be able to use coot to
align the maps after aligning two PDB files corresponding to the
coordinates of interest. Its the "Transform map by LSQ model fit ..."
menu under Map Tools...
Is that helpful at all? (I should really come up with a better name for
bin_stuff.)
-James Holton
MA
tps://github.com/jmholton/refmac_tools_jmh/blob/main/refmac_occupancy_setup.com
(note that I have uploaded it into github so that it looks like I know
what I'm doing)
Does that help?
-James Holton
MAD Scientist
On 11/20/2024 6:09 AM, Kyle Gregory wrote:
Dear all,
I have a 1.5 angstrom resol
r a shared resource.
Examples that come to my mind are: fragment screening, AI/ML data
analysis, and, of course, synchrotrons. But synchrotrons already exist!
They are looking for resources that are not currently on the list.
-James Holton
MAD
atulations to our latest Nobel Laurates! But the
battle for the "Last Angstrom" is far from over.
-James Holton
MAD Scientist
On 10/9/2024 10:25 AM, Frank von Delft wrote:
So Randy, what should we be saying/using, and where do we find it...
and (not least!), /when/ in the experime
sound
exciting, but finding the right answers to my users questions is what
made me into a MAD Scientist on this BB.
https://sjobs.brassring.com/TGnewUI/Search/home/HomeWithPreLoad?PageType=JobDetails&partnerid=6495&siteid=5861&Areq=79597BR#jobDetails=3558174_5861
-James Holton
M
ground truth of this
Challenge. Easily worth $1500.
-James Holton
MAD Scientsit
On 1/21/2024 7:07 AM, Herbert J. Bernstein wrote:
Have you considered the impact of tunneling? Your rope crossings are
not perfect barriers.
On Sat, Jan 20, 2024 at 6:09 PM James Holton wrote:
Update:
eters and try to extract the physically meaningful reality they are
trying to capture. Restraints are very helpful in preventing many types
of unrealistic situations, but ultimately it is up to you to decide if
the fitted model makes sense.
-James Holton
MAD Scientist
On 7/30/2024 11:30 AM, Ian T
f chains spread out in the loopy
regions you are concerned about. This might be the way to go?
You can also do ensemble refinement in the latest Amber. That is, you
run an MD simulation of a unit cell (or more) and gradually increase
structure factor restraints. This would probably result in t
here fill out that survey?
-James Holton
MAD Scientist
On 6/13/2024 12:24 PM, John R Helliwell wrote:
Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago,
there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its
E MSR. If the beamline scientist who supported you was one of
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg
Hura, Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony
Rosalez, Daniil Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros,
then you used an MSR
that brings us back to the "weak image limit". What if instead of
images we just collected a list of x-y coordinates of photon hits vs
time? Anyone have a suggestion for the name to give to the program that
can process such data?
-James Holton
MAD Scientist
On 5/15/2024 3:28 PM, James
it might
be faster than the cloud.
Sorry if any of this sounds gruff, I don't mean to shout down on anyone,
but I want the message to be clear. This is something Gerard B and I
have struggled to communicate for decades:
Collecting one wavelength at a time is not MAD, but rather M-SAD.
Multip
://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg51707.html
-James Holton
MAD Scientist
On 5/6/2024 12:19 PM, Liliana Margent wrote:
Greetings everyone,
I'm currently in the process of modeling a disulfide bond in two structures.
However, when I attempt to model single occupancy for the cyst
ting out that energy
doesn't always have to come from burning carbon. Carbon doesn't even
have the highest energy density. You can see from this table:
https://en.wikipedia.org/wiki/Energy_density_Extended_Reference_Table
that other fuels are much more effective.
HTH,
-James Holton
MAD
?
Sent from tiny silly touch screen
*From:* James Holton
*Sent:* Monday, 1 April 2024 08:01
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] request for applications
Hey Everyone,
It may sound like an incredibly boring thing that
more carefully next time.
Best of luck,
-James Holton
MAD Scientist
On 4/1/2024 8:03 AM, Phil Jeffrey wrote:
:: I expect to have ~ $1e12 USD on current ledgers.
Presumably via the Bankman-Fried algorithm
Phil
On 4/1/24 3:01 AM, James Holton wrote:
Hey Everyone,
It may sound like an incredibly b
For you, Eleanor? Of course! I look forward to it.
But do you have an "elevator pitch"?
I feel that a lively exchange of short messages conveys ideas much more
efficiently and effectively than an annual exchange of hyper-dense
documents.
Cheers,
-James Holton
MAD Scientist
On
s in
science: the intellectual and technological hurdles that money can't
overcome. I'm hoping this will be an opportunity for all of us to focus
on those. I know we're all not used to thinking on this scale, but, at
least for today, let's give it a try!
Looking for
specify a rotamer. I say try doing that
in coot and record the session. However, if that gets too complicated,
another way to do build-by-rotamer is with these awk programs that I
wrote long before coot was a thing. I still find them useful for
certain tasks. I have created a git repo for them h
han the
ground truth. This implies the "right interpretation" of correlated
motion is recognizable and provable. I find that motivating.
-James Holton
MAD Scientist
On 1/21/2024 4:07 AM, Herbert J. Bernstein wrote:
Have you considered the impact of tunneling? Your rope crossings are
.als.lbl.gov/~jamesh/challenge/twoconf/#tangle
-James Holton
MAD Scientist
On 1/18/2024 4:33 PM, James Holton wrote:
Greetings Everybody,
I present to you a Challenge.
Structural biology would be far more powerful if we can get our models
out of local minima, and together, I believe we can f
, and it will not
only explain the data to within experimental error, and have the best
possible validation stats, but it will reveal the true, underlying
cooperative motion of the protein as well.
Unless, of course, you can prove me
e got something
cooking while I sleep...
Cheers,
-James Holton
MAD Scientist
On 1/18/2024 3:04 AM, Robert Oeffner wrote:
Hi,
I am wondering if authors of refinement programs would like to consider putting
on their users wish list the ability of refinement programs to automatically
terminate on
like non-isomorphism will
start to be overcome. No doubt borrowing from our cryo-EM friends who
have been stretching, pulling and sharpening 3D images for decades.
Happy New Year everyone!
-James Holton
MAD Scientist
On 12/21/2023 11:37 AM, Tom Peat wrote:
Hello All,
I think Randy makes a ve
Are you thinking of "othercell" ?
On 12/27/2023 10:38 AM, Kay Diederichs wrote:
Dear all,
I seem to remember a tool called "nearestcell", a command-line equivalent of
the Oxford Nearest-Cell web server which appears to be offline.
However I cannot locate that tool in CCP4 nor elsewhere. Can an
ng a bulk
solvent mask should be?
You might also want to try the Babinet inverse type of bulk solvent
model. refmac supports this if you use "scale type bulk".
-James Holton
MAD Scientist
On 12/14/2023 2:40 AM, Palm, Gottfried wrote:
I can only guess that the solvent at
trick question and that I already have a
beautiful answer I'm waiting to reveal. That is not really the case.
What I have is a handful of rather unsatisfactory solutions, and I'm
wondering if I'm just not aware of an existing solution to this problem.
Hope everyone had a
Thank you Paul. This is interesting!
I have not played with super-sampling yet. I am assuming you mean
creating a new map 8x the size? If so, did you fill the interstitial
grid with zeroes? Local maximum? Linear interpolation? Tricubic spline?
And when you say "sharpen/blur" with a factor
y some real-space "feathering" is called for before performing FFTs.
Same goes for masked density like that used to compute CCmask. It may
also be worth looking into the digitization process of "image first"
structural biology methods?
My question for the BB: can someone e
low enough to be dominated by
experimental noise only. Nevertheless, despite the phase problem being
cracked by direct methods in the 1980s, your local chemistry department
has yet to shut down their diffractometer. Why? Because they need it.
And for macromolecular structures, the systematic e
quot;,pre,X,Y,Z,post)}' |\
cat > roundoff.pdb
These rounded-off structures look ... weird. And yes they really do
crash validation programs. Food for thought perhaps on what
"resolution", rmsd, and especially GDT_TS really mean?
-James Holton
MAD Scientist
On 4/1/20
to protect them from the dangers
of too many decimal places.
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
I have never met a computational chemist who did not "notice" when a
side chain is modeled as more than one conformer.
-James Holton
MAD Scientist
On 3/31/2023 8:31 AM, Olga Moroz wrote:
Hi everyone,
I always thought it is better to truncate so that biologists looking
at the stru
~jamesh/trimnotrim/testdata.tgz
-James Holton
MAD Scientist
On 3/19/2023 10:02 PM, Lijun Liu wrote:
Hi James:
First of all, I think all those trim-or-not-to-trim practices are kind
of compromises when the data did not really offer local density strong
enough to model side chain relia
as well as information on how to apply for beamtime. For more
information, see the announcement here
<http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10th-2023/>.
http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10th-2023/
Hope to see you there,
-
ight think that with enough copies in the ensemble it should
be possible to fit any density with geometrically reasonable molecules,
but that is not what happens in practice. This is actually quite
remarkable! So many "free parameters" and yet the tug-o-war between R
factors and geometry
seeing 1-electron changes. This
is because hydrogen is only 17% of a carbon. But 3-5% error, which is a
typical experimental error in crystallographic data, anything bigger
than one electron is clear.
-James Holton
MAD Scientist
On 3/18/2023 2:10 PM, Nicholas Pearce wrote:
Not stupid, but essent
PanDDA ?
On 1/3/2023 7:14 AM, Harry Powell wrote:
Hi folks
I was wondering what people’s favourite program is to find binding pockets in
proteins. I’ve had a look at a couple but each has its own idiosyncrasies.
HNY
Harry
##
re many more questions, and better suggestions. I look
forward to enlightening discussions! GRCs have always been about
discussion, and I hope to keep that tradition alive in this community.
-James Holton
MAD Scientist
To uns
rmal. This tends to prevent these mysterious "Killed" errors.
HTH?
-James Holton
MAD Scientist
On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote:
Dear all,
I do not know if this is the right list and I would like to apologize
if it is not.
We have repeatedly experienced xds cras
ption used is that it can be potentially infinitely large. It
still is a decent metric I think.
P
P
On Tue, Nov 8, 2022 at 3:25 PM James Holton wrote:
Thank you Ian for your quick response!
I suppose what I'm really trying to do is put a p-value on the
"geometry&q
l has a finite probability of occurring by chance), as would be
finding no deviations > 3 sigma (for a reasonably large sample to
avoid sampling errors).
Cheers
-- Ian
On Tue, Nov 8, 2022, 22:22 James Holton wrote:
OK, so lets suppose there is this bond in your structure that is
count as 1000 deviates
together? Or separately?
I'm sure the more mathematically inclined out there will have some
intelligent answers for the rest of us, however, if you are not a
mathematician, how about a vote? Is a 3-sigma bond length deviation
significant? Or not?
Looking forward to
s_occ.txt" that you can
import into your refmac run. Possibly using the "@" keyword?
HTH
-James Holton
MAD Scientist
On 9/13/2022 6:59 AM, Evgenii Osipov wrote:
Dear CCP4 community,
I am refining several structures of multimeric protein-ligand complexes and I
wanted to
plain a given blob I
don't think is solved. But I imagine this would make for a good AI project?
Cheers,
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/
One might even want
to compare integrated density to occupancy-refined recovered electron
count? There is the old adage that "a person with two thermocouples
never knows what temperature it is", but personally, I'd rather know the
error bars.
And the overall accuracy? I doubt it w
t to
the masked-off difference map before doing the "new Fobs" structure
factor calculation. Include these same atoms in the new refinement. They
won't move, but they will keep the scale stable. Oh, and don't forget to
turn off the bulk solvent correction! The bulk solvent has
Venue%20Information%20.pdf
Looking forward to a safe and productive GRC!
-James Holton
MAD Scientist
On 5/7/2022 10:11 AM, James Holton wrote:
One more thing:
Some may also recall that in 2020 we were accepting tax-deductible
donations to help attendees from underrepresented groups overcome the
o miss you!
If you need help paying for registration please do reach out to me
off-list and I will let you know what kinds of assistance are
available. In some cases a financial need itself can qualify.
Cheers, and hope to see you there,
-James Holton
MAD Scientist
On 5/3/2022 7:35 AM, Ja
agine
it is not an uncommon situation where you might want help from more than
just the reviewers on how to revise your application. I know I always
try to get all the help I can get.
Might even be able to use biorxiv to do it? Or am I missing something?
-James Holton
MAD Scientist
On 6/27
lps. Not as
good as using CDL, but it helps.
-James Holton
MAD Scientist
On 6/27/2022 8:38 AM, SUBSCRIBE CCP4BB rkrishnan wrote:
I am refining a structure at 2.2A resolution. I find that all my arginines show
distortion after refinement with refmac5 even though they fit into the density
really
community thinks. Please share your views!
On- or off-list is fine.
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&
cks do you use? For many beamlines you may have to buy
different ones.
Looking forward to the June 21 APS/U town hall discussions, as well as
the ACA's "Bridging the APS dark period" session. We will definitely be
discussing this at the Diffraction Methods GRC, which is July 24
starting now: Dave Case on simulating macromolecular crystals with AMBER :
https://lbnl.zoom.us/j/99255547757?pwd=TWozZm9NNDBZZFpIZER6U0JmMmYvQT09
To unsubscribe from the CCP4BB list, click the following link:
https://www.
her on- or off-list is
fine. I expect this community will be interested in the digest.
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.
they may qualify please self-identify to me, off-list, in an email. It
is my goal to bring as many diverse backgrounds and points of view as
possible into this meeting, because that is what makes for the most
productive discussions.
-James Holton
MAD Scientist
On 5/2/2022 12:35 PM, James
g toward a brighter future, will inspire even more visionary and
collaborative ideas for the role structure will play in that future. I
can't imagine a better theme of discussion for this next meeting.
-James Holton
MAD Scientist and Chair of the 2020/2022 Diffract
I have found I usually need to run an mtz through "CAD" in order to
sanitize it after doing things in sftools and other programs that . CAD
is kind of my "make it a cannonical mtz again" program.
HTH
-James Holton
MAD Scientist
On 4/5/2022 6:47 AM, Eleanor Dodson wrote:
running shelxd.
-James Holton
MAD Scientist
On 3/16/2022 5:21 PM, Jessica Bruhn wrote:
Hi all,
I am wondering if there is a way to limit the number of CPUs that can
be used by SHELXD. It seems that this program uses all that are
available until it hits the NTRY you specified or it finds a
? If you don't have a working N2 gas stream and are on
a budget they are not that hard to build:
https://doi.org/10.1107/S0021889894006357
Cheers,
-James Holton
MAD Scientist
On 1/26/2022 9:25 AM, Guenter Fritz wrote:
Dear Dom,
thanks a lot. Yes, this might work sending a combipuck alon
With x-ray data in hand, I've been multiplying this whole thing by Rwork
and trying to find clever ways to minimize the product. Rfree is then,
as always, the cross-check.
Or does someone have a better idea?
-James Holton
MAD Scientist
On 1/13/2022 11:14 AM, Tristan Croll wrote:
Hard
ut alternatives.
I.E. What if we could train an AI to predict Rfree by looking at the
coordinates?
-James Holton
MAD Scientist
On 12/21/2021 9:25 AM, Pavel Afonine wrote:
Hi Reza,
If you think about it this way... Validation is making sure that the
model makes sense, data make sense and
u have the time!
Free and open to all, and be sure to mute your mic.
Here is the link:
https://lbnl.zoom.us/j/91028154433
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following l
Thank you everyone for your interest in Erica's talk, which went great!
Not up on the website yet, but here is a quick gdrive link to the
video. enjoy!
https://drive.google.com/file/d/1uyCJpOkJxE77l5jsMzgfEp_BNBPdhxTI/view
-James Holton
MAD Scientist
On 12/8/2021 9:06 AM, James H
Starting in 10 min!
https://lbnl.zoom.us/j/97680529569
On 12/8/2021 9:06 AM, James Holton wrote:
Greetings all!
At 3pm PST Dec 8, 2021 (California time),
I managed to get Erica Saphire to speak about her recent work at the
ALS Colloquium. It is a forum for users and staff of the Advanced
Good news! Erica's talk will be recorded! I will update on this thread
when the link is up.
Goodnight Europe,
-James Holton
MAD Scientist
On 12/8/2021 11:16 AM, Gerlind Sulzenbacher wrote:
Dear James,
thank you so much for putting into place all these outstanding seminars.
Here a
Thank you all,
I appreciate the convenience if it can be recorded. I know Jennifer
Doudna's talk was recorded, but there seems to have been some delay
getting it hosted.
I will provide updates ASAP. Hopefully before Europe falls asleep tonight.
-James Holton
MAD scientist
On 12/8/20
ht be of interest if you have the time!
Free and open to all, and I'm not sure if this is being recorded or
not. Here are the links:
https://lbnl.zoom.us/j/97680529569
https://als.lbl.gov/news-events/seminars/
-James Holton
MAD
ree started
to take a turn for the worse, and you can do this without ever looking
at Rfree!
Of course, it is always better to not put in bad waters in the first
place, but sometimes its hard to tell.
Anyway, I suggest using a watershed-ed model as your reference.
Hope that is helpful in som
just
the right compression ratio I could get slightly better Rfree. But that
is not something I'd recommend as a good idea.
-James Holton
MAD Scientist
On 11/1/2021 2:22 AM, David Waterman wrote:
Hi James,
What you wrote makes lots of sense. I had not heard about Rsleep, so
that
just being processed in different ways, first
make a choice about what you are interested in, and then optimize on
that. just don't optimize on Rfree!
-James Holton
MAD Scientist
On 10/27/2021 8:44 AM, Murpholino Peligro wrote:
Let's say I ran autoproc with different combinations
Hello all,
Jennifer Doudna Lecture starting in 30 minutes! 3 pm CA time (PDT).
Zoom link: https://lbnl.zoom.us/j/96095492358
See you there,
-James Holton
MAD Scientist
On 26 Oct 2021, at 22:19, James Holton wrote:
Greetings all,
This year I have the honor of co-organizing the ALS
ntibody Therapeutics and
Stabilized Spike"
See you in the zoom!
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP
t me if
I'm getting something wrong. And the community benefits from the
discussion.
Thank you for your thoughtful and thought-provoking insights!
-James Holton
MAD Scientist
On 10/19/2021 2:05 AM, Gergely Katona wrote:
Dear James,
I am sorry to nitpick, but this is the answer to "wh
le prior distribution is Poissonian with
mean=variance= N/F/Q photons/pixel ?
-James Holton
MAD Scientist
On 10/17/2021 11:30 PM, Frank von Delft wrote:
Thanks, I learnt two things now - one of which being that I'm credited
with coining that word! Stap me vittals...
If it's s
pixel case:
Iobs = 1
sigIobs = 1
but in both cases the distribution is NOT Gaussian, but rather
exponential. And that means adding variances may not be the way to
propagate error.
Is that right?
-James Holton
MAD Scientist
On 10/18/2021 7:00 AM, Kay Diederichs wrote:
Hi James,
I'
Bayesian perspective then this will not help,
unfortunately.
Best wishes,
Gergely
-Original Message-
From: CCP4 bulletin board On Behalf Of James Holton
Sent: den 16 oktober 2021 21:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] am I doing this right?
Thank you everyone for yo
currently aware of.
I am confident a solution exists, but only recently started working on
this. So, I figured ... ask the world?
-James Holton
MAD Scientist
On 10/17/2021 1:51 AM, Frank Von Delft wrote:
James, I've been watching the thread with fascination, but also the
confusion of
mple and loop in microns
exposure = exposure time in seconds
flux = incident beam flux in photons/s
1.2e-5 = 1e-4 cm/um * 1.2 g/cm^3 * 0.2 cm^2/g (cross section of oxygen)
If you don't know anything else about the sample, you can at least know
that.
Or am I missing something?
-James Holto
s, but I think at least two of
those are incorrect,
-James Holton
MAD Scientist
On 10/13/2021 2:34 PM, Filipe Maia wrote:
I forgot to add probably the most important. James is correct, the
expected value of u, the true mean, given a single observation k is
indeed k+1 and k+1 is also the mean sq
r than one, but these days with
small crystals and big detectors N=1 is no longer a trivial situation.
I look forward to hearing your take on this. And no, this is not a trick.
-James Holton
MAD Scientist
To unsubscribe fro
Talk on laser plasma x-ray light sources starting in 5 min!
Here's the zoom link. Open to all.
https://lbnl.zoom.us/j/95338327083
On 9/29/2021 12:24 PM, James Holton wrote:
Greetings all,
This year I have the honor of co-organizing the ALS Colloquium Seminar
series. This is norma
antibody technology from all over the world together to fight SARS-CoV-2.
I think we've got a pretty good lineup!
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www
ack
One final run through "cad" to clean things up and make sure you have
the right asymmetric unit.
That's what I do, anyway,
-James Holton
MAD Scientist
On 8/31/2021 3:04 AM, Eleanor Dodson wrote:
Espec. Jan & Kay,
I had better check this out - ville wrote the code I
I use pdbset, coordconv and sftools a LOT. Usually for things no other
programs do, like converting to fractional coordinates, and performing
math operations on mtz data. Always from command line scripts.
-James Holton
MAD Scientist
On 8/26/2021 3:29 AM, Robbie Joosten wrote:
Dear CCP4
ny help or advice is much appreciated.
Thank you for maintaining pdb2ins !
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP
What about proteins where the crystals don't diffract well? I've found
in my teaching experience that students take your advice much more
seriously when they see it work on 3.5A data than they do when they see
it work on 1.5 A data.
-James Holton
MAD Scientist
On 6/17/2021 7:40
ely, both bash and tcsh recognize "|" in
the same way. Unfortunately, they differ on how to re-direct output to a
file.
Oh, and that magic little "#!" that you put at the start of the first
line of the script is called a "shebang".
-James Holton
MAD Scientist
cupancy group alts incomplete 10
occupancy group alts incomplete 11
#--
Where, for this last one I demonstrate how you can select for various
things by making a scratch PDB file that contains only the atoms you
want to occupancy-refine.
Hope this helps!
Cheers,
-James Holton
MAD Scien
et" as a second command-line argument.
You can then perhaps copy-and-paste this to the relevant GUI window.
-James Holton
MAD Scientist
On 6/7/2021 3:35 AM, Marina Gárdonyi wrote:
Hi,
I didn't know that I can also enter keywords without a file! That is a
good note, thank you!!
Best regar
why leave the mean variation squared? I expect it is because it
is supposed to be proportional to temperature. Hence the name
"temperature factor".
-James Holton
MAD Scientist
On 5/27/2021 11:09 AM, Gergely Katona wrote:
Dear Jonathan,
In 1D sd may be intuitive, but in 3D it
Shiny!
On 3/31/2021 10:36 AM, David Schuller wrote:
https://www.haaretz.com/archaeology/.premium-somebody-in-the-kalahari-had-a-crystal-collection-105-000-years-ago-1.9670735
Somebody in the Kalahari Had a Crystal Collection 105,000 Years Ago
--
===
.
-James Holton
MAD Scientist
On 12/11/2020 4:42 AM, Phil Evans wrote:
Alpha-fold looks great and is clearly a long way towards answering the question
“this is the sequence, what is the structure?”
But I’ve always thought the more interesting question is “this is the
structure, what does it do
rystal form" or
different "crystal habit"? Or is it the same form, and just really
non-isomorphous?
Opinions?
-James Holton
MAD Scientist
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htt
a favorite
trick for this?
And in general, any suggestions or comments, or best of all home
experiment results would be great to hear. I believe that if we
collectively work the problem we will inspire more breakthroughs like
the Fozouni et al. paper below, and that will have a strong positi
ou have to distort the geometry. Turn the geometry
weight up too high and your R factors blow up. Turn the X-ray weight up
too high and you get badly distorted geometry. I think we've all
experienced that?
-James Holton
MAD Scientist
On 12/3/2020 8:29 PM, Jon Cooper wrote:
Hello James
turn the X-ray weight term down to zero ... the
molecule blows up in my face?
-James Holton
MAD Scientist
On 12/3/2020 3:17 AM, Isabel Garcia-Saez wrote:
Dear all,
Just commenting that after the stunning performance of AlphaFold that
uses AI from Google maybe some of us we could ded
I use mapslicer
-James Holton
MAD Scientist
On 10/8/2020 2:21 PM, Gloria Borgstahl wrote:
What is the best way to display Harker sections... these days?
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I think if we work together this might actually work. Please do let me
know if I missed anything!
-James Holton
MAD Scientist
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ein, but flatten the
solvent. You can get this map out of refmac using the MSKOUT feature.
You then smooth it in reciprocal space by applying refmac's best-fit
solvent B factor using sfall and fft, then finally scale it with
mapmask. I should admit, however, that I have not tried this in a
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