Given that the I/sigma(I) is quite low the high R-merge values are probably to be expected. If the data were stronger, an R-merge that high would indicate that the space group was wrong or the data misindexed. If the multiplicity was higher you could process the data in lower symmetry space group (
Hello, have you tried refining anisotropic B-factors? It should lower R-free a few percent at that resolution.On 7 Nov 2019 13:42, Robert S Phillips wrote:
I have several data sets of Salmonella tryptophan synthase with different ligands bound in the beta-site. The data look good, with high re
I am interested to know the resolution on the basis that the better it diffracts, the lower the solvent content, generally. Have you tried Bernard Rupp's server which gives you probabilities for the No mols per AU, partly based on resolution? The LLGs look challenging - I've seen higher ones refine
Hello, it should be alright especially if you have NCS. Diffraction anisotropy also springs to mind. Best wishes, Jon.C.On 25 Nov 2019 13:11, Matthias Oebbeke wrote:Dear ccp4 Bulletin Board,
I collected a dataset at a synchrotron beamline and got the statistics
(CORRECT.LP) after processing
Re: "In our lab we generally use BL21 for plasmid replication."I am interested because on the occasions that I prepared plasmids in BL21 (usually by mistake), they were never any good for cloning or sequencing. I always had to transform them back into a cloning strain and do another plasmid prep!
Hello Rafael
No problem, thank you for confirming.
Best wishes
Jon Cooper
Original Message
On 10 Jul 2020, 14:27, Rafael Marques wrote:
> Thank you for pointing me this out. I don’t know why I said BL21...maybe in
> the rush to say to use Rosetta for protein expressi
Hello,
being a pedant, I guess you mean 'cell':
http://xray.chem.ualberta.ca/xray/shelxl/cell.htm
rather than 'unit':
http://xray.chem.ualberta.ca/xray/shelxl/UNIT.htm
;-?
Best wishes, Jon Cooper
Original Message
On 15 Jul 2020, 17:55, Jeffrey B Bonan
last round. However, the last time I
tried this, the GLOREF option had disappeared!! Perhaps there is an equivalent
approach these days.
Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com
Original Message
On 16 Jul 2020, 15:35, Edward Snell wrote:
> Not completely
3.72 Angstroms (not 2.72, sorry).
Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com
Original Message
On 16 Jul 2020, 16:56, Jon Cooper wrote:
> That's interesting. I remember the days of wax rings, we even used to do
> several at different X-D distances. I so
case anyone else
(who is yet to upgrade) was confused, there seems to be no need to panic, just
yet!!
Best wishes, Jon Cooper,
E-mail: jon.b.coo...@protonmail.com
To unsubscribe from the CCP4BB list, click the following
Hello, do you have any negative difference density for the current position of
the His side chain? If so, it may be in two confirmations. Just a thought.
Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com
Original Message
On 20 Jul 2020, 17:16, samer halabi wrote
Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide?
Coot is pretty good at fitting known ligands, and unknown ones, too!
Original Message
On 23 Jul 2020, 17:53, Reza Khayat wrote:
> Hi,
>
> Can folks suggest programs for objectively docking ATP/ADP mol
wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 29 Jul 2020, 14:56, Eleanor Dodson wrote:
> Sometimes ghost like this mean there is a spacegroup error - absences can be
> the result of the non-crystallographic translation and not be truly
> indiciti
Hello, it should be possible to get the example data, at least for SAD, thru
the i2 interface. It worked last week...
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 30 Jul 2020, 15:10, Rafael Marques wrote:
> Hello folks.
>
> During the qua
e map as good as possible.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 6 Aug 2020, 16:39, Silvia Napolitano wrote:
> Dear CCP4BB community,
>
> I am working on a crystal structure and I am a bit stuck with the refinement.
>
> To build
have
not really been around for some time:
https://1.bp.blogspot.com/-Y3HEe2KTczg/X0rPRm3ffNI/AfQ/EeSLElXobsUG-uIlWpU4BruLO3J6CChjACLcBGAsYHQ/s2048/IMG_1032.JPG
(Picture c/o P. McArdle)
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 30 Aug 2020
Apologies, I see that MAR now sell the Pilatus 200K detector, which may partly
explain things.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 30 Aug 2020, 18:03, Jon Cooper wrote:
> Hello, have you installed the latest version of ccp4 or could
Re: "I think MAR is the default detector, so I guess for some reason the image
header is not getting read correctly or is missing..."
Thanks for the proper explanation, Mark.
Indeed the manual says:
"Default: DETECTOR defaults to MAR"
Best wishes, Jon Cooper. jon.b.c
be corrected on this.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 12 Sep 2020, 11:06, Luca Mazzei wrote:
> Dear CCP4 people,
>
> I am approaching in these days to the new CCP4i2 interface and, in
> particular, to REFMAC. Can anyone quic
question, but when you say the space group is P32, I guess you mean P3
subscript(2) rather than P321, and I take it you have tried alternative space
groups in the MR like P3 subscript(1). Are the systematic absences good, or is
it all a bit ambiguous?
Best wishes, Jon Cooper.
jon.b.coo
Hello, all you ever need is:
https://www.ebi.ac.uk/pdbe/pisa/
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 25 Sep 2020, 14:35, Smith Lee wrote:
> Dear All,
>
> For pdb ID 1g4a, it is of space group P 3 2 1. In the paper for this pdb
&
centre? If you are
only predicting 25% of the spots it sounds, as you implied, like a cell and
symmetry problem.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 2 Oct 2020, 16:04, Xu, Shenyuan wrote:
> Dear CCP4 community,
>
> I have two ch
Hello, can you possibly show us a couple of screenshots with atom labels of the
affected side chain and a normal one?
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 15 Oct 2020, 15:07, Sam Tang wrote:
> Dear colleagues
>
> I am trying to
ishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 16 Oct 2020, 06:57, Sam Tang wrote:
> Dear all
>
> I attach herewith the Arg concerned. I actually saw no issue in Coot when I
> checked residue info. The issue was repeatable using both Refmac from
7;s very much less hassle than doing it yourself, esp. in
current situation. You will find equivalent services in the US, etc.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 16 Oct 2020, 19:22, Xiong, Jian-Ping wrote:
> Sorry for an unrelated request.
s and weights is to _minimise_
overfitting, not eliminate it. It is not possible to eliminate it completely:
if it were then Rwork and Rfree would become equal (apart from that small
effect from random sampling). " " "
That was Ian, not me, of course!
Best wishes, Jon Cooper. jon.b.coo
Hello, I am interested to know why "it is conventional to delete/omit
first/last image". Forgive my ignorance.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 21 Oct 2020, 19:23, Doo Nam Kim wrote:
> Dear all,
>
> What I knew is
to be stable. Hope this helps a bit.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Original Message
On 25 Oct 2020, 20:54, amit gaur wrote:
> Hi All,
> I have a question that, I have a loop region with hydrophilic
> residues(TNETRERE) that lie close to m
Hello,
does the protein you added cysteine to (I assume you mean by mutagenesis) have
another cysteine which could make an intra molecular disulphide with it? That
would probably not show on non-reducing SDS?
Best wishes, Jon Cooper
Original Message
On 31 Oct 2020, 15:58
data even with monoclinic. HTH a bit. Jon Cooper
Sent from ProtonMail mobile
Original Message
On 4 Nov 2020, 16:30, Almudena Ponce Salvatierra wrote:
> Hello everyone,
>
> I have collected 6 small datasets from a crystal, each from a different point
> on the crys
versus 31k Friedel pairs
available). Did you have to cut the resolution back somewhat in refinement? If
so I can't see an obvious problem. Can you just provide an explanation or does
the web form not let you proceed?
Best wishes, Jon Cooper
Original Message
On 21 Nov 2020, 19:
saying the obvious...
Best wishes, Jon Cooper
Original Message
On 24 Nov 2020, 11:28, Nika Žibrat wrote:
> Hello,
>
> I have a question about protein-ligand, of which ligand displays an ambiguous
> electron density. I am solving a structure of protein with ligand whi
Hello, I think this thread from a few months ago will help.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2007&L=CCP4BB&D=0&P=49210
Best wishes, Jon Cooper
Original Message
On 25 Nov 2020, 03:24, Cheng Zhang wrote:
> Hi everyone,
>
> This question
ients
could be used as refinement targets and I think the answer to that one is
probably 'no', at least in the X-ray field ;-)
Best wishes, Jon Cooper
Original Message
On 24 Nov 2020, 16:02, Dale Tronrud wrote:
> Hi,
>
> To me, this sounds like a very dan
Hello, yes, I tangled with this about a year ago so my memory is a bit vague. I
think you can get the mean protein B-factor from the refmac log file, but for
ligands, etc, I had to write a script. I can dig it out this evening if that's
any use.
Best wishes, Jon Cooper
Sent from Proto
Hello, if you are depositing the structure, a workaround might just be to use:
https://pdb-extract.wwpdb.org/
I suspect that was obvious, sorry!
Cheers, Jon. Cooper
Original Message
On 26 Nov 2020, 17:56, Nikolas wrote:
> Hi all,
>
> I am trying to prepare and e
resorting to
jokes about artificial intelligence, I couldn't make that out from the CASP14
website or the many excellent articles that have appeared. Best wishes, Jon
Cooper.
Sent from ProtonMail mobile
Original Message
On 3 Dec 2020, 11:17, Isabel Garcia-Saez wrote:
&
expected RMSD? AlphaFold, no matter how impressive, still
> gets things wrong.
> c. will the AI efforts now gear to ligand (fragment?) prediction with
> similarly impressive performance?
>
> Exciting times.
>
> A.
>
>> On 3 Dec 2020, at 21:55, Jon Cooper
>> <000
Hello James, that's really strange - I've used refmac et al., to do poor man's
energy minimizations of models and they've generally come out fine, unless the
restraints, etc, are wildly off-target. I wasn't playing with X-ray weights
though, since there never was a dataset, of course.
Cheers, J
-like pattern. I
think those lunes of spots in the first image are some sort of disorder in the
crystal, which I fear is zinc acetate. Best wishes, Jon Cooper.
Sent from ProtonMail mobile
Original Message
On 8 Dec 2020, 15:46, Joseph Ho wrote:
> Dear all:
> We recentl
Hello, have you tried the 'pointless' option to use one of the
structures/datasets as a reference, then there should not be a need to do MR on
the others, since they will all be indexed consistently. Sorry if that is what
you meant below. Cheers, Jon Cooper.
Sent from ProtonM
Just received a query from someone:
"Can you tell me when working with Coot maps how to make the atom names and
numbers more prominent."
Sorry, I've not looked at manual yet but, being idle, I thought someone might
just know the answer instantly ;-)
Best wishes, Jon.C.
Sent from ProtonMail mo
Thanks! Works well.
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Original Message
On 15 Dec 2020, 17:50, Paul Emsley wrote:
> On 15/12/2020 17:41, Jon Cooper wrote:
>> Just received a query from someone:
>>
>> "Can you tell me when working with Coot maps how to
Hello, when you say the (4, 0, 0) intensity goes down, I was wondering what is
actually changing? Likewise for the shift in (2, 0, 0). If every atom lay in a
particular diffraction plane, they would all scatter in phase and the
diffraction from that plane would be nice and strong! The relative p
Hello, it might be to do with the TLS group refinement which is mentioned in
your log file. Maybe try without TLS and see if it makes a difference, to the
B-factors at least.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent with [ProtonMail](https://protonmail.com) Secure Email
Hello, there is atomic-absorption. Breaks your heart to see the protein going
into the flame, but we got good results for Se and transition metals with a
superoxide dismutase. I doubt if there'll ever be one of those on a beam line
;-0 Cheers, Jon Cooper.
Sent from ProtonMail m
Hello again, re: amount, yes, from memory, it was a few milligrams. We also
used EDAX on dried samples IIRC. Cheers, Jon.C.
Sent from ProtonMail mobile
Original Message
On 7 Jan 2021, 14:13, Andrew Lovering wrote:
> Dear CCP4ers
>
> We have a protein with moderate resolution (
Pentagons of water are quite common in ordered water structure. Is it isolated or do the waters H-bond to other waters?The dimer interface looks, if I may say, a bit borderline to me. How does it fare in Pisa? Best wishes. On 27 Sep 2019 12:33, Vijaykumar Pillalamarri wrote:Dear Community,I sol
Does anyone know the pH of JCSG+ condition A3 which is stated as 0.2 M ammonium citrate dibasic, 20% (v/v) PEG3350. I can't really measure it myself, so any help much appreciated!
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1
/product-PEG-Ion-PEG-Ion-2-PEG-Ion-HT-11.html under the Support Material(s). Hope this helps.
Kind Regards, Bob Cudney
From: CCP4 bulletin board
On Behalf Of Jon Cooper
Sent: Saturday, October 5, 2019 2:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] A crystallisation screen pH query.
Does
omes which programs allow
specific torsion angles to be restrained to certain values?
Best wishes
Jon Cooper
Sent from ProtonMail mobile
Original Message
On 16 Jan 2021, 01:56, Flemming Goery wrote:
> Dear All,
>
> Is any server or script which can change the phi or psi a
Dear Sam
I can only suggest trying the old trick of editing the pdb file and giving all
the DNA bases the same residue number. As you are using the old gui you might
be able to do the same with pdbset or pdbcur, or maybe a graphics program.
Cheers, Jon Cooper
Sent from ProtonMail mobile
Take care ;-
https://www.wicys.org/
Seems genuine enough group & everything to me. The referees should have spotted
that one ;-0
Sent from ProtonMail mobile
Original Message
On 22 Jan 2021, 23:03, Bernhard Rupp wrote:
> Dear CCP4 Fellows,
>
> for the subscribers of my immens
Hello Sir,
Just confirming PPI is Protein-Protein Interactions rather than Proton Pump
Inhibitors?
Anyway, I knew someone who used UCSF Chimera a lot for that sort of thing.
Hope this helps. Jon.C.
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Original Message
On 25 Jan 2021, 19:02, Sergei St
Hello, in the self-rotation function the peaks arising from the NCS rotation
axes are good at hiding under the peaks for the crystallographic rotations,
which is because they are actually translational NCS elements, I think. Also,
sorry Eleanor, a double-check on wikipedia confirms the space gro
I am finding slightly similar-looking pictures of twinned pyrite crystals and
therefore hoping they are not fool's gold ;-)
Best wishes, Jon.C.
Sent from ProtonMail mobile
Original Message
On 16 Feb 2021, 21:00, Gerlind Sulzenbacher wrote:
> Dear Dale,
>
> A warm thank you fo
Hello, there usually is noise in the difference map near electron-dense
elements. Maybe refining against I(+) and I(-) might help, as someone suggested
a few months ago or perhaps you have already done that. It would be interesting
to know if it helps. Cheers, Jon.C.
Sent from ProtonMail mobile
Definitely water pentamer, no doubt at all ;-0
Cheers, Jon.C.
Sent from ProtonMail mobile
Original Message
On 22 Mar 2021, 14:16, Mark J. van Raaij wrote:
> The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so
> it’s probably mainly water molecules.
> P
Jeremy Cockcrofts web stuff is quite good:
http://pd.chem.ucl.ac.uk/pdnn/symm2/pntgrp1.htm
You can click through to the stereograms.
Best wishes
Jon.C.
Sent from ProtonMail mobile
Original Message
On 6 Apr 2021, 12:34, careinaedgo...@yahoo.com wrote:
> Can anyone send me a
Good point. It looks like a mac to me ;-
Best wishes, Jon.C.
Sent from ProtonMail mobile
Original Message
On 8 Apr 2021, 19:52, Tim Gruene wrote:
> Dear Luca, did you click at the empty line below where it says 'automatic'?
> Maybe the word 'manual' is just not visible for in
Hello, there's another one at 1.1 A in 5JK4 which was a contaminant that
crystallised over 2 years. No mass-spec, though! Cheers, Jon.C.
http://scripts.iucr.org/cgi-bin/paper?S2059798316010433
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Original Message
On 21 Apr 2021, 17:01, Isabel Moraes wr
If you want to try co-crystallisation again, if you dissolve your ligand in say
DMSO or anything that works, e.g. isopropanol, then add it to your protein up
to its maximum tolerable level (i.e. the level up to which the protein is not
denatured/inactivated by the solvent - you need to test this
:33, Jon Cooper wrote:
> If you want to try co-crystallisation again, if you dissolve your ligand in
> say DMSO or anything that works, e.g. isopropanol, then add it to your
> protein up to its maximum tolerable level (i.e. the level up to which the
> protein is not denatured/inacti
Hello, just to double check, I assume that you input the correctly oriented and
positioned structure of each domain from successive runs as a 'fixed' model?
Cheers, Jon.C.
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Original Message
On 11 May 2021, 02:53, Lande wrote:
> Hi everyone, I starte
The hard bit is to get the rmsd's into the B-factor column, but it shouldn't
stretch you too much, Harry ;-
There is ProtSkin on the web which does something similar with sequence
alignments.
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Original Message
On 26 May 2021, 16:28, Harry Powell - C
otonMail mobile
Original Message
On 26 May 2021, 16:51, Harry Powell - CCP4BB wrote:
> Yes, Jon, but I was hoping I wasn’t the first person to ever want this…
>
> Harry
>
>> On 26 May 2021, at 16:34, Jon Cooper
>> <488a26d62010-dmarc-requ...@jiscmail.ac.u
d the resulting picture (attached)
looks about right, I think/hope.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent with ProtonMail Secure Email.
‐‐‐ Original Message ‐‐‐
On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB
wrote:
> Hi Jon
>
> The RMSD data (also NOEs, c
I am thinking this could be done using pdbset to apply symops and origin
shifts, etc, with a bit of checking in Coot, creative chain-ID's and some trial
and error? Or using Coot to apply symops and save the resulting pdb's with
different chain ID's and then concatenate them into a mini-lattice?
Agreed, ANIS is the command to try.
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Original Message
On 3 Jun 2021, 20:18, Philip D. Jeffrey wrote:
> R1 of 17% is bad for small molecule.
> 0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs
> then these might be too aggre
Hello, the keywords can be entered in refmac gui (in one of the dropdown
things), so you don't need a file, as such, but it's useful to keep a record.
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Original Message
On 5 Jun 2021, 16:39, Marina Gárdonyi wrote:
> Hello everyone,
>
> I am trying to
Correct me if I'm wrong, but the first papers to stop reporting R-anything were
XFEL ones so I assumed it was a particularly bad estimator of data quality for
those expt's ;-
With a more normal expt, again correct this if it's wrong, the problems with
R-merge only throw it off by a few percent?
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.
Sent from ProtonMail mobile
Original
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.
Sent from ProtonMail mobile
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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Original Message
On 5 Jul 2021, 14:54, Robert S Phillips wrote:
> I collected da
Or Bernard's:
http://www.ruppweb.org/new_comp/anomalous_scattering.htm
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Original Message
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
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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Original Message
On 20 Jul 2021, 23:36, Murpholino Pe
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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Original Message
On 27 Jul 2021, 15:21, Afshan Begum wrote:
> Hi E
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
On
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.
Sent
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 D
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 i
Hello, could the His be partially acetylated?
Best wishes Jon.C.
Sent from ProtonMail mobile
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 po
n the 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
del 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
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 inc
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
On
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 affect
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,
>
Or, you can start Coot in the terminal. Little CueMol gives the same info.
Sent from ProtonMail mobile
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 overla
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 use
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 left-ha
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 on
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
2, Krieger, 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
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 getting
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 Me
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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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 you
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,
>
>
e available from the PDBe
EBI.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
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