Hi folks
It seems that with the version of Firefox on my (old-ish) Mac, there are no
Zoom links.
However, if I use Edge or Chrome (or Firefox in my Ubuntu VM) they appear as if
by magic.
Many thanks
Harry
> On 7 Jan 2025, at 09:51, Andrea Smith wrote:
>
> there are links, clic
Hi folks
Almost certainly something I’ve overlooked, but I don’t see any links to Zoom
for the SW on the page https://studyweekend.ccp4.ac.uk/programme/
Any ideas?
Harry
To unsubscribe from the CCP4BB list, click the
studies, but not as
cofactors *unless* they appear as cofactors in UniProt.
A person has to know their limitations… to paraphrase another Harry.
Harry
> On 20 Dec 2024, at 12:11, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi folks
>
> Befor
encounter with a protein
unless it had been dehydrated thoroughly and was under an argon atmosphere.
Best wishes
Harry
> On 20 Dec 2024, at 12:09, Martin Malý wrote:
>
> Dear Harry,
>
> You can check this structure of an FAD-dependent monooxygenase with bound FAD
>
poses, I’m using the UniProt nomenclature because I’m parsing
files from them. I’ll worry about what’s _really_ a cofactor at a later date!
Best wishes
Harry
> On 20 Dec 2024, at 11:47, Harry Powell wrote:
>
> Wow. I was right about one thing - this _is_ a good place to ask.
>
>
ere’s only one cofactor (or worse,
none), then I will rapidly move on (unless someone can provide a solid
justification as to why UniProt is wrong and they’re right…).
Enjoy a solstice-oriented break!
best wishes
Harry
> On 20 Dec 2024, at 10:37, Harry Powell
> <1933
Hi
It seems that East London (the one in the UK, not South Africa) is more similar
to Germany in this respect than Austria is - I get identical figures to Kay’s
(or does the LLM know that we’ve both developed integration programs, and bias
accordingly?)
Harry
> On 19 Dec 2024, at 15:00,
Presumably DSSP is still available -
https://swift.cmbi.umcn.nl/gv/dssp/
Harry
> On 13 Nov 2024, at 12:18, Marc Graille wrote:
>
> Dear Vitali,
>
> I used to do it with Stride server.
>
> Stride
> wzw.tum.de
>
>
>
> Hope this helps,
>
&g
Hi
I was wondering if moorhen might be useful for this?
Harry
> On 18 Jul 2024, at 18:35, Paul Emsley wrote:
>
> On 7/18/24 15:33, Andrea Smith wrote:
>>
>> I have a “green blob” in my map and I want to create a picture of it. What
>> is the best option to do t
“Images” window after you
have loaded images - for “modern” crystals I find that a value of 5 - 10
microns here is often useful.
Best wishes
Harry
> On 18 Jul 2024, at 05:01, Arpana Shikha wrote:
>
> Dear CCP4 Users,
>
> I recently updated the CCP4 package from version 8 to
Hi
Pandora’s box comes to mind…
Harry
> On 10 Jul 2024, at 07:14, Grant Hansman
> <db9e83c7f6ed-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi,
>
> I sent a message yesterday on the CCP4BB (below). I received so many
> enquires. Can I edit or stop this messa
Ok, it seems to be back again. Maybe the servers had a hangover after
yesterday’s celebrations…
Harry
> On 5 Jul 2024, at 11:43, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi folks
>
> https://www.ebi.ac.uk/pdbe
>
&g
Hi folks
https://www.ebi.ac.uk/pdbe
HTTP Status 404 - Not Found
??
Harry
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This message
predicted
models from the DB).
Harry
> On 26 Jun 2024, at 06:00, YASH MISRA PHD222012
> wrote:
>
> Dear all,
>
> Can someone help me with this?
>
> Until yesterday it was working fine but today when I tried running this task
> I am getting the following error. I tr
Hi folks
I’m just having issues seeing the PDBe website - does anyone know if this is
scheduled or if there is another issue?
Harry
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk
people to raise the issue directly with me…)
Once more, I knew this would be the place to ask!
Harry
> On 24 Jun 2024, at 13:40, Robbie Joosten wrote:
>
> Hi Harry,
>
> A BSc student in our lab just had a look at this. Here is the list of
> mappings pdb-redo uses:
> h
recently), but a quick search through ccp4bb postings has not revealed it to me.
Can anyone help?
Harry
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Hi
Presumably Wladek would know about this - I believe that he is an occasional
visitor to this BB!
Harry
> On 13 Jun 2024, at 10:40, Martin Malý wrote:
>
> Dear John,
> Thank you for the link. It would be great if https://proteindiffraction.org/
> (IRRMC) was rescued. I
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 Bleic
Hi Robbie
I’m not actually using PDB files of proteins - I’m using the PDB format files
in PDBeChem, because at the moment I’m interested in doing stuff with
ligands/substrates/etc. The charges I’ve seen so far seem to be not quite what
I’d expect, but I’m prepared to work around that.
Harry
read the atomic charge as well, which is
useful for my purposes) so I’m hoping that this will be reliable.
Harry
> On 15 May 2024, at 12:38, Marcin Wojdyr wrote:
>
>>
>>> • Alignment of one-letter atom name such as C starts at column 14, while
>>> two-letter
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
Hi Ezra
Thanks for this.
In other words, would it be true to say that there are no actual rules about
what appears in columns 13-16 because “it's a rose by any other name”?
Harry
> On 15 May 2024, at 11:38, Ezra Peisach wrote:
>
> If you take a look at
> http
8.307 6.456 -11.669 6.00 11.00 C
> HETATM 1075 CHD HEM A 1 6.928 4.145 -15.725 6.00 13.25 C
I’m sure that someone here will say “why don’t you look at *, it’s
obvious”, in which case - many thanks!
help
Harry
t Outlook for Android
>>>> 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 Reproducibil
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, Ra
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 ; Pedr
?
Harry
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hoste
have
their own webcam utility to turn your DSLR/mirrorless into a suitable device,
and this would be most likely to use the SLR mount. E-Bay have Nikon bodies
starting at around $200 today.
Harry
> On 24 Apr 2024, at 22:15, Patrick Loll wrote:
>
> Greetings, hive mind,
>
>
Hi Clemens
I’m “quite”* surprised. Do the authors of these programs offer any explanation
as to why the scaling programs (given that these are the ones that usually
provide F/I information for subsequent programs) bother to calculate sigmas if
they’re going to be ignored?
Harry
* for “quite
tion limit is (I’d choose CC -1/2 = 0.30, as
Doeke suggests)? Do HKL or XSCALE do the same (sorry, I haven’t looked at their
output for quite some time)?
Just my two ha’porth
Harry
> On 17 Apr 2024, at 21:35, Hekstra, Doeke Romke
> wrote:
>
> Hi Matt,
>
> I appreciate disagree
be able to answer you directly - 30 years ago I *would* have been
able to spot problems in these files at a glance, but lack of practice means
that I doubt I could do the same these days!
best wishes
Harry
> On 12 Mar 2024, at 09:00, Fred Vellieux wrote:
>
> Hi folks,
>
>
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
was an unrecognised system, and
the most recent binary was built in 2008).
Many thanks to everyone who took the time to read and answer my question!
Harry
To unsubscribe from the CCP4BB list, click the following link:
https
(when) things go
wrong!
best wishes and thanks again
Harry
> On 23 Feb 2024, at 14:00, Nicholas Clark
> <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Harry,
>
> Unfortunately, I did not see that the latest binary update was from 2008. I
> do not have
wonderful - that’s why there are so many of them.
Have a great weekend
Harry
> On 23 Feb 2024, at 12:46, Ida de Vries wrote:
>
> Dear Harry,
>
> You could also try to use pdb2cif from the cif-tools:
> https://github.com/PDB-REDO/cif-tools. The only strict requirement for
higher
> Linux .. any version
> SGI IRIX ... version 5.3-6.4
> make: *** [Makefile:32: compile] Error 1
which is odd, because this is a new Linux system installed this week
> [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> Rocky Linux release 9.3 (Bl
til I
retire ;-)); I’ve found with other web resources that this can trigger DDOS
protection systems (e.g. being temporarily banned…).
best wishes
Harry
> On 23 Feb 2024, at 11:41, Marta Martínez wrote:
>
> Hi Harry
>
> I use this link: https://mmcif.pdbj.org/converter/
>
A-coot-0.cif filled.cif
> Error reading file ‘protein_A-coot-0.cif'
> >> parse error at line 2: This file does not seem to be an mmCIF file
Harry
To unsubscribe from the CCP4BB list, click the following link:
https
values of the angles from the data processing showed unambiguously that I had a
high symmetry solution. I believe that Pointless arose after a
hexagonal/C-centred orthorhombic ambiguity arose (but my memory could be faulty
here).
Best wishes
Harry
> On 23 Feb 2024, at 09:58, Winter, Graeme (DLS
collection.
You don’t say which beamline at ALS you used, but if it’s got a kappa or
similar fitted the beamline staff should be able to help.
best wishes
Harry
> On 20 Feb 2024, at 09:20, Pedro Matias wrote:
>
> Hi Marco,
>
> Further to Zhen's comment, that can also happe
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
detailed than people have mentioned
here, there’s a “Methods in Enzymology” chapter by Charlie Carter (?) et al
from the early part of this century on the subject - again, I can’t remember
exactly who or when.
Have a good break (which reminds me to register for the CCP4 Study Weekend)!
Harry
alignment of the first three models in the file
Harry
> On 14 Dec 2023, at 21:55, Krieger, James M wrote:
>
> I don’t have one for pymol, but there is a function in prody for it.
>
> Best wishes
> James
>
>> On 14 Dec 2023, at 21:41, Srivastava, Dhiraj
>>
,
some places will also grow your crystals for you on site, using your
conditions. Unfortunately, I don’t know where “yahoo” is, so I can’t make a
suggestion as to which might be closer/easier for you to access!
best wishes
Harry
> On 24 Nov 2023, at 08:59, careinaedgo...@yahoo.
get samples to (from
Birmingham) than one of the European facilities.
Harry
> On 23 Nov 2023, at 09:31, Jose A. MARQUEZ wrote:
>
> Dear Elizabeth,
>
> In situ data collection is a good approach to try in your case. You could use
> the CrystalDirect technology for automated
be associated with the project losing funding (which is a
huge loss to the community at large).
Harry
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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,
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 Iu
iber) -
> https://cen.acs.org/careers/great-tenure-debate-again/101/i29
If you have a free 10 -15 minutes…
Harry
> On 16 Oct 2023, at 08:15, Tim Gruene wrote:
>
> On Sun, 15 Oct 2023 19:44:45 +
> "Hekstra, Doeke Romke" wrote:
>
>> Mark is, of cour
in the right
direction.
Best wishes
Harry
> On 10 Oct 2023, at 06:17, Vyankatesh Rajmane wrote:
>
> Dear all,
> We have collected diffraction data on a Rigaku FR-X machine with a
> HyPix-6000HE detector. The images are in .rod_img format. We are trying to
> export t
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
to
keep it… so it should be somewhere in my “archives"
Harry
> On 3 Oct 2023, at 14:22, F.Xavier Gomis-Rüth wrote:
>
> You can purchase it from Amazon.
>
> On 3/10/23 15:21, Burak Veli Kabasakal wrote:
>> Dear all,
>>
>> Sorry I realized the movie is
to see if I can find it.
Do you have a deadline?
Harry
> On 3 Oct 2023, at 11:02, Chris Ulens wrote:
>
> Dear members of the ccp4bb,
> I have a somewhat unusual question. For many years I have shown the movie
> “Naturally Obsessed - the making of a scientist” for educative
effort on your part - another
tool to your collection.
Harry
> On 25 Sep 2023, at 07:00, Guillaume Gaullier
> wrote:
>
> A good example of such expected outliers can be found in structures of
> nucleosomes: the validation report always flags almost all DNA bases as
> geometr
occupancy); the structure
solution was actually carried out in the laboratory of one G.M. Sheldrick,
using software that I think may have never been released to the public.
See
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20809/
for details...
Harry
> On 19 Sep 2023, at 20:53, Di
them appearing in Acta D),
available at -
https://legacy.ccp4.ac.uk/courses/proceedings/1997/h_powell/main.html
Contributions at the same meeting by others whose names will be instantly
recognizable may well be more use than mine…
Best wishes
Harry
> On 19 Sep 2023, at 19:32, Wag
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 ther
whatever text editor you have on your system - so on LInux or Mac,
something like vim, emacs, nano, on Windows Notepad. No need for anything
special.
But I’d also be wary about screwing up the file completely with your edits -
it’s easy to turn a compliant file into something invalid.
Harry
> On
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
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:
> http
y takes a short time...
best wishes
Harry
> On 2 Aug 2023, at 20:20, Phil Jeffrey wrote:
>
> 1. Completeness is primarily an issue with using the right point group and
> crystal system, not the actual space group (e.g. in primitive point group mmm
> the space groups P222, P2221
”
with a pleasing appearance?
Harry
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clear of lawyers and the law...
Harry
> On 28 Jul 2023, at 12:36, John R Helliwell wrote:
>
> Dear Graeme,
> Yes indeed, interesting.
> There are clearly aspects of microED of proteins which might be documented as
> non-obvious otherwise it wouldn’t have been a bit st
sy to run (submitting
a job would take less time than it’s taken me to type this sentence), and has
very helpful user support (see
http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index)
It would at least give you something to think about before spending time in the
lab.
Harry
> On 26 Jul
) because they had the
set-up your pictures are of.
However, these pics may still be of use to me.
Thanks everyone who has replied to this - I knew this would be the right place
to ask!
Harry
> On 25 Jul 2023, at 00:23, Jon Cooper
> <488a26d62010-dmarc-requ...@jiscmail.ac.
Hi Alastair
YES! Those are the ones.
Many thanks
Harry
> On 24 Jul 2023, at 16:46, Alastair MC EWEN wrote:
>
> Hi Harry,
>
> Are these the ones you mean?
>
> Best,
> Alastair
>
> ~
> Alastair McEwen, PhD
> Integrated Structural Biology Platform
&
Can’t have been a PS300 in that case!
I’ve since been reminded that they were made of wood (the stereo viewers, not
the Evans and Sutherland. But I’m probably wrong about that as well…)
Harry
> On 24 Jul 2023, at 16:03, Wim Burmeister wrote:
>
> Hi,
> the E&S PS300 alread
were used for advanced
computer graphics machines like E&S PS300.
From my somewhat dim memory, they had an adjustable mirror on one side so that
the two views could be coalesced (with the adjustment knob on the top of the
box).
More in hope than expectation…
H
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:
&
tps://journals.iucr.org/e/issues/2020/01/00/su5533/index.html
>
> https://doi.org/10.1107/S2056989019016244
>
> checkCIF validation ALERTS: what they mean and how to respond
>
> Anthony L. Spek
best wishes
Harry
>
> On 12 Jun 2023, at 10:29, Aaron Finke
>
read the entries? (the refinement program
for 6p9o is given as both REFMAC and “PHENIX” in the CIF - presumably
phenix.refine, but I wouldn’t bet my house on it).
Harry
To unsubscribe from the CCP4BB list, click the following
quite 100%) that work for Linux will also
work for Macs (as you suspect).
Harry
> On 5 Jun 2023, at 12:31, David J. Schuller wrote:
>
> I am not familiar with Macs, but on Linux the first problem could be easily
> solved by having the desktop shortcut call a brief shell script rather
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 sur
sive and the results were not that good.
>
> But I agree that many (all?) of the talks will be of lasting value. I will
> think about how we could record it without incurring great expense.
So (being an optimist, as those who know me well know :-)) I’d say “maybe”.
Harry
>
&g
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:
>
> Indeed! Will it perhaps be possible to watch the event by zoom? Or will a
> recording of it be availabe later on? Any idea?
> Cheers,
&
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-crystallog
, Rfree 0.222) is at #6 - why? looking at the PDB-REDO
entries is educational), so it’s challenging to write scripts that will scrape
the whole DB and give the “best” model for each.
Harry
> Hi Harry,
>
> A useful starting point when looking for the 'best' [insert criteria here]
these are from the same paper, so
may be in different conditions (e.g. pH). All except the first (1A3P) cover the
same bit of sequence.
Specifically, what should I look for in the downloadable files (mmCIF, for
example) from the PDB?
Thoughts?
Harry
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:
>
> D
previous events held by the IUCr Commission for Crystallographic Computing
which are are available here -
> https://www.iucr.org/resources/commissions/computing/schools
Harry
> Begin forwarded message:
>
> From: "Lutz, M.H. (Martin)"
> Subject: Crystallographic Co
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 2
Hi Jürgen
You might think so, but I’d disagree. Not going too far away from your line of
reasoning I could also put in a completely fictitious ligand or cofactor and
assign its occupancies to zero (I really, really knew it was there but I just
couldn’t find any evidence… :-))
Harry
> On
there in the crystal
_before_ exposure to the beam.
The coordinates are supposed to be what you actually find, not what you hope is
there.
Just my two ha’porth
Harry
To unsubscribe from the CCP4BB list, click the
Hi Eleanor
According to
https://www.ccp4.ac.uk/html/gesamt.html
"Gesamt aligns two or more structures…”
and
https://www.ccp4.ac.uk/html/superpose.html
"superpose aligns and superposes two or more protein structures…”
But the real expert is probably Eugene.
Har
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 di
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:
>
we’re processing > 1000 models a day (project
supervised by Prof Mike Sternberg). Missense-3D predicts the structural changes
introduced by an amino acid substitution (project supervised by Dr Alessia
David).
> http://www.sbg.bio.ic.ac.uk/phyre2/
> http://missense3d.bc.ic.ac.uk/mis
ha’porth
Harry
> On 30 Jan 2023, at 11:54, Frank von Delft wrote:
>
> Whether cross-pollination happens depends on the session chairs, and the
> remit they're given, and the instructions given to the speakers: if early on
> everybody sets the tone, to inform as much as adve
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:
>
>
Hi Mike
Interesting. I haven’t looked at Java stuff for quite some time…
Harry
> On 4 Jan 2023, at 12:53, Mike S wrote:
>
> Have you tried P2Rank? It is quite fast, and there is a standalone version
> that has command line options to run against all coordinate files in a
>
tons gets a little
boring!
Sorry my initial post wasn’t clearer
Harry
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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
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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) for d
Hi Julie
Ta.
Do you know if there’s an API (pref. Python 3.9 or later) for downloading the
3D coordinates from ChemSpider?
Harry
> On 6 Dec 2022, at 12:04, Julie Tucker
> <20908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Chemspider can also provide you with a
Hi Oliver
I’d just worked that out when I tried an obviously non-planar molecule (that I
didn’t include with my breakfast this morning)!
PubChem looks like a useful way forward - many thanks.
Harry
> On 6 Dec 2022, at 11:55, Oliver Smart wrote:
>
> Hi Harry,
>
> The SDF foun
!
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
0
> 8 3 1 0 0 0 0
> 4 3 2 0 0 0 0
> 7 4 1 0 0 0 0
> 1 5 1 0 0 0 0
> 5 3 1 0 0 0 0
> 12 5 1 0 0 0 0
> 6 2 1 0 0 0 0
> 6 4 1 0 0 0 0
> 11 6 2
atoms in different partially occupied conformations, but
I’m not sure there is a real justification for this apart from making the
solution refine more stably. No doubt someone here will correct me!
Harry
> On 28 Nov 2022, at 19:31, Michael Colaneri wrote:
>
> Dear colleagues,
&g
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