Hi Jon
“Preaching to the choir”!
Harry
> On 23 May 2023, at 23:16, Jon Cooper
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> I am biased, but this looks like an interesting meeting:
>
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
>
> Best wishes,
gt; Boaz
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel
>
> On May 24, 2023 11:26, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi Jon
>
> “Preaching to the choir”!
>
> Harry
>
Hi Gerard
I’ve mentioned it to the organiser - we shall see how long the Garmen will be
there!
Harry
> On 24 May 2023, at 10:27, Gerard Bricogne wrote:
>
> Dear Jon,
>
> Quite a line-up indeed.
>
> Might someone at the RSC correct the typo in Elspeth's surname (in two
> places)? Or
t; On 24 May 2023, at 10:17, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Boaz
>
> No informaiton on the website about this but I have asked the organiser.
>
> Harry
>
>> On 24 May 2023, at 09:58, Boaz Shaanan wrote:
>>
Hi David
This is *exactly* what I did when implementing iMosflm’s double-clickable icons
for Mac, Windows (“proper” Windows, not WSL, CygWin or MSYS) and Linux, many
years ago…
Since MacOS is based on (may well actually be, I can’t remember…) BSD UNIX,
loads of shell things (nearly but not
Apropos Phil’s last point -
>
> 4. On the model front, go find an AlphaFold model, they have worked for me
> multiple times in molecular replacement so far.
If there is no extant Alphafold model, it may be worthwhile creating your own
via colabfold (duckduckgo it like I did…). Only takes a
Hi Armando
At the risk of appearing flippant, why not submit the sequence of the
full-length protein to something like Alphafold (readily available to all via
ColabFold (see
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)?
I suspect that each of the
Hi folks
I was wondering if anyone has a photo of the old-style head-mounted stereo
viewers that used to be used to see 3D images from wall-eyed stereo pairs? I
don’t mean the ones that were used to view the side-by-side stereo images that
once appeared in printed journals, but the ones that
gt; IGBMC
> 1 rue Laurent Fries
> 67404 ILLKIRCH - FRANCE
> tel: +33 (0)3 69 48 52 82
> From: CCP4 bulletin board on behalf of Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> Sent: 24 July 2023 16:58:26
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] 1990s-
ed LCD-based shutter glasses connected with a wire
> although awfully flickering with a switching frequency in the 8 Hz range!
> Wim
>
> - Mail original -
> De: "Harry Powell" <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> À: "CCP4BB"
> Env
hand drew each vectors line by line - and my god that
>> flickered awfully with “complex” objects.
>>
>> Adrian
>>
>> Sent from my iPhone
>>
>>> On 24 Jul 2023, at 18:53, Harry Powell
>>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wro
Hi
> Has anyone seen similar density to this before and/or can suggest how to
> model this positive density? Many thanks.
Romulan bird of prey?
Harry
>
> Regards,
>
> Yue Li
>
>
>
> To unsubscribe from the CCP4BB list, click the following link:
>
I’m left wondering which aspects of the patent application are novel and
haven’t already been published elsewhere in the list of references (which
include a number of Tamir’s other papers).
Others will know - can you patent something that you have already published in
a paper? I try to steer
Hi folks
I note that the installation pages for ccp4i2 tell me that I need _exactly_
version 2.8.0 of XQuartz so that things like Coot, iMosflm, etc will work. The
problem with that is that my TrueType fonts seem to have disappeared from
XEmacs and I’m left with the spidery bit-mapped fonts (I
to tell me that the chain ID in
legacy PDB format in _atom_site.auth_asym_id in the mmCIF, and not in either of
the two items I mentioned previously.
best wishes and happy Solstice!
Harry
> On 9 Jun 2023, at 15:57, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
&
Hi folks
I was wondering.
If there is a UniProt entry (for example, P01132, but there are plenty of
others) for which I want the “best” (whatever that might mean) representative
_experimental_ structure (i.e. not one of these new-fangled predicted models
that some folk say have removed the
if high-resolution restraints as RDCs had been used.
> Recall that NMR structures are build using monomer libraries that are
> seriously different from the x-ray ones.
>
> Best,
>
>
> E.
>
>
>> On 3 May 2023, at 11:45, Harry Powell
>> <193
Hi Marco
Further to Pedro’s comment, one way to avoid missing data in cusps is to use a
multi-sweep strategy for data collection (as championed by the good folk at
Global Phasing over many years). Many of the problems encountered in structure
solution can be traced back to a sub-optimal data
Hi
Didn’t Francis Crick have something to say about this in the early 1950s? I’m
sure it was published but off the top of my mind I can’t think where (one of
the more “established” members of this community will be able to give chapter
and verse)!
If you want to read something a little more
Hi
Not PyMol, but relevant to the ccp4BB - why not try “gesamt” for this?
e.g. for the nmr structure 1q01 -
> gesamt pdb1q01.ent -s '/1/A' pdb1q01.ent -s '/2/A' pdb1q01.ent -s '/3/A'
> -r0=1.5 -sigma=1.0 -o 1q01_cluster.cif -o-cf -a align.seq
gives me an alignment of the first three models
AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue
RMSD
Harry
> On 5 Jan 2024, at 10:49, Tomas Malinauskas
> wrote:
>
> Dear All,
>
> I apologize for asking a somewhat off-topic question.
>
> I have multiple aligned PDB files loaded in PyMOL, each representing
>
Hi
Well worth contacting your favourite (or favorite…) synchrotron about in-plate
data collection - I’d imagine that APS has something in-place (there was a
report way back in the depths of time [2015, when I still worked in the field…]
about a prototype on ID-19?), and that might be easier to
Hi
I can’t see any (obvious) suggestions in the current list of answers to try
room temperature diffraction before introducing cryoprotectants and cryocooling
your crystals (but I might just have missed it).
Often, just the act of changing the conditions that your crystals sit in will
Nick
>
>
>
> -- Forwarded message -
> From: Nicholas Clark
> Date: Fri, Feb 23, 2024 at 8:03 AM
> Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
> To: Harry Powell
> Cc: Harry Powell
>
>
> Hi Harry,
>
> MAXIT binar
Hi Graeme (I may well have mentioned this when we shared an office) et al
I’ll add something from my small-molecule crystallography days, when we used
point detectors - so this would be pre-1996 which was the last time I used one
of these machines.
I don’t remember which structure it was (feel
Hi folks
I am in the situation of having coordinates of apoproteins (i.e. polypeptide
chains without prosthetic groups) in PDB format - but I need them in mmCIF
format so I can run them through a locally built copy of AlphaFill.
I need something I can install locally, so web services are a
gt;
> to convert pdb to mmCIF . Hope, it was usuful for your modelled coodinates.
>
> Regards
>
> Marta
>
>
>
> El 2024-02-23 12:32, Harry Powell escribió:
>
>> Hi folks
>>
>> I am in the situation of having coordinates of apoproteins (i.e. polypep
at Buffalo
>> Department of Structural Biology
>> Jacob's School of Medicine & Biomedical Sciences
>> 955 Main Street, RM 5130
>> Buffalo, NY 14203
>>
>> Cell: 716-830-1908
>>
>>
>> On Fri, Feb 23, 2024 at 7:36 AM Harry Powell
>>
Hi folks
I’ve made considerable progress in getting to the bottom of this problem. From
what I can gather, AlphaFold writes “modelCIF”, which is not quite the same as
“mmCIF”, and just saying “CIF” is not unambiguous. So I guess I should have
been more aware of this when posting my original
Hi Marco
You could always try the CCP4 tools (since this is the CCP4 BB…) “superpose” or
“gesamt” to superpose (or is it “superimpose”? discuss…).
Harry
> On 28 Feb 2024, at 00:53, Marco Bravo wrote:
>
> Hello all,
> Does anyone know how to save a superimposed pymol or chimerax session as a
Hi Martin, Marcin, Arturo, Avinash
First off, I’m **NOT** saying that there’s anything wrong with the CIF files
produced by these routes - just that AlphaFill doesn’t like them (it *does*
like CIFs from AlphaFold -
> alphafill process alphafold.cif filled.cif
> 1DKE
Hi Fred
There *used* to be CCP14 (for small molecules and powders), but this lost
funding many years ago.
In the UK, I’d contact the National Crystallography Service at Southampton to
see if they have any pointers to bulletin boards - I have a vague recollection
of one but can’t remember the
Hi
Only comment is that (surely) any decent refinement program these days would
down-weight any reflections with negligible I/sig(I) (for example, those in the
“unobserved” high resolution regions) so that they do not contribute
(significantly) to the refinement. Or am I wrong (I don’t mind
” surprised, read “you could have knocked me down with a feather”.
> On Thu, Apr 18, 2024 at 09:22:04AM +0100, Harry Powell wrote:
>> Only comment is that (surely) any decent refinement program these days
>> would down-weight any reflections with negligible I/sig(I) (for ex
Hi Pat
Depends on how much you want to spend.
I’d start with a web search for “webcam astrophotography”, which should show
options on how to remove a webcam’s lens and mount the cam (not the kens, of
course!) on another optical instrument.
Back in the day, I had a Philips webcam that had a
Hi folks
For many years I’ve been using Scientific Linux as my OS of choice (when not
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.
What do people here recommend as a replacement?
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
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
/introduction.html
<https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver730/introduction.html>
As an aside, there are some subtle changes to the installed package in the CCP4
distro which mean that you can’t just swap in the new version.
Harry
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 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
> 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
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
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
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
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
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
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
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
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
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
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:
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
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
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
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,
the field, and haven’t really paid CASP much attention
in the past I wouldn’t want to comment about past methods. I’ve got a lot to
learn.
Harry
> On 9 Dec 2020, at 12:35, Bryan Lepore wrote:
>
> On Dec 9, 2020, at 07:16, Harry Powell wrote:
>>
>> ...the importa
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:
>
>
it was
last updated in 1997…).
Harry Powell
> On 21 May 2021, at 03:45, Dirk Bussiere
> <5f8efc77064a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear colleagues,
>
> I have an old data set collected on a Nonius Kappa CCD (.kcd format). I
> would like to convert the
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
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
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
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
; 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
> ‐‐‐ 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
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
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
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
>>>
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
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
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
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 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
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
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
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…
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
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:
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
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
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
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
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
>
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