this is suitable for a
solvent molecule disordered on a special position of higher symmetry
than the molecule can take".
I use PART 1/PART 2/PART 0 all the time in "small molecule world" but
I've used PART -1 precisely once.
Phil Jeffrey
Princeton
On 2/6/20 4:15 PM
gt to resume his quest for
overextended naming rationales, of which ValLigURL is a personal
'favo[u]rite'. But I'm just old-fashioned.)
Ironically,
Phil Jeffrey
Princeton
[* I too have collected 540 degrees in P1 to solve a SAD structure, just
because I could, hence "
me issues in phenix.refine are: real
space refine subprocess sometimes "unrefines" my structure (try turning
it off); there appears to be enough of a difference between first and
subsequent passes of the weight estimation that the weight-refinement
scheme gets thrown off.
Phil Jeff
s beyond just lowering the expected %
homology. Or if anyone has had success with other programs. This is
perhaps a rare edge case but I naively expected Phaser to work.
In the end I used the weak SeMet sites to locate the monomer and the
occupancy appears to be around 0.32 in refinemen
he advice of Dale, I would play around
with the % homology to find the value which works best.
My 2 cents,
Herman
-Ursprüngliche Nachricht-----
Von: CCP4 bulletin board Im Auftrag von Phil Jeffrey
Gesendet: Donnerstag, 10. Dezember 2020 14:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Finding par
n fraction approaches 0.5. The
latter difference can easily be less than sigma(I), and so the
signal/noise of your data plummets.
Better to use REFMAC and phenix.refine's abilities to compensate for the
twin fraction directly in refinement and leave your data as it is.
Phil Jeffrey
Princet
ing
much changes. That would need to be quantified in some way(s).
Phil Jeffrey
Princeton
[* Your R-free is also initially model-biased in cases where the data
are significant non-isomorphous or you're using two different xtal
forms, to varying extents]
I still don't understand how
ake it a SAD dataset. ALL datasets contain some
anomalous/dispersive signals, most of the time way down in the noise.
Phil Jeffrey
Princeton
On 1/18/12 12:48 PM, Francis E Reyes wrote:
Using the terms 'MAD' and 'SAD' have always been confusing to me when
considering more
own fluorescence scan. The advantage of
structural metals is full occupancy and relatively lower B-factor.
That map was actually pretty good, and since it came out of MLPHARE I
don't doubt modern programs like SHARP could make it quite a lot better.
Phil Jeffrey
Princeton
On 3/6/12 3:
e new map coefficients - so I don't see the benefit of Fc.
The map coefficients, on the other hand, are a checkpoint of the maps
being looked at by the author at the time of deposition and don't
require programs beyond a typical visualization program (i.e. Coot) to view.
Phil Jeffrey
Pr
Wolfram,
Did you solve these structures independently by molecular replacement ?
It sounds like your two solutions might be related by alternative
origins (0,1/2 along a,c). If you translate the second example along
the a axis by -a/2 does it refine with similar R-factors ?
Phil Jeffrey
ion data from
Scalepack differs depending on what space group you tell it, since
systematic absences along h00, 0k0 and 00l in P2x2x2x are not written
out. The number of reflections affected is quite small, of course.
Phil Jeffrey
Princeton
On 5/7/12 4:48 PM, Jacob Keller wrote:
Is it true th
Faculty Position
Department of Molecular Biology
Princeton University
The Department of Molecular Biology at Princeton University invites
applications for a tenure-track faculty position at the assistant
professor level. We are seeking an outstanding investigator in the area
of biochemistry a
s, so it's impossible to
tell which statistic they are reporting. The editorial/proof-reading
staff at journals aren't catching this ambiguity.
I personally report but wrote my own program to do it from
the .sca files.
Phil Jeffrey
Princeton
olicy about handling reflections
with |F|=0. The loss of reflections would manifest in a difference
between the completeness in data collection and the completeness in
refinement.
Phil Jeffrey
Princeton
find . -name '*.osc' -or -name '*.img' -type f -size +3000 -print -exec
bzip2 '{}' \;
is a personal favorite, along those lines, with ample opportunities for
customization. (If the above command line wraps, it's all supposed to
be on one line)
Phil J
n one case that ritually defeats me with quite strong pseudo-centering,
this seems to be true for heavy atom searches also.
Phil Jeffrey
Princeton
On 2/9/11 5:08 PM, Jon Schuermann wrote:
I would NOT use Phaser for MR with PTS present. It doesn't handle it
correctly yet, since the likeliho
Postdoctoral position at Princeton University
A position is available in the laboratory of Prof. Fred Hughson to apply
biochemical and structural approaches to the study of bacterial
cell-cell communication, also known as quorum sensing. We are especially
interested in the receptors bacteria u
The CCP4 program UNIQUE does this.
http://www.ccp4.ac.uk/html/unique.html
"UNIQUE creates a unique list of reflections for a given unit cell with
a given symmetry up to a specified high resolution limit. The output
file can be used to complete a dataset (i.e. to give an MTZ file with
all allow
from the dot product of the
direction cosines of VL:VH and CL:CH1.
Phil Jeffrey
Princeton
tarique khan wrote:
Dear all,
I am trying to calculate elbow angle of my fab structure using a online
software developed by Robyn L. Stanfield /et. al/. but it is giving a
solution with the following
ac5 5.4.0077 (I'm apparently a Luddite)
Phil Jeffrey
Princeton
t.
However this thread appears to have reached the point where not much new
ground is being broken.
Phil Jeffrey
Princeton
.
Alternatively: everyone tries harder before synchrotron trips
Phil Jeffrey
Princeton
On 9/28/10 1:27 PM, Francis E Reyes wrote:
Hi all
I'm interested in the scenario where crystals were screened at home and
gave lousy (say < 8-10A) but when illuminated with synchrotron radiat
not let you change the Reply-To feature.
Phil Jeffrey
Kjeldgaard Morten wrote:
Unfortunately, It appears that JISCMAIL is using the outdated LISTSERV
software to run it's mailing lists, so there is not much hope of getting
such things as the [ccp4bb] subject tag and "reply to sender
Angstrom
data, then this may well give you enough information to proceed with at
least some laborious form of molecular replacement (and/or averaging
with the MAD/SAD map).
Phil Jeffrey
Princeton, NJ
Yi Xue wrote:
Dear all:
We already got nice crystals of a drug-protein complex, however, MR
Individual B's can also be restrained by non-crystallographic symmetry
and as far as I can tell grouped B's are not.
I think one has to explore all possibilities rather than take one fixed
approach to working at modest resolutions, and the optimal solution is
likely to be different fo
l for tests
other than twinning), both of which list the twin operators that they try.
Phil Jeffrey
Princeton, NJ
siva charan wrote:
hello
I have a data set to 2.4 A, which has space group of *P21 *. From the
cumulative intensity distribution graph, indicates that data is
twinned . To
Wouldn't the desirability of this depend on the extent to which the
molecule has moved between the high-resolution and low-resolution
datasets ? I would have thought that there was an effective information
transfer between R-work and R-free once the rigid body movements became
too large, which
k fix is to make your own copy
of scatter.lib and edit the files that reference it to pick up the local
copy.
Phil Jeffrey
Princeton
Jian Wu wrote:
Dear all,
I am refining a structure in which there is an fluorine atom in the
inhibtor. When I go on the energy minimization in CNS, an unusua
the CCP4 talk with
all these numbers in it, but I regret it's sitting on my iBook at home
as of writing.
Phil Jeffrey
Dean Madden wrote:
It is true that multicopy refinement was essential for the suppression
of Rwork. However, the whole point of the Rfree is that it is supposed
to be i
h the
inappropriate use of multi-copy refinement at low resolution.
Phil Jeffrey
Princeton
Dean Madden wrote:
Hi Dirk,
I disagree with your final sentence. Even if you don't apply NCS
restraints/constraints during refinement, there is a serious risk of NCS
"contaminating" your Rfree. C
t at anything
less than quite high resolution - I'm thinking in particular of a
comment in Chen & Chapman (2001) Biophys J vol. 8, 1466-1472. So I see
no reason to suggest NCS is having a particularly extreme, perhaps
unprecedented, effect.
Phil Jeffrey
(still working on converting Micro$loth Powerpoint to html)
imited
datasizeunlimited
stacksize 65536 kbytes
coredumpsize0 kbytes
memoryuse unlimited
descriptors 256
memorylockedunlimited
maxproc 100
Hope this helps,
Phil Jeffrey
Princeton
hari jayaram wrote:
Hi
Since I am not on the cnsbb yet I am posting this here.
I
timately it worked rather well.
Others might have more elegant ideas.
Phil Jeffrey
Princeton
Partha Chakrabarti wrote:
Hi,
Apologies for a non CCP4 question in strict sense. I am trying to work
out the NCS operators for a three wavelength
Se-MAD data which has only one site. The map is hardly inte
This is on OSX "Tiger" 10.4.11 on a G5 machine.
Phaser 2.1.1, CCP4 6.0.2
Is anyone else seeing the following ?
In a feature that seems new-ish in Phaser, intermediate solutions get
culled after translation function and before packing tests:
(begin snippet)
Purge solutions according to highest
37,451.8
Chain AC 35,576.6
Difference 1,875.2
Difference/2 937.6
For buried S.A. I agree with Steve Darnell's definition. However PISA
appears to be reporting half that value, or what it calls "interface
area".
out.
OSX has minor quirks, like the patch to make OSX treat e.g. the
filenames MyJunkData.sca and myjunkdata.sca as the same file rather than
the expected Unix behavior. But in practice I rarely find this to be an
issue.
Phil Jeffrey
Princeton
Sheemei wrote:
Dear all,
I am thinking of
, you should
consider tolerating a few ill-humored replies - at least that particular
responder didn't post to the entire list.
Phil Jeffrey
Marius Schmidt wrote:
Interesting, isn't it? :-), nice person.
[rest of content removed]
et to update the JRNL reference.
I believe that the lead time is unnecessarily long. Perhaps one day
might be more reasonable.
Phil Jeffrey
Engin Ozkan wrote:
I agree that the pdb deposition process has gotten better, but I still
regularly have issues with releasing of newly published struc
It also has the same/analogous bug in space group P3 with Pointless
v1.2.10 - I wasn't sure if I was missing something obvious and went back
to using my default combination of REINDEX/SCALEIT for the tests and
reindexing.
Phil Jeffrey
Princeton
Robert Nolte wrote:
An output file is cr
ke if one is familiar) but the
helices in one of the other subunits (A) were actually nicely resolved.
Excitement may be warranted, even at 6 Angstrom.
Phil Jeffrey
Princeton
The cadmium-utilizing marine diatom carbonic anhydrase (CA) protein has
three consecutive CA domains that have very similar structures but
non-identical sequences.
See:
Structure and metal exchange in the cadmium carbonic anhydrase of marine
diatoms.
Xu Y, Feng L, Jeffrey PD, Shi Y, Morel FM.
PCMBS etc so if you were especially concerned about that, start with the
latter compounds. I'd also probably try Me3Pb(OAc) as an alternative to
mercurials.
Phil Jeffrey
Princeton
ts from the Chooch analysis of the
scan from the actual crystal.
Cheers (and good luck)
Phil Jeffrey
Princeton
Jerry McCully wrote:
Dear All:
Next week we are going to try some seleno-Met labeled crystals.
We checked the literature to try to find out the peak wavelength
that has
You could always use a larger mask for
this step and a smaller one for the MAVE/Expand step.
Phil Jeffrey
Princeton
Rana Refaey wrote:
Hi,
I have two maps from two different crystals with the same space group, both
show an unknown density in the same place. I wanted to superimpose the ma
is, none of the data processing
programs or suites of programs has implemented this as far as I know. A
Phil Jeffrey
Princeton
solve it in P1 and find the space group "by
inspection" afterwards
Phil Jeffrey
Princeton
e the TRUNCATE YES option in Truncate ?
Does the output MTZ from Scalepack2mtz show the number of reflections
you expect ?
Phil Jeffrey
Princeton
On 7/5/13 3:24 PM, Ursula Schulze-Gahmen wrote:
Sorry for the non-CCP4 question.
I am confused about the sigma cutoff used by HKL2000 for scaling. I
sca
imately whatever
formats come next)
Using mmCIF as an archive format makes sense, but I doubt it's going to
make building structures any easier except for particularly large
structures where some extended-PDB format might work just as well or better.
Phil Jeffrey
Princeton
On 8/5/13 9:5
On 8/7/13 8:27 PM, Ethan Merritt wrote:
That would be a bug. But it hasn't been true for any version of coot
that I have used. As you say, this is a common thing to do and I am
certain I would have noticed if it didn't work. I just checked that
it isn't true for 0.7.1-pre.
Thanks.
Turns out I
correlation
between the two halves of the P21 asymmetric unit if it was really
P212121 and you could overlap the maps corresponding to the different
monomers using those programs.
Phil Jeffrey
Princeton
m via URLs like:
ftp://ftp.rcsb.org/pub/pdb/data/structures/obsolete/XML/js/1jsq.xml.gz
Phil Jeffrey
Princeton
On 10/17/13 10:26 AM, Nat Echols wrote:
On Thu, Oct 17, 2013 at 6:51 AM, Lucas mailto:lucasbleic...@gmail.com>> wrote:
I wonder if there's a list of problematic structures
rystal form. I hope you don't have something like that, but it's possible.
Phil Jeffrey
Princeton
On 11/14/13 5:22 PM, Niu Tou wrote:
Dear All,
I have a strange MR case which do not know how to interpret, I wonder if
any one had similar experiences.
The output model does not fit into th
ve things, consider the possibility
that the fourth molecule is not what you think it is, or may be
statistically disordered
Phil Jeffrey
Princeton
On 11/21/13 12:35 PM, Meisam wrote:
Dear CCP4ers
I have a data set that diffracts 1.96 Å. It scales in P21 Space group with 7%
linear Rfactor.
The
x27;m a Luddite so I use emacs and/or
grep for this.
Phil Jeffrey
Princeton
11/21/13 1:11 PM, Appu kumar wrote:
Dear All,
I think i have not explained my problem precisely. This
may be weird one but let me elaborate more. I have have a protein
moleculeA, having N-term,
o the expedient thing and drop an Au in
there with e.g. 0.5 occupancy (or a range of occupancies) and see what
the refinement does.
Phil Jeffrey
Princeton
On 12/10/13 7:44 AM, PriyankMaindola wrote:
dear members
i am trying to solve this crystal structure but
I am puzzled with an
undefined
mple chamber and about 80x the Kd in the injector. That's not exactly
the same situation, but 80x vs 170x suggests the the considerations are
much the same.
Phil Jeffrey
Princeton
On 2/14/14 12:52 PM, Keller, Jacob wrote:
What a nice idea this ITC dilution is--a great example of
d with the relevant PDB
file(s).
Phil Jeffrey
Princeton
On 5/14/14 1:37 PM, Gloria Borgstahl wrote:
I vote for Z's idea
On Wed, May 14, 2014 at 12:32 PM, Zachary Wood mailto:z...@bmb.uga.edu>> wrote:
Hello All,
Instead of placing the additional burden of policing on the good
del is in
fact the only reasonable explanation of your data.
But as it stands it is rather atypical and it warrants further investigation
Additional evidence that your C2 cell is the only reasonable model would
be identifiable electron density differences between each chain in your
(presumed) multi
axis
so that refinement programs will treat this as a special position water
and eliminate the extra one - i.e. make it as close as possible to its
symmetry mate.
Phil Jeffrey
Princeton
On 3/11/19 12:09 PM, Firdous Tarique wrote:
Hello everyone
I am having a difficult time fitting a water
t problems
with the molecular replacement search.
Phil Jeffrey
Princeton
On 8/29/19 11:28 AM, Napoleão wrote:
Deal all,
Sorry for the long post.
I have a data set obtained from a crystal produced after incubating a
protease with a protein which is mostly composed by an antiparallel beta
te
deviations between previously identical monomers in the map and probably
consider using NCS to reduce the random deviation between monomers that
actually are identical by symmetry. You may have assigned the
crystallographic 21 down the wrong unit cell axis in that P21 test case.
Phil Je
respect to fractional - for most space groups "ncode 1" is often used
but for primitive monoclinic "ncode 3" is sometimes used, and I think
the matrix shown in Kevin Cowtan's document above corresponds to "ncode 1".
Phil Jeffrey
Princeton
On 9/4/14 3:55 PM, Ch
find the
*other* fragment in the context of that first solution.
Phil Jeffrey
Princeton
On 10/5/14 3:34 AM, Luzuokun wrote:
Dear all,
I’m doing molecular replacement using Phaser. My protein is predicted to
have two domain with a “hinge” linking them. The model sequence identity
is 0.27. But
the phases are
pretty good. It's usually not as strong as difference density for
hydrogens, before you put them in, but it's often pretty clearly visible
once you have.
(I use SHELXLE as an interface for small molecule refinements because of
a somewhat Coot-like experience in view
I would have thought that what the indexing routine defined as [001] vs
[00-1] would be essentially random as one would obtain the equivalent
indexing in 622 in both "up" and "down" alignment of the
crystallographic a/b/c axes with respect to crystal morphology.
Phil Jeffr
CIF but I do for the reverse
case).
Thanks
Phil Jeffrey
Princeton
d not _refine.ls_d_res_high but there are several where the resolution
of refinement is apparently significantly higher than the resolution of
the source data: 1AU7, 1AW7 etc.
Cheers
Phil Jeffrey
Princeton
On 7/8/15 10:04 AM, Jose Manuel Duarte wrote:
This looks like the mapping you are after:
nd Lp-corrected so I want to avoid applying things twice.
Thanks
Phil Jeffrey
Princeton
ked the "I/sigI" reported by
Scalepack in the log file is / and not for the
shell. The PDB format in REMARK 200 wants the latter.
One of these days one hopes RCSB might include Rmeas in REMARK 200.
Phil Jeffrey
Princeton
On 7/31/12 8:54 AM, Faisal Tarique wrote:
Dear all
i have two
90.000
EOF
#
#
scala hklin scalepack.mtz hklout scala.mtz \
scales scala.scales \
rogues scala.rogues \
normplot scala.norm \
anomplot scala.anom <Corrections, comments or outright repudiation of this script quite
welcome - this was my first attempt.
Phil Jeffrey
Princ
, rotation function peaks relating
different domains in the same molecule should show very similar alpha,
beta and differ in gamma.
Good luck,
Phil Jeffrey
Princeton
On 10/26/12 8:27 AM, Seijo, Jose A. Cuesta wrote:
Hi all,
I am dealing with a molecular replacement problem for a 60KDa protein
Perhaps it's an artisan organic locavore fruit cake.
Either way, your *crystal* is not vitrified. The solvent in your
crystal might be glassy but your protein better still hold crystalline
order (cf. ice) or you've wasted your time.
Ergo, "cryo-cooled" is the descr
work.
I'd echo Nat's suggestion of going 3rd party for the memory and putting
in as much as you can afford.
(Modern Mac Minis and even my 13" Macbook Pro outperform my older
octacore tower on a per-core basis. They're quite capable machines.)
Phil Jeffrey
Princeton
On 1/22
ure for you, starting from the molecular replacement solution
(or, perhaps with it stripped to ALA). While you could use Autobuild,
this is the CCP4 list and so you should use CCP4 programs.
Phil Jeffrey
Princeton
On 3/27/13 12:22 PM, Tom Van den Bergh wrote:
Dear members of ccp4bb,
I need so
guidance that RCSB gives about this field is very weak, which accounts
for the variation.
I'm interested in what "ab initio phasing" really means, but I've been
too lazy to mine the actual entries for details.
Phil Jeffrey
Princeton
On 4/15/13 9:48 AM, Raji Edayathumang
n Truncate or Xtriage I
wouldn't suggest that.
A final question is how much disordered structure is missing from your
models ? Could a partly ordered but unmodeled segment be driving up
R-free ?
Cheers
Phil Jeffrey
Princeton
On 4/26/13 5:38 PM, Patrick Loll wrote:
Hi all,
Here is a p
ese
scripts, but that would make this post too long.
If still in print I recommend the "C shell Field Guide" by Anderson and
Anderson if you want to get further into Csh scripting. Python's also
not a bad option. At all costs avoid Perl.
Phil Jeffrey
Princeton
On 5/8/1
http://skuld.bmsc.washington.edu/scatter/AS_periodic.html
http://skuld.bmsc.washington.edu/scatter/data/Sr.dat
Would probably work for initial values. 9700 eV for that wavelength.
https://people.mbi.ucla.edu/sumchan/crystallography/ang-eV_convertor.html
Phil Jeffrey
Princeton
On 1/22/21 2:36
olecule disorder so that comes ahead of adding
hydrogens, and refining unrestrained anisoB (as is the default) for
disordered atoms is asking for trouble. It's not as cookie-cutter as
you represent, and I stick to all my suggestions.
Phil Jeffrey
Princeton
On 6/4/21 4:27 AM, Harry Powell
CCP4's PEAKMAX program would be quite scriptable.
Phil
On 10/27/21 1:58 PM, Murpholino Peligro wrote:
So... how can I get a metric for noise in electron density maps?
First thing that occurred to me
open in coot and do validate->difference map peaks-> get number of peaks
(is this scriptable?)
o
maps at 1.4 Å, although the bond length issue could be quite subtle.
Phil Jeffrey
Princeton
mimicking like ATP bound state, surrounded and
coordinated by two metal ions(resolution is 1.4A). There is a change in
space group (from I212121 to P212121 ) and further important
conformation changes are
to invert one. Unless you actually wanted Fourier coefficients it
shouldn't be impossible to create a masked volume of the difference
between two maps after rotating one of them.
Phil Jeffrey
Princeton
On 3/10/17 5:24 PM, Oleg Zadvornyy wrote:
Dear All,
We are working on a tetrameric pro
not to the list.
Thanks
Phil Jeffrey
Princeton
0Å with 75%
solvent - PDB 4U6U). If you were missing half your asymmetric unit from
your model, Rwork would be held up in the mid-30% range and there would
be regions of relatively high difference density outside the model.
Phil Jeffrey
Princeton
On 7/11/17 12:31 PM, Koromyslova, Anna wrote:
embraces both excellence and
diversity.
See the link:
https://puwebp.princeton.edu/AcadHire/apply/application.xhtml?listingId=2821
Applications must be received by October 31, 2017.
Note: I'm just the messenger and not involved at all in the search process.
Phil Jeffrey
Macromole
protected by law.
For questions not covered by the application URL above, email Prof.
Hughson at hugh...@princeton.edu
Cheers
Phil Jeffrey
Princeton
t implicit. You must
specify it but preferably don't report it at all, and just use it for
diagnostic purposes.
Phil Jeffrey
Princeton
On 10/16/17 11:02 AM, James Holton wrote:
If you suspect that weak data (such as all the spot-free hkls beyond
your anisotropic resoluiton limits) ar
R=50% at a resolution of 2.2 Å is a lot different to 50% at, say, 3.5 Å
resolution. What happens if you refine it at 3.0 or 3.5 Å ?
What's the model vs sequence % identity ?
Phil Jeffrey
Princeton
On 11/17/17 3:23 PM, Yue Li wrote:
Dear all,
I have several datasets (one best resol
? Do I simply define a new version of the
monomer (w/o errant hydrogen) and hope that it overwrites the previous
definition ?
I'm doing this at borderline atomic resolution.
Thanks
Phil Jeffrey
Princeton
e
atoms are.
Put your disordered Arg in with 10 alternate conformations, each with a
refined relative occupancy, and then let the B-factors smear that lot
out, and that's your better model.
Phil Jeffrey
Princeton
To uns
will inherently allow their correct
relative placement to be modeled. If you managed to get TFZ of 42 with
flawed models, this should be a pretty easy thing to pull off, but if
not please contact me off list.
Phil Jeffrey
Princeton
On 3/27/23 1:52 PM, Kher, Gargi M wrote:
Hello,
I obtained di
files.
Phil Jeffrey
Princeton
On 4/20/23 4:02 PM, Ning Li wrote:
Hi all,
Does anybody know why I got this error message:
/Checking for embedded fcf data in CIF .../
/No extractable fcf data in found in CIF/
as I uploaded the CIF file to https://checkcif.iucr.org/
<https
be
able to feed it into POINTLESS and AIMLESS for scaling
4. On the model front, go find an AlphaFold model, they have worked for
me multiple times in molecular replacement so far.
Phil Jeffrey
Princeton
On 8/2/23 3:00 PM, CENGIZ KAAN FERAH wrote:
Hello,
So I'm trying to get
n't love being cross-linked, and I would call this a
successful instance of a desperation maneuver.
Good luck.
Phil Jeffrey
Princeton
On 11/22/23 11:44 AM, Blake, Morgan Elizabeth wrote:
Hello
I am a PhD student working on a crystallography project to wrap up my
dissertation research. I h
:: 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 boring thing that there has never been a
formal mathematical proof that finding the prime factors of very l
ould fix that. Also that chem_comp.name seems to be
associated with a variety of ligand IDs with different formulae and also
turns up as a synonym of others. Things seem to be a little wayward in
there.
Phil Jeffrey
Princeton
On 4/26/24 10:40 AM, Diana Tomchick wrote:
But I think that is a m
It says in aforementioned docs:
"Alignment of one-letter atom name such as C starts at column 14, while
two-letter atom name such as FE starts at column 13.
"
and no, hopefully they don't mean that, since their example shows plenty
of 2-letter and 3-letter atom names starting at column 14 in t
Laboratory, Warrington,
UK (1980)
Phil Jeffrey
On 7/30/24 11:44 AM, Pavel Afonine wrote:
From this perspective, all refinable atomic model parameters can be
viewed as trash bins, with the size of these bins being proportional to
the amount of prior information (restraints) imposed on these
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