Hi Lucas
This one?
https://www.iucr.org/resources/commissions/crystallographic-computing/schools/kyoto-2008-crystallographic-computing-school
IUCr’s Commission on Crystallographic Computing still holds these - next one
(probably) in Alberta!
Harry
> On 16 May 2024, at 01:51, Lucas Bleicher
n the CCD are correct, but
> they are much more reliable. If you find errors, please report them to the
> proper authority. See it, say it, sorted.
>
> Cheers,
> Robbie
>
> On 15 May 2024 14:41, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> H
Hi
This is very, very useful and hits on the four-letter name problem that I am
encountering - thank you. Saves me trying to produce a new design for a
circular object with an axle…
For the files that I am trying to use, columns 77-78 are present (actually,
columns 79-80 are there so I can
Sorry - just read that
> • Alignment of one-letter atom name such as C starts at column 14, while
> two-letter atom name such as FE starts at column 13.
indicating a rule does exist.
Harry
> On 15 May 2024, at 11:54, Harry Powell
> <193323b1e616-dmarc-requ...@jiscma
comes from the chemical component dictionary.
>
>
> Ezra
>
>
>
> On 5/15/24 6:28 AM, Harry Powell wrote:
>> Hi folks
>>
>> I’m sure that this has been answered many times before (I’m sure that when I
>> was young I even read it here…), and
Hi folks
I’m sure that this has been answered many times before (I’m sure that when I
was young I even read it here…), and I *know* that we should all be using
mmCIF, but I’m using PDB format files generated by a popular Python module and
I wanted to check the output against a definitive
ndroid
>>>> From: CCP4 bulletin board on behalf of Rafael
>>>> Marques
>>>> Sent: Monday, May 13, 2024 3:13:16 PM
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
>>>
Hi
With this in mind, I have found the easiest way to generate AlphaFold models
(for those not in the DB) is actually in CCP4 Cloud-remote - makes MR using AF
models a real doddle.
See the Tutorials (in particular on MR) available with CCP4 Cloud.
Harry
> On 14 May 2024, at 09:20, Randy
Hi folks
This arrived in my inbox this morning, and I believe that it may provoke some
discussion…
Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν
Best wishes!
Harry
>From: Stephanie Wankowicz
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao
>
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 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
” 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
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
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 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 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
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
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 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
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
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
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 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
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
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
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
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 folks
I was wondering if anyone on ccp4bb could give me a hand with some queries I
have about HHBlits and HHSearch?
The “issues” page on github (https://github.com/soedinglab/hh-suite/issues)
seems to be completely moribund and no-one has answered any queries for quite
some time - this may
Hi Jon
many thanks for this!
For those interested in Peter Morris, there was an interview with him in
Chemical and Engineering News at the end of September -
https://cen.acs.org/people/CEN-talks-with-Peter-J-T-Morris-science-historian/101/i32
Harry
> On 9 Nov 2023, at 22:57, Jon
Hi
I’ve never actually used it in anger (one should never be angry when processing
data…), but doesn’t AutoProc, developed by the good folks at Global Phasing do
a lot of these analyses? Clemens, Claus etc may have something pertinent to say.
Harry
> On 30 Oct 2023, at 13:23, Jorge Iulek
On the general topic of tenure, I read an interesting article in the news organ
of the American Chemical Society (Chemical and Engineering News) about the
future of tenure in the US recently - it’s available free-to-view (C allows
viewing one article a month without being a paid subscriber) -
Hi
If you’re not in a hurry, I should be able to take a look and see what needs to
be done (I’m a little busy right now, but I do know more than a ittle about
Mosflm and image formats). Otherwise I’d contact Mathias Meyer directly at
Rigaku Oxford Diffraction, who should be able to point you
Okay, I’ve found a DVD with it on…
Harry
> On 3 Oct 2023, at 14:51, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Good idea, but amazon.com.be tells me -
>
> "Actuellement indisponible.
> Nous ne savons pas quand cet article sera
Good idea, but amazon.com.be tells me -
"Actuellement indisponible.
Nous ne savons pas quand cet article sera de nouveau approvisionné ni s'il le
sera.”
and amazon.co.uk -
"Currently unavailable.
We don't know when or if this item will be back in stock.”
and amazon.com -
"This item
Hi Chris
I seem to remember arranging a showing or two of it at the 2011 IUCr meeting in
Madrid (Frances Bernstein asked my about doing this, to give credit where it’s
due). I have a vague memory of having obtained the DVD but couldn’t swear to it
now. I’ll have a look through my bits and bobs
Hi
I think It may be worthwhile submitting your model and data to PDB-REDO to see
if (inter alia) you have applied any unconscious bias to your building that has
resulted in these outliers, or over- or under-interpreted the data. It’s quick
and easy to submit and requires remarkably little
Hi
I am also reminded that I was involved in the data collection but not structure
solution of a DNA cyclic octamer from a single wavelength dataset collected to
atomic resolution (on image plate…), which was solved after locating a Ba
(which turned out to be one of several with partial
Hi folks
just my two ha’porth.
Back in the mid 1990s, when MAD was becoming common and tunable beamlines were
being installed at every synchrotron you could shake a stick at, I was involved
in several successful projects involving 5-Br-U in oligo-DNA crystallography.
In my (very, very) naïve
Hi Matt
Call me old-fashioned but I’d use Mosflm for this. The multiple lattice
autoindexing is easy to run and easy to interpret.
Harry
> On 30 Aug 2023, at 16:20, Matt McLeod wrote:
>
> Hi all,
>
> I have a lot of large datasets that I want to screen to determine if there
> are one or
Hi
There is no particular special editor from PDB (or from anywhere else, as far
as I know) for doing this - mmCIF is basically a simple text file with a
defined set of contents. It frees you from the tyranny of fixed-width columns
that your have in the historic PDB file.
I’d just use
Hi
Since this is the ccp4 bulletin board, it’s always worth mentioning CCP4MG for
producing images & movies of macromolecules. Comes with the package, and you
can get help from the author directly if you have any issues.
Harry
> On 17 Aug 2023, at 02:09, khaja faisal tarique
> wrote:
>
>
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:
>
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 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
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 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
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
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
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
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
One small issue with Aaron’s answer - the alert specifically says “Not (SHELXL)
Weight”, so I suspect that you may not be using SHELXL for your refinement, in
which case the “OMIT” instructions may not be available or may take a slightly
different form.
There’s an open-access IUCr paper
Hi folks
I’ve noticed that for some structures, the PDB file seems to have the mmCIF
entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB
files it has the “_atom_site.label_entity_id”.
e.g. for 4bpq, for ATOM 1 I see -
> CIF: ATOM 1N N . UNK A 1 1 ? 14.187
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
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:
>>
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 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,
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 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
I hadn’t noticed until just now, but this also happens on Linux machines at
SLAC -
> Distributor ID: Debian
> Description: Debian GNU/Linux 10 (buster)
> Release: 10
> Codename: buster
:-(
Harry
> On 29 Mar 2023, at 15:02, Joseph Cockburn wrote:
>
> Dear BB,
> Quite a few
Dear all
Those of you who are travelling to Melbourne for the IUCr Congress and General
Assembly in August may be interested in this (which finishes in time to get to
the opening ceremony of the main Congress).
To get an idea of the content of the workshop, you may wish to look at tetails
of
Whoops!
A quick glance at the PDB entry indicates I must have been clairvoyant to have
read it 20 years ago.
Harry
> On 20 Mar 2023, at 10:35, Harry Powell wrote:
>
> And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or
> not cramin is a protein, since
And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or not
cramin is a protein, since it has “only” 46 amino acids) where (from memory, I
haven’t read the paper for at least 20 nyears…) they modelled multiple water
networks.
3NIR, for reference.
Harry
> On 20 Mar 2023,
10 Mar 2023, at 16:58, Jurgen Bosch wrote:
>
> Going back to RIP phasing methods :-)
> So Harry in your particular case occupancy of zero would actually reflect
> reality for those “combusted” atoms.
>
> Jürgen
>
>> On Mar 10, 2023, at 11:56 AM, Harry Powell
&
Hi folks
One other thing that I haven’t noticed anyone mentioning yet (sorry to those
who have mentioned it!!) is that you may not see your sidechain atoms in
density because they are not there at all, in spite of what you may have had in
the original protein, or even if the atoms were really
ry
> On 6 Mar 2023, at 14:55, Eleanor Dodson wrote:
>
> Does Superpose or GESAMT align multiple structures?
> And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2
> etc?
> Eleanor
>
> On Mon, 6 Mar 2023 at 14:53, Harry Powell
> <193323b1
Or you could use Gesamt - also in CCP4.
Harry
> On 6 Mar 2023, at 13:15, Kay Diederichs
> wrote:
>
> Dear Armando,
>
> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign
> (https://zhanggroup.org/US-align/).
> In my tests, THESEUS sometimes crashed in different ways. USalign is
Hi Manoj
If the structures are in the PDB, then PDB-KB may have already done the work
for you -
https://www.ebi.ac.uk/pdbe/pdbe-kb/
They run Gesamt on homologous structures for the whole PDB every week (as I
understand it).
Harry
> On 2 Mar 2023, at 07:45, Manoj N wrote:
>
> Dear
Hi folks
Please let anyone know who may be interested in working in the heart of South
Kensington, funded by the Wellcome Trust.
Job Opportunity for Experienced Bioinformatics Software Developer (Phyre and
Missense3D) See:
My (limited) experience of the Diffraction Methods GRC suggests that the most
valuable part of these meetings is when people get together outside the talks -
so independent of the session chairs (apart from the people that they invite)
and of any instructions given to speakers.
Just my two
is the surface of the pocket as vertices and faces in a file with
the extension “.obj” (the other programs fill the pocket with dummy atoms).
Result looks most similar to that from parKVFinder.
Again, many thanks for the input
Harry
> On 12 Jan 2023, at 11:26, Harry Powell wrote:
>
>
> occasionally split a larger pocket into smaller ones, similar to the fpocket
> behavior, but perhaps not quite as frequent.
>
> -Mike
>
> On Wed, Jan 4, 2023 at 6:31 AM Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> THX for the replies -
>
>
THX for the replies -
> On 3 Jan 2023, at 22:56, Bernhard Rupp wrote:
>
> There is also a service from our Polish friends:
> called Spaceball (jokes aside) that calculates the volume of protein cavities
> (http://www.ifpan.edu.pl/~chwastyk/spaceball/).
> and the services in Hamburg are useful
Hi folks
I was wondering what people’s favourite program is to find binding pockets in
proteins. I’ve had a look at a couple but each has its own idiosyncrasies.
HNY
Harry
To unsubscribe from the CCP4BB list, click the
g that with “64119” as the argument gives me a file ChEBI_64119.sdf
with 3D coords.
Many thanks to all who got me out of my hole!
Harry
> On 6 Dec 2022, at 12:19, Harry Powell wrote:
>
> Hi Julie
>
> Ta.
>
> Do you know if there’s an API (pref. Python 3.9 or later) f
would be possible to
> programatically find the equivalent PubChem CID.
>
>
>
>
>> On 6 Dec 2022, at 11:31, Harry Powell
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Hi folks
>>
>> Can anyone help with this?
>>
>> I m
!
Harry
> On 6 Dec 2022, at 11:31, Harry Powell wrote:
>
> Hi folks
>
> Can anyone help with this?
>
> I must have missed something in the documentation, because I don’t understand
> why the .mol and .sdf files downloaded from
>
> https://www.ebi.ac.uk/chebi
Hi folks
Can anyone help with this?
I must have missed something in the documentation, because I don’t understand
why the .mol and .sdf files downloaded from
https://www.ebi.ac.uk/chebi
seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now
since I solved any
Hi MIke
Beyond the obvious that they should sum to no more than unity, if they are
similar to or not hugely greater than other temperature factors in your
structure, they are probably okay.
People often apply restraints or constraints to keep the temperature factors
similar for equivalent
ach SMILES string.
> Note: you have to first convert each SMILES in the database to canonical form.
> I hope this helps.
> Thanks
> Jitendra Kuldeep
> Postdoc researcher
> Machine learning and precision oncology group
> Cancer research center of marseille, INSERM
> France 1300
Hi
Probably a silly question, but I was wondering how to search for a ligand in
ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning
mind ...
Harry
To unsubscribe from the CCP4BB list, click the
cross this
> number of data sets at non-cryo temperatures
>
> Best wishes Graeme
>
>> On 8 Sep 2022, at 10:21, Harry Powell
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> hi folks
>>
>> I’ve been away from data processing for
hi folks
I’ve been away from data processing for a while, but am I alone in thinking
that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I
seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3.
Harry
> On 7 Sep 2022, at 19:46, Matt McLeod wrote:
>
Crambin (quick search for “Martha Teeter” and “Crambin” should yield
dividends)? There are some very high resolution structures of that with
multiple conformations.
Harry
> On 23 Aug 2022, at 23:02, Pavel Afonine wrote:
>
> Dear community,
>
> I’m looking for an example of a crystal
forge that does not have those changes, but I can make a
> point release if it is helpful.
>
> If the PAE code or your installation still does not work, please create an
> issue on GitHub and we can sort it out.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Bioph
Hi folks
No doubt someone will tell me that I should be posting this on the Phenix BB,
but since everyone on there reads ccp4BB as well (:-)), I’m likely to reach the
right audience anyway!
Two Qs -
(1) most important - scitbx.array_family seems to have disappeared (see stuff
below Q2).
Hi
The mosaicity (as Herman and Andrew have pointed out) is very high - so I’d
contemplate collecting at least some images at ambient temperature to see if
the cryocooling has increased it substantially. If images from RT data
collection shows that the mosaicity has blown up during cooling (I
Sorry - meant to add this: I know that (of the “free” programs) Mosflm, DIALS
and Eval15 can process multiple lattices.
Harry
> On 28 Jul 2022, at 14:36, Harry Powell wrote:
>
> Hi Sayan
>
> If you have multiple lattices showing in your diffraction pattern, it may be
> wo
Hi Sayan
If you have multiple lattices showing in your diffraction pattern, it may be
worthwhile using one of the programs that can process multiple lattices for
your integration.
It may also be a good idea to share a few of your images that show the problem
with an expert (don’t post the
Hi Saurabh
It looks like the “tdom” package (which is used by iMosflm to parse the XML
output from Mosflm in order to produce all the graphics) is missing from the
tcltk used by iMosflm in the ccp4 distribution.
CCP4 central should be able to help (see this web-page:
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
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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
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