Hello Harry
Any of the top 50 on distrowatch.com will basically be fine and the next 20 or
so on the list will probably be fine. Then you start getting into the twilight
zone. I am sure that will help greatly to narrow down your choice ;-0
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
I can see the file here:
https://github.com/martynwinn/Uppsala-Software-Factory/tree/master/voidoo
Hope that will help.
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Original Message
On 10 Apr 2024, 12:05, Ankur Kumar Singh wrote:
> D
Gemmi is probably easiest.
gemmi sf2map -s3 --mapmask=my.pdb my.mtz my.map
Vary s (sampling) according to taste ;-0
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Original Message
On 6 Apr 2024, 12:00, Cryo EM wrote:
> Hi all,
&g
how I know, but you can get Rfree values lower than Rwork at
this point. Combine this with low completeness and perhaps that is what is
happening.
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Original Message
On 28 Feb 2024, 16:21, Justin Cru
This should all go fine. You can maxi- or mini-prep the plasmid DNA from the
expression strain and transform it back into a cloning strain for sequencing,
etc.
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Original Message
On 19 Feb 2024
Thank you for clarifying that. It may not be much consolation but I thought it
might be useful to know that there are no problems with running mapslicer from
the command line on linux but my font could be better ;-0
https://u.cubeupload.com/jbcooper/mapslicer.png
Best wishes, Jon Cooper
You could search for peaks of decreasing height by stepping back through
through alphabet with your text searches. Of course, peakmax will do a good job
of finding them anyway.
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Original Message
searching with a text
editor pretty easy just by searching for the characters corressponding to the
high values. I don't know if that's any use.
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Original Message
On 18 Feb 2024, 03:29, Bernhard Rupp
From your refmac refinement job in i2, this should give you the combined mtz?
[test.jpg]
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On Friday, 9 February 2024 at 17:54, Palm, Gottfried
<b793af054fc6-dmarc-r
- bit hard for mac
users, I know ;-0
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Original Message
On 9 Feb 2024, 17:54, Palm, Gottfried wrote:
> Dear all,
> I have problems preparing my experimental data (XRD) for deposition. I have
>
Limited proteolytic might help, too.
https://www.nature.com/articles/nmeth1118
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Original Message
On 5 Feb 2024, 10:27, kavyashreem wrote:
> Dear All,
>
> Has anyone worked on a prot
I have one or two in my garage ;-0
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Original Message
On 27 Jan 2024, 19:46, Randy John Read wrote:
> Hi, The current policy of the PDB is that you can deposit a re-refinement of
> a str
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Original Message
On 25 Dec 2023, 09:52, Dale Tronrud wrote:
> Hi, I wanted to correct a statement by Prof. Peat about the ionic state of
> phosphate in solution. Phosphate has four
, but the fractional atomic coordinates remain
relatively unchanged (right?) so bigger unit cell differences still allow the
method to work.
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Original Message
On 21 Dec 2023, 09:07, Harry Powell wrote:
>
ay, 20 December 2023 at 22:21, Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> Unless you have a degree in maths, the IUCr's "Little Dictionary of
> Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension on
> this matter (it
n for dumb biologists might
be to say that A and B are isomorphous, but C isn't.
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Original Message
On 20 Dec 2023, 20:15, Hekstra, Doeke Romke wrote:
> Dear colleagues,
>
> Something
Hello, you seem to have positive difference density for the Cys sulphur/sulfur
atom. It would be worth checking it's occupancy.
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Original Message
On 18 Dec 2023, 17:03, Liliana Margent wrote
Hello, it doesn't look like a phosphate very much, to be honest, and being so
close to the carboxylate suggests it isn't. Is there any chance that it is an
alternative conformation of the Arg side chain? If you model it as water, is
there residual positive difference density?
Best wishes, Jon
).
- - - - - - - - - - - - - - - - - - - - - - - - - -
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Hello, it sounds like a monomeric protein which has been cleaved in 4 places so
that would not give it 'quaternary' structure. If the nicked monomers assembled
into dimers or timer, etc, then it becomes quaternary.
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an implementation
of NCS refinement that was a bit different from current progs. Ian will know ;-0
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Original Message
On 21 Nov 2023, 20:27, Albert Castellvi Toledo wrote:
> Also forget to obse
How does it look with gl gl... glycerol fitted ;-?
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Original Message
On 15 Nov 2023, 14:00, Rafal Dolot wrote:
> Hello everyone,
>
> I need help identifying the ligand I found on the
of RSC Networks for
uploading them to YouTube.
Best wishes,
Peter Morris
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Hello Oliviero
If you look in the ccp4bb archive (my apologies if you already have) there are
quite a few posts about this at the end of July - early Aug 2020 i.e. >3 years
ago. A quick look shows that the options then were mainly based on 2nd hand
bits and bobs, though.
Best wishes,
Hello, unless it's changed over the last couple of years, the pdb rightly used
to let you deposit a structure with outliers, hopefully not too many, though ;-0
I take it the stalling you reported probably comes from whoever is looking over
your shoulder.
Best wishes, Jon Cooper. jon.b.coo
page:
https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
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--- Original Message ---
On Wednesday, September 20th, 2023 at 22:23, Jon Cooper
wrote
I am also asking about remote access and recording as I not up to date on that
either. There will be a fairly detailed report in Crystallography News and
volunteers for writing it are most welcome ;-0
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Folk are reporting that registration is full, sorry. I will contact the
organiser and ask if there might be an overflow option.
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Original Message
On 20 Sept 2023, 22:23, Jon Cooper wrote
A reminder that the registration deadline for the free one-day RSC meeting on
British X-ray Crystallographers is fast approaching. More details can be found
here:
https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent
Hello, is it definitely due to the TLS refinement? I guess you have tried
without TLS and don't see the same effect i.e. the B-factors are more
consistent. It would be good to know.
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It looks like it is not applying the 90 degree phase shift for anomalous data.
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Original Message
On 2 Aug 2023, 14:32, Andrea Smith wrote:
> Dear Eleanor,
>
> yes, I made the pr
Hello, I don't do anything MAC but maybe shipping dewars would be a good
situation for an Apple Airtag, which I read about recently, or equivalent, if
there are any?
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Original Message
On 28 Jul
.
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Original Message
On 21 Jul 2023, 04:10, Lande wrote:
> Dear Eleanor and Jon,
>
> Thank you for your replies. My good datasets are in P212121 space group and
> unit cell 56.67 60.53
is just rotational NCS with a screw translation?
Others will probably disagree ;-0
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Original Message
On 18 Jul 2023, 10:06, Lande wrote:
> How to deal with tNCS? Dear all, I have read topics talk
The organiser has confirmed it is free.
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Original Message
On 26 May 2023, 22:30, Jon Cooper wrote:
> I've just registered as a non-member and there's no fee, right?
>
> Best wishes, J
Hello, is the CSO going into the PDB file as ATOM'S or HETATM's?
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Original Message
On 27 May 2023, 00:43, Nicholas Clark wrote:
> I have a cysteine residue that is oxidized and ne
I've just registered as a non-member and there's no fee, right?
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Original Message
On 24 May 2023, 09:26, Harry Powell wrote:
> Hi Jon “Preaching to the choir”! Harry > On 23 May 2023, at
I am biased, but this looks like an interesting meeting:
https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
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.
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Original Message
On 28 Apr 2023, 08:41, StrBio wrote:
> Hello,
>
> Can you suggest how to make isopeptide bond in coot and generate .cif file to
> refine the structure in phenix?
&
Hello, can you give us a screenshot of a diffraction image, with the caveat
that they never look all that good with fine-slicing, still it might help ;-0
Also, an idea of the R-merge, R-meas, CC-half in some of those space groups.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from
Hello Ian,
if I understand you and Eleanor correctly, this is the philosophy of the
mini-MTZ, i.e. if you are doing anything independent of i2, you have to dig
around a bit to find which output file contains the columns you need.
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Sent from
. it almost works reliably, unlike
before.
-
Better memory management - it can go through several hundred residues without
crashing!
-
New virtual server!
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--- Original Message
Hello, yes, the trimming and occupancy tricks can be confusing and they can be
a bit of a cheeky way to improve the model statistics. I prefer to build the
whole side chain and if you can't see all or part of it, then that's just too
bad, but I have erred.
Best wishes, Jon Cooper. jon.b.coo
Coot's ssm superposition does give the C-alpha rmsd, though, most easily seen
if you run it from a terminal window? I guess it can't be miles different from
a least-squares fit ;-?
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Original Message
Cheeky question: if its 'just' an asp script, a virtual private server is about
£10 per year. Does it need a huge database or something?
Cheers all, Jon Cooper
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Original Message
On 17 Jan 2023, 20:34, Janet Newman wrote:
> CSIRO has ta
Hello, are the data from serial crystallography? The redundancy and the CC's
are very good but the R-merge (an unpopular metric these days) is quite high?
Cheers, Jon Cooper2
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Original Message
On 6 Jan 2023, 08:17, 조규혁 wrote:
> Dear all,
>
> I
Dear Boaz
I think your original answer must have been steganographic ;-0 Maybe white text
on a white background ;-? Anyway, I can see it below now that I have started
typing this reply, and advice is excellent.
My answer to Rafael's question would be to look at apbs:
Hello, this sounds like a good case for electron density averaging which would
allow you to build one chain into the averaged density and then generate the
full set of 12 by NCS for refinement. Even better would be using the NCS in
refinement of the one chain you have built. Anyway, I would
I used to use the riding hydrogens from shelx when I was doing a neutron
refinement a few years ago, now. It might be worth looking at some recent
neutron papers to see how the H/D atoms are handled. I think it is mainly done
with phenix these days ;-0
If you have electrostatic calculations or
wishes, Jon Cooper.
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It'll just be Hugh hacking your system again ;-0
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Original Message
On 25 Sep 2022, 15:37, David J. Schuller wrote:
> CCP4 8.0.004
> Scientific Linux 7, kernel 3.10.0-1160.76.1.el7.x86_64
> mate-desktop-1.16.2-1.el7.x86_64
>
> This morning I updated
Cool, typed a long reply but only about 1/3 of it is still relevant and is
given below.
The crystal would have to be capillary mounted for these data collections or
the humidity controlled somehow. Only 253 K would be a good one to use.
Pre-cryo, this used to give good data at SRS! Interested
Hello, K will always have a higher B-factor for a given piece of density due to
it having a larger atomic number. Is the K B-factor much higher than those of
neighbouring atoms and, if not, it's probably the best interpretation? Cheers,
Jon.C.
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Original
Hello Jan
Not a very helpful suggestion, but using rcsb's ligand-expo site I did find
some structures of similar resolution in the PDB with jeffamine present. I
don't know if looking at them would be helpful and you have probably done that
already.
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Thank you very much for all the helpful replies. I have summarised the
discussion here:
https://justpaste.it/9cfl9
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s artificially introduced, could
> provide a clever algorithm (AI?) with the data basis to figure out those
> "fingerprints". Maybe even for the ASN/GLN/HIS side-chain orientations when
> the sequence is actually correct. Cheers Clemens On Fri, Jul 29, 2022 at
> 1
sequences, this may give you some answers for the ambiguities you might be
> seeing, if nothing else ..
>
> Jan
>
> On Fri, Jul 29, 2022 at 12:15 PM Jon Cooper
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, I am looking for suggestions of ways
Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray
sequence for a protein where it is impractical to do experimental sequencing,
protein or DNA. The structure refines to publishable R/R-free and the main
ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where
Hello again, as far as I can tell, the question is about two already
merged/unique datasets which Mirek wishes to merge into one. As far as I can
tell/remember, Scaleit is for scaling datasets side-by-side to get isomorphous
differences, etc, and I don't know of a way that you could get it to
Hello, I looked thru the program list in ccp4i and Combat caught my eye. Seems
you can input an MTZ file of amplitudes and output a multirecord MTZ, and you
can specify a batch number. If you did the same for your second dataset with a
different batch number you could then append them with
th best regards,
>> Sayan Saha
>>
>> On Fri, Jul 1, 2022 at 8:04 PM Jon Cooper
>> wrote:
>>
>>> Hello, I wonder if it is disorder i.e. alternative conformations of the Asp
>>> and flexible Lys.
>>>
>>> Do let us know your final i
Hello, I wonder if it is disorder i.e. alternative conformations of the Asp and
flexible Lys.
Do let us know your final interpretation as we don't often, or indeed ever,
hear the final outcome of these mystery density competitions and I would love
to learn more from them.
Cheers, Jon.C.
Sent
Hello, in P21, FFT swaps the axes around so Y will be the slowest changing axis
i.e. along W in the Patterson, I think.
How many atoms are in your model? Very hard to be sure it's not working as the
Patterson is so very convoluted with a large model.
Cheers, Jon.C.
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!
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--- Original Message ---
On Saturday, May 21st, 2022 at 00:20, Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> For info, barring disasters, the
.
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Original Message
On 7 Apr 2022, 01:03, Jon Cooper wrote:
> Thank you to those who replied a week or two ago about this. In the end, I
> put a revised version here:
>
> http://minimapai.de/
>
> I'm not sure if that (econo) dom
Hello, scaleit is for derivative-to-native scaling whereas the Fox and Holmes
method is generally for batch scaling and merging, as done, for example, by
scala and its successors, but it is all non-linear least squares, so the
methods will be fundamentally the same. Hope this helps a bit,
Hello, something like:
ccp4prog xyzin input.pdb > output.log
Or:
ccp4prog xyzin input.pdb > & output.log
if output.log already exists.
HTH, Jon.C.
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Original Message
On 11 May 2022, 15:48, Rafiga Masmaliyeva wrote:
> Hi.
>
> I run CCP4 CONTACT
Hello, I would try deleting the header records i.e. REMARKs, etc, leaving only
ATOMS and possibly HETATMs. Also, your filename (_2H ?) suggests the PDB file
has riding hydrogen atoms in it which might throw naccess off course. Best
wishes, Jon.C.
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Original
Hello, naccess and psa are golden oldies but there is areaimol in ccp4 which
might also help. For naccess, the best contact would be the author (Simon
Hubbard, Manchester). You could even say you were sent by his examiner ;-0
Good luck with it. Jon.C.
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Hello, could this be a case of the ZN not being shifted one place to the left
in the PDB file to give it the right scattering factor ? ? The progs are
pushing neighbouring atoms into the Zn density to account for its scattering
power ? ? Maybe these problems don't happen any more.
Sent from
, which might even be useful to somebody ;-?
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--- Original Message ---
On Monday, March 28th, 2022 at 16:33, Jared Sampson
wrote:
> Hi Phoebe -
>
> Your ema
PDBe
EBI.
Best wishes, Jon Cooper.
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I don't know for sure, but I think the -origin-hand thing would be for heavy
atom work where both enantiomers of the solution can fit the data. Cheers,
Jon.C.
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Original Message
On 18 Mar 2022, 04:02, 付兴科_201928000807036 wrote:
> Dear Colleagues,
>
One practical point: I had the same experience recently with a structure that
had been worked on by others previously. Refmac was automatically picking up a
data column from some earlier work, unknown to me, rather than the observed
data from XDS and the R-factors were sticking at the values
Hello, the ligand needs to be treated as one occupancy group since refining
individual occupancies would be a case of refining too many parameters, unless
it was a very fragmentary compound!! It is one keyword in refmac, but I can't
remember for phenix, sorry! Ta jc
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The diagonal elements of the scale matrix are 1/a, 1/b and 1/c for orthogonal
cells. It converts orthogonal coordinates to fractional. There should be more
info on the rcsb.org website or in the ccp4 documentation e.g. for pdbset.
Cheers, Jon.C.
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Original
I thought it was tryptophan but the nitrogen and extra bond are in the wrong
places so it must be a ligand and, if so, have you tried refining the
occupancy? Cheers, Jon.C.
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Original Message
On 22 Feb 2022, 05:34, S wrote:
> Hi All,
>
> I am
, James M wrote:
> Probably arginine and tyrosine do like each other a fair bit. They can form
> both cation-pi interactions and hydrogen bonds.
> Best wishes
> James
>
>> On 1 Feb 2022, at 16:41, Jon Cooper
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Hello, I did wonder if it might be an alternative conformation for the
quanidinium group of that nearby arginine. Being such high resolution, quite
low occupancy groups would show up, I think, but it may just be too far away
and I don't know how much tyrosine and arginine like each other!
Sent
Hello, it's a while since I ran Shelx and I imagine that you are running it
through the i2 GUI, which isn't something I've tried yet. Unless it's changed a
lot recently, shelx itself accepts the reflection data as h, k, l, F and
sigma(F) (HKLF 3) or h, k, l, I and sigma(I) (HKLF 4). Bit rusty
I think that's pretty unusual. Can you give the PDB code or map pictures? Does
it have D-amino acids? Cheers, Jon.C.
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Original Message
On 12 Jan 2022, 20:15, Prasun Kumar wrote:
> Hi All
>
> Happy New Year to All.
> I have a PDB file that has
I was going to suggest returning to this topic in 3 months time. It has that
sort of quality ;-?
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Original Message
On 31 Dec 2021, 15:17, Robbie Joosten wrote:
> Hi Eleanor,
>
> This seems to be a caused by a bug in an older version of Phenix. We
Or, you can start Coot in the terminal. Little CueMol gives the same info.
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Original Message
On 14 Nov 2021, 07:24, Eleanor Dodson wrote:
> Well I do this by overlapping one domain of protein A onto protein B - you
> can do that in coot - then
You could replace the OXT with a hydrogen, note O-H bond length is about 1
Angstrom, a la neutron style refinement. Phenix has this sort of thing inbuilt,
I think.
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Original Message
On 23 Sep 2021, 10:06, Schreuder, Herman /DE wrote:
> Dear Rohit,
Maybe turning off smooth re-centering would help our mac-using friends ;-?
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Original Message
On 16 Sep 2021, 11:29, Weiergräber, Oliver H. wrote:
> Hi,
>
> You may want to check the number of "steps" used in re-centring.
> This setting strongly
How long and specific is the motif? If its something like GxxG, then I can't
help, sorry, but if it's something like a domain then will the search by
sequence tool at RCSB help at all or have I missed the point? Good luck, Jon.C.
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Original Message
Hello Engin, we discussed this a year or two ago in relation to NCS when Ian
Tickle convinced me that since overfitting is due errors in the data, there is
no reason to expect these errors to be correlated by NCS and picking the R-free
set uniformally or in shells doesn't matter. No doubt my
model the malonate in the different conformation, but that didn't
> work. But I'll check about the protease inhibitor. Thanks!
>
> Kind regards
> Ana
>
> On Tue, 17 Aug 2021 at 14:48, Jon Cooper wrote:
>
>> Hello, only other thought was that malonate might be binding in two
>>
crystals that grew with malonate. In other conditions
> doesn't show anything like that. So I thought it'd be the malonate. But I'll
> check on that.
> Thanks for the suggestion.
>
> Kind regards
> Ana
>
> On Mon, 16 Aug 2021 at 16:56, Jon Cooper wrote:
>
>> He
Hello, could the His be partially acetylated?
Best wishes Jon.C.
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Original Message
On 16 Aug 2021, 14:52, Ana Ebrecht wrote:
> Dear all,
>
> I am building the structure of a protein that was crystallized in 0.2 M
> sodium malonate pH 5.0, 20% w/v
As Joel has suggested before, alphafold on an IDP would be interesting and
would seem like a zero-cost starting point - perhaps one you have tried already.
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Original Message
On 15 Aug 2021, 15:53, Scott Horowitz wrote:
> Hi Sorin,
>
> I hate to say
Hello, my numpty-level understanding is that being intrinsically disorder and
giving high-resolution structural data are mutually exclusive. I will re-read
your e-mails. Hope this helps. Cheers, Jon.C.
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Original Message
On 15 Aug 2021, 09:16, Sorin
Hello, do you start with a loop and coot/refmac give you back a loop or do you
start with a strand and get a loop back? Which fits the density best and how
good is the initial fit? Are there any extra restraints which always make it
loop back on itself when it shouldn't ;-?
Cheers, Jon.C.
Have you tried including a small amount of chymotrypsin? There were quite a few
papers about this technique 10-15 years ago. It worked for one of our proteins,
but I'm not sure about its success with complexes.
Good luck, Jon.C.
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Original Message
I don't know about solving this in Coot but would using a plain text editor on
the PDB file be a way to work around the issue? There is also the
spreadsheet-style PDB editor in i2??
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On 27 Jul 2021, 15:21, Afshan Begum wrote:
> Hi
Kay's program makes a system call to grep so I think it needs to be run on a
unix/linux/X machine or virtual machine or to have grep installed on windows,
which looks possible.
Good luck, Jon.C.
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On 20 Jul 2021, 23:36, Murpholino
Or Bernard's:
http://www.ruppweb.org/new_comp/anomalous_scattering.htm
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On 20 Jul 2021, 12:45, Tim Gruene wrote:
> Dear Eleanor, not sure how to make Chooch happy, but maybe Ethan Merrit can
> make you happy: there is his excellent
Hello, yes, the difference map looks great. If this one diffracts to
near-atomic resolution, maybe you have a tetramer with a very low solvent
content. Cheers, Jon.C..
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On 5 Jul 2021, 14:54, Robert S Phillips wrote:
> I collected
It's not important, but I am curious what 'Save relative to model/map' actually
means in that widget. Is it just a case of copying the relevant CRYST1 card? I
think Faisal is asking how to save new/modified coordinates but probably I
misunderstood...
Cheers, Jon.C.
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Hello, you could also try:
http://www.ic50.tk/kmvmax.html
Or
http://ic50.org/kmvmax.html
The former has an exponential decay thing that might help with your substrate
inhibition and other things if you have biphasic behaviour ;-0
Cheers, Jon.C.
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