Also, of course, you could get the up-to-date version from -
https://swift.cmbi.umcn.nl/gv/dssp/
Harry
> On 7 Apr 2022, at 09:29, Harry Powell - CCP4BB
> wrote:
>
> Hi Ines
>
> DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file
>
Hi Ines
DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file
“Oldie but goodie”...
Harry
> On 7 Apr 2022, at 09:24, Munoz.Ines wrote:
>
> Dear all,
>
> Is there any program or server that automatically assign the secondary
> structure elements into a pdb generated
Isn’t that what we all say every year on the day after March finishes?
Harry
> On 1 Apr 2022, at 23:46, Paul Emsley wrote:
>
> That, for the record, is more or less what Ralf said 18 years ago.
> On 01/04/2022 23:38, Pavel Afonine wrote:
>> It's April 1st today, isn't it? -;)
>>
>>
>> On
Hi folks
Just my two ha’porth; if you go back to one of the first two structures
determined by protein crystallography, haemoglobin (horse?) has multiple oxygen
binding sites) which are potentially different (the binding of oxygen ion one
affects the binding in the other - “allostery”). I’m
Jul 2013)
Harry
> On 21 Feb 2022, at 10:04, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi
>
> Is this _really_ the most recent reference for cctbx?
>
> Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P
Hi
Is this _really_ the most recent reference for cctbx?
Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002).
J. Appl. Cryst. 35, 126–136.
(from one of Dorothee Liebschner’s recent papers)?
Harry
> On 21 Feb 2022, at 09:44, Harry Powell -
Hi
I didn’t find this in a couple of minutes searching so I thought I’d ask -
what’s the current literature reference for the cctbx toolkit?
Harry
To unsubscribe from the CCP4BB list, click the following link:
Hi
Last year there were a few reports in the chemical press (e.g.
https://doi.org/10.1039/D1SC02708E, and references therein) of studies of glass
catalysing reactions - it seems that it isn’t as benign as one might imagine.
Of course, this will not be news to the old chemical hands on this
e with MG.
>
> On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi folks
>
> Been a while, but I’ve been doing some work on checking that some files are
> valid PDB files and went back to the documentation; a
Hi folks
Been a while, but I’ve been doing some work on checking that some files are
valid PDB files and went back to the documentation; as far as I can work out,
the best solution to this is John Walker’s, because “MODEL 0” is not allowed in
the standard (maybe it is for mmCIF…) -
> On 27
Hi
Forgive me if I’ve missed something, but I can’t find a way to run AlphaFold
without installing it locally - in which case I need a reasonable GPU.
On the other hand, RoseTTAFold does pretty much the same thing and is available
via David Baker’s web server - upload your sequence and sit
Hi
Just my two ha’porth.
I’m currently involved in a project where my collaborators are investigating
the interactions between protein pairs (both hetero and homo) - they
specifically asked me _not_ to give them any models from ensembles (actually,
they said “no NMR structures because they
Hi folks
This is probably a good time to mention that both Melanie and Andrea will be
giving presentations at the IUCr in Prague in a couple of weeks or so in the
Commission for Crystallographic Computing session chaired by Rita Giordano -
MS-73 Machine learning in biological and
Readers of this BB may be interested in the following paper from DeepMind -
https://www.nature.com/articles/s41586-021-03819-2_reference.pdf
referenced from
https://www.nature.com/articles/s41586-021-03819-2
Of course, you should never just open a link contained in an e-mail…
gnificant main-molecule 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
&g
Hi
Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å
data most small molecule crystallographers would do this as a first step after
fitting all the non-H atoms.
One thing I can’t agree with is to cut the resolution of your data _unless_ you
have a very, very good
> ‐‐‐ Original Message ‐‐‐
> On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB
> wrote:
>
> Hi Jon
>
> The RMSD data (also NOEs, chemical shifts, etc) are not in the original
> PDB so I would have to calculate them - which takes me to my original
> question
; scaled by NMR variability
>
> in ccp4mg?
>
> This changes the size of the worm but not the colour.
>
> On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Anyway, thanks to all those who answered
Anyway, thanks to all those who answered my original question - especially
Tristan: Chimerax (+ his attached script)
Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/)
Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
Rasmus CYRANGE
gt;>>
>>>> The superpose/overlay of all the structures in PyMol should inform you the
>>>> rigid part of the protein as well as the flexible part. The rigid part
>>>> would have very low backbone RMSD or overlay tightly and the flexible part
>>>
s of the protein may have been studied through NMR relaxation.
>
> Smita
>
>
> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Hi
>
> Given that there are plenty of
hot areas?
> Jürgen
>
>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Hi
>>
>> Given that there are plenty of people on this BB who are structural
>> biologists rather than “ju
Hi
Given that there are plenty of people on this BB who are structural biologists
rather than “just” crystallographers, I thought someone here might be able to
help.
If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures
that fit the NOEs, is there a tool available
Hi Dirk
Converting to a form that Mosflm can read is not too much of a problem - the
problem arises because Kappa CCD images are not corrected for spatial
distortions, which can be significant.
I think you would need a correction table (or similar - maybe “brass plate”
images if you have
and its link /usr/local/lib/libssl.dylib)
looks like it’s solved my problem.
Talk about needles in haystacks…
Harry
> On 21 Apr 2021, at 10:42, Harry Powell - CCP4BB
> wrote:
>
> Hi folks
>
> I have an old-ish Mac (Mac Pro, mid-2010, 3.46 6-core Intel Xeon, 32GB RAM)
>
Hi folks
I have an old-ish Mac (Mac Pro, mid-2010, 3.46 6-core Intel Xeon, 32GB RAM)
running High Sierra (OSX 10.13.6) - the box will not support newer versions of
OSX or MacOS, so I can’t “upgrade” any further on the OS front (well, I could
if I really wanted to hack beyond Apple’s
Hi Alex
Have a look at Auspex - it may be able to help
AUSPEX (www.auspex.de)
Harry
> On 4 Mar 2021, at 15:39, Alexander Brown
> wrote:
>
> Hi all,
> I'm struggling with a dataset I have which shows very poor data quality
> around 3.6A, or exactly where I can see a significant ice ring in
The “something” is what gives them their edge (and which they’ve hinted at, but
avoided being explicit)…
The main quality score used to distinguish their results is GDT_TS (Global
Distance Test - Total Score - you can look it up on Wikipedia like I did).
Although it doesn’t say in Wikipedia,
Hi
Actually, since Deep Mind is a commercial organization (funded by shareholders
and people who buy their services), I don’t think they are subject to the same
rules as academia as regards making their source code public. It would be very
nice if they would (could?) make their code public,
represents a typical spread of homologous
> models in the PDB. So yes very competitive if you're desperate for a MR
> starting model, but not quite yet there for a refined high-resolution
> structure.
>
> Cheers
>
> -- Ian
>
>
> On Tue, 8 Dec 2020 at 12:11, Harry Powell
Hi
It’s a bit more than science by press release - they took part in CASP14 where
they were given sequences but no other experimental data, and did significantly
better than the other homology modellers (who had access to the same data) when
judge by independent analysis. There were things
Hi
To be fair to Apple, the original Rosetta that allowed Power PC executables to
run on their Intel chipped computers worked really well. I still have a machine
that can run Snow Leopard (OSX 10.6.8), which uses Rosetta to run a very old
version of PPC MS Word. The main issue appears to be
Hi
If it’s just organic, use 18 Å^3 per non-hydrogen - e.g. glucose (C6H12O6)
occupies around 12*18 ~= 216Å^3. Atoms like S and P add a little more, but for
mental artihmetic and a quick estimate it doesn’t amount to a hill of beans.
H
> On 5 Nov 2020, at 09:25, vincent Chaptal wrote:
>
>
Hi
I haven’t looked at this for a few years, but I can’t see why you couldn’t; as
far as I remember, Mosflm reads Saturn images okay.
You would probably need to do low and high resolution runs since the detector
is (I think) only 72mm square.
Best option would be to try with something like
even received my own message
from the BB…
Harry
> On 21 Sep 2020, at 09:47, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi folks
>
> SInce early last week I have had no messages from the BB - and also received
> a message
Hi folks
SInce early last week I have had no messages from the BB - and also received a
message telling me that I had been unsubscribed automatically because of
bounced messages.
I _should_ have now been resubscribed, but am not getting anything - and the BB
is no longer on JISCMAIL’s list of
Hi folks
Thank for the name-check Jon - I haven’t been employed on the Mosflm project
since 2016, but it’s nice to be remembered.
The place to look for a more definitive answer to the problem is in the
date-stamped mosflm.lp file (called something like mosflm_202008319_124743.lp)
which will
nd users may think they just have bad crystals despite pretty
> diffraction.
>
> So yes, there are people these days who collect powder data for wavelength
> and beam position reference.
>
> Cheers,
>
> Tom
>
>
> On 16/7/20, 9:26 pm, "CCP4 bulletin board
s diffraction-free method, then a Si powder allows a precise calibration
> of detector distance (and location of beam centre).
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB wrote:
>> H
Hi
Does anyone bother collecting a powder image (e.g. Si powder) these days so
they actually have a reference that can be used to check both the wavelength
and the beam centre? Or is this considered just something that old folk do?
Harry
> On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt wrote:
Dear all
I’ve been persuaded that MPR is a useful name (and see that there are
shortcomings with both “multiplicity” and “redundancy") and I agree with much
of what’s been said most recently in this thread.
BTW, just because the Physics definition of a measurement/quantity/whatever is
given
Why not just use QTMG rather than Pymol? This is, after all, the _CCP4_
bulletin board…
H
> On 14 Jun 2020, at 23:56, Javier Gonzalez wrote:
>
> Thank you so much Vijaykumar and Kevin, it worked smoothly!
> Best wishes,
> Javier
>
> On Sun, Jun 14, 2020 at 5:04 PM Kevin Jin wrote:
> My OS
Hi
I’d make the decision based largely on where I was going to use it, and how
much I was going to have to carry it (and if I ever wanted to use it in coach
class). If it was going to be my machine for “on the road”, I’d go for the 13”
one, but if it was going to sit on my desk most of the
Hi
Just to echo what has been said before, and expand a little.
(*) 5mm NMR tubes are wonderful for growing small molecule crystals in the way
Artem describes - partly because they have _extremely_ smooth interior surfaces
with few nucleation points - so you tend to get fewer, bigger
ignored or a parser will throw an error.
>
> Cheers,
> Robbie
>
>> -Original Message-
>> From: CCP4 bulletin board On Behalf Of Harry
>> Powell - CCP4BB
>> Sent: Friday, May 29, 2020 16:57
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp
Hi
Is there something about “MODEL ” lines (i.e. five characters followed by a
space) in PDB files that is completely beyond the pale?
I’ve got some PDB files from a protein structure prediction server based in the
US that Coot fails to read and that cause QTMG to crash on my Mac. I’ve
Hi Tim
You could send out an SOS to some of the other authors in the same issue, who
might have kept a copy - several are “regular" posters on this forum, e.g.
Sacha Urzhumtsev
Gerard Kleywegt
Eleanor Dodson
There’s a good chance they’ll be stuck at home at the moment
Hi folks
I can’t help feeling that if there are data extending to 0.97Å and there are
multiple conformations/multiple components occupying the same region of (real)
space/non-unity occupancies, the problem is crying out for SHELXL…
Harry
> On 27 Apr 2020, at 07:53, Schreuder, Herman /DE
>
Hi folks
I don’t know if this has been announced anywhere else yet, but this year’s IUCr
meeting in Prague has been postponed to 2021 - see
https://iucr2020.org/news/
I doubt this will be a surprise to anyone.
Keep well
Harry
Hi
> While those text files would be heavy, they'd be still lighter than raw
> images and the whole useless white space they carry with them between
> reflections.
At the risk of extending this thread into a different direction, the "white
space (the images) carry with them between
Hi folks
I’ve noticed that the Mosflm help line has recently received several messages
regarding problems processing Eiger 2 images with iMosflm (e.g. those collected
on IMCA-CAT)
Invariably, the users have been trying to use iMosflm/Mosflm 7.2.* series -
also inevitably, this will not work!
Hi
Something else I should have mentioned - in iMosflm you can sum your images for
viewing only if you have them as HDF5 or Pilatus CBF (as well as summing them
for processing if you have HDF5).
Harry
> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE
> wrote:
>
> Hi Daniele,
>
> I agree
Hi
Apropos Mosflm - if you have HDF5 files from ESRF (or Diamond, probably
elsewhere) you can sum the images internally to whatever rotation range per
pseudo image you want (so if you have, say, 0.05º physical images you could
process 0.1, 0.15, 0.20º, etc), provided you have installed Mosflm
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