D.
Principal, Himmel
Another recommendation: Increase the concentration of your pH buffer, if
possible, for better results (possibly a larger yield). I agree that some
components, especially the sugars, should not be autoclaved and should be
filtered instead.
Daniel
Daniel M. Himmel, Ph. D.
Principal
sulfate instead of
phosphate)?
Daniel
___
Daniel M. Himmel, Ph. D.
Principal, Himmel Sci Med Com, LLC
E-mail: danielmhim...@gmail.com
URL : https://www.HimmelSciMedCom.com
On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. wrote:
> Hello All,
>
>
I had the pleasure of editing and accepting an article that Alexei Vagin
and his colleague Alexei Teplyakov submitted to the International Tables
for Crystallography Volume F (2nd edition) on the Molrep software. I'm
sorry to hear the news and extend my condolences to all who knew him.
Sincerely,
The Schrodinger software suite may also have a module that you can use
(https://www.schrodinger.com/platform#product-list-collapse). You can
contact technical help
for advice.
Daniel
On Wed, Jun 24, 2020 at 7:54 PM Andre LB Ambrosio wrote:
> Dear Sorin, many thanks for this. Very useful.
>
>
That's fascinating! Can such an interferometer actually be constructed for
an
X-ray beam line or is this still in the realm of the theoretical possible?
Daniel
___
Daniel M. Himmel, Ph. D.
E-mail: danielmhim...@gmail.com
On Tue, Mar 31, 2020 at 10:01 PM Bernhard Rupp
Dear colleagues,
Since when does being a structural biologist make us experts in
climatology,
and isn't it a breach of basic ethical practice and professionalism as
scientists
to sign on as authors to an article for which we have neither contributed
research nor intellectual content of the ma
You're welcome to boo this one down, but how about something like, "With a
some coaxing,
a protein can be X-cited to expose its structure." I think that's poor,
but maybe it's a starting point.
-Daniel
On Thu, Aug 15, 2019 at 7:42 AM Gerard DVD Kleywegt
wrote:
> Dear CCP4BB-ers,
>
> Once agai
-- Forwarded message -
From: Daniel M. Himmel, Ph. D.
Date: Mon, Aug 5, 2019 at 12:45 PM
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to
phosphate bound to Zn2+
To:
Pentagonal phosphate geometry would be a transition state, except that
three oxygens
acilitates crystallization at higher temperatures).
Daniel M. Himmel, Ph. D.
E-mail : danielmhim...@gmail.com
URL : http://www.DanielMhimmel.com/index_Xtal.html
<http://www.danielmhimmel.com/index_Xtal.html>
On Thu, Aug 1, 2019 at 5:24 AM Sergei Strelkov
wrote:
> Dear all,
>
>
>
During the few years that I had the opportunity to work with Michael
Rossmann,
I found him to be not only a great scientist but a fine and humble
gentleman,
who will be missed.
-Daniel
On Tue, May 14, 2019 at 9:13 PM Hasan, Syed Saif
wrote:
> Dear Colleagues,
>
>
> It is with profound sadness
Fisher Scientific makes 22 inch square plastic cover slips, which are
labeled "Fisherbrand Unbreakable
Cover Slips".
I and my colleagues have used them for over 15 years instead of siliconized
glass coverslips.
Just dip each one in ethanol to clean before use, dry with an air blower,
and use it to
(try especially
> >> to improve
> >> your Ramachandran Plot). Use MolProbity to help in identifying errors
> >> and clashes.
> >> If a few rounds of simulated annealing and model building don't improve
> >> things, try some
> >> refinement
By the way, I would recommend running simulated annealing with each
composite omit map you generate to help in overcoming model bias.
-Daniel
On Sat, Nov 10, 2018 at 9:31 PM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:
> Anandhi,
>
> Assuming the data reduction
to another model and then correct the geometry in
Coot.
If B-factors don't come down no matter what you do, you could be in the
wrong space
group or have problems with the original data that need to be addressed.
I hope this helps.
Daniel
_______
Daniel M. Himmel, Ph. D.
URL:
esult from weak overall attractions between the protons in the nucleus of
one atom
and the electron cloud of another atom and therefore increase as the atomic
number
of the atoms increase.
-Daniel
On Thu, Sep 20, 2018 at 10:04 AM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:
>
rgy
> for the formation of the interface.
>
>
> Sheila
>
>
>
> --
> *De:* Daniel M. Himmel, Ph. D.
> *Enviado:* terça-feira, 18 de setembro de 2018 15:10
> *Para:* sheila_bore...@hotmail.com
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Assunt
Sorry. I may have been unclear. H-bonds are actually a subset of dipole
interactions.
On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:
> By the way, distinguishing between dipole and ionic (salt bridge)
> interactions could
> be a
By the way, distinguishing between dipole and ionic (salt bridge)
interactions could
be a slippery slope, because which one you have sometimes depends on the
protonation
state of the protein(s), which is pH dependent.
-Daniel
On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. <
danielm
Sheila,
Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions
are often collectively called
electrostatic interactions. Note that dipole interactions involve partial
charges. If you want to exclude
dipole interactions, you have say so specifically in your manuscript.
Non-bond
Dear JL,
Years ago, this was a common problem when I was crystallizing myosin
constructs for my doctoral work. Some of the most beautiful crystals I
got showed little or no diffraction. Often this occurs when there is a very
large water content in the asymmetric unit and in proteins that have a
Just be careful when drawing conclusions from B-factors. If you
look at the mathematical way that a B-factor modifies a structure factor,
you can see that as a B-factor's numerical value increases, the
corresponding structure factor's contribution to a calculated diffraction
pattern is reduced. I
If I may jump in, I wonder if there are any hardware configurations
(monitor, 3D glasses, graphics cards, etc.) that allow 3D graphics
with a MacIntosh OSX platform.
-Daniel
On Wed, Jan 3, 2018 at 4:42 AM, Wim Burmeister
wrote:
> I answer a bit late, but I repost a message on 3D graphics from M
I skimmed your paper, and overall it looks like a good overview
of high-throughput protein crystallization. However, I was surprised
that no mention was made of Formulatrix Rock Maker software,
which is an excellent computer-aided graphical tool for designing
crystallization screens rapidly. This
it-cell parameters. (these are XFEL
> data so indexing wouldn't give the point and space groups). I checked the
> PDB, but no luck the PDB structures have the different space group
> assigned, no definitive answer
> hopefully, somebody can point me in the right direction
>
> Best,
&
Gihan,
The best way, in my opinion, to choose a suitable (and correct) space group
is to combine your own understanding and knowledge with the available
software tools.
I’ve never indexed XFEL data, so I don’t know if this data can be sampled
and
run through hkl2000/3000 or Mosflm to get some f
Have you tried using the CNS script rmsd.inp? You can explicitly list
the atoms to superimpose and set "coord_fit=true;".
-Daniel
On Mon, Apr 16, 2018 at 3:30 PM, Carter, Charlie wrote:
> I think I’ve asked this question before and I was pointed in a number of
> unsuitable (for various reason
Oliviero,
We published a paper in 2003 in which we normalized B-factors
to do a comparison of relative mobility or flexibility. The reference
is: Gourinath et al. Structure 11:1621-1627 (2003). The jargon
we used for Bave of the protein is . In our case, to be
conservative in our interpretatio
(or try combination of PEG 400 and PEG 200), or
vary the MPD concentration. Good luck.
I hope this helps.
-Daniel
[image:
RnNZfQn2o2xpggJQqefCOervMbPIci5mujDPJnvl43kv6Rtxjyh5gHN_JKVzeU-aaGz3pePFgxfoAAtZJZNx8mveVTc-11j98EfuAJVcumUenA=s0-d-e1-ft.gif]Daniel
M. Himmel, Ph
Oops. I meant to say that Ca2+ usually has seven coordinating atoms.
Mg2+ usually has six. Sorry for the error.
-Daniel
On Wed, Mar 7, 2018 at 2:27 PM, Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:
> Rajesh,
>
> Ca2+ usually is coordinated by five atoms, whereas
Rajesh,
Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is
coordinated by six. I've seen that a lot in structures that I've
determined.
-Daniel
On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> You just calculate a anom ma
-- Forwarded message --
From: Daniel M. Himmel, Ph. D.
Date: Wed, Mar 7, 2018 at 12:23 AM
Subject: Re: [ccp4bb] suggestions on a microscope for Crystallography
To: Chandramohan Kattamuri
My best experience was with Leica microscopes, such as the S6E.
Leica microscopes have
I'm looking for some computer hardware advice.
I have a MacBook Pro with a "Retina" screen and
an Intel HD Graphics 4000 1536 MB graphics card,
running OS X 10.11.16 ("El Capitan"), and I would
like to view structures in 3-D in Coot.
Which computer monitors and which 3-D glasses brands
would allow
ment about what type of structural element
is always ordered.
I hope this helps.
-Daniel
____
Daniel M. Himmel, Ph. D.
On Tue, Nov 28, 2017 at 9:44 AM, vincent Chaptal
wrote:
> Hi,
>
> I've been searching but can't find what I am looking for so I thought I
> ask special
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