Re: [ccp4bb] PDB to AlphaFold via Uniprot

2022-08-02 Thread Paul Bond 
Hi Paul,

You have probably solved this already, but in case you are interested I
have written a script to superpose AlphaFold models using PDBe mmCIF
annotations, AlphaFold DB and Gemmi (link below), as I had already done
something similar in a previous project. It is probably better to use
3D-Beacons as Robbie suggested however as it has a documented API.

https://gist.github.com/paulsbond/e4806e878c578218d0ae56bb5067a330

Cheers,
Paul B

On Sat, 30 Jul 2022 at 13:45, Nicholas Larsen <
5741fb55e4af-dmarc-requ...@jiscmail.ac.uk> wrote:

> Or you can go straight to uniprot.  Every available PDB + alphafold model
> is linked to the uniprot entry.
>
> On Fri, Jul 29, 2022 at 4:46 PM Robbie Joosten 
> wrote:
>
>> Hi Paul,
>>
>> From the PDB file get the Uniprot primary accession code (see DBREF) and
>> use this to get the Alphafold model using 3D-beacons (
>> https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/).
>> You can also use 3D-beacons to get the related AlphaFill model (just
>> saying...).
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Paul
>> > Emsley
>> > Sent: Friday, July 29, 2022 20:31
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: [ccp4bb] PDB to AlphaFold via Uniprot
>> >
>> > I wonder if others are curious about (or know how to solve) the
>> > following problem:
>> >
>> > I am looking at a PDB file that I've downloaded from a wwPDB site and I
>> > would like to see the AlphaFold model(s) overlaid. What the best (or
>> > easiest) way of doing that? (let's imagine that I can do a bit of
>> > scripting in python (including urllib) and can use the functions in Coot
>> > for the superposition).
>> >
>> > Thanks,
>> >
>> > Paul.
>> >
>> > ###
>> > #
>> >
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>
>
> --
> Nick Larsen
> Director - Lead Discovery
> H3 Biomedicine | an Eisai Oncology Company
> 300 Technology Sq #5
> Cambridge, MA 02139
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[ccp4bb] Job advert: Postdoc CryoEM

2022-08-02 Thread Panne, Daniel (Prof.) 
Dear all,

We currently have an open postdoc position in our Institute!

The Panne group focuses on signal processing on enhancers and how 3D genome 
organisation contributes to various aspects of genome function. For examples of 
recent work see Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 
562, 538–544 (2018).

We are located at the the Leicester Institute of Structural and Chemical 
Biology (LISCB) is a cross-disciplinary entity that brings together 
internationally renowned research in structural biology, single molecule 
approaches and chemical biology at the University of Leicester. The Institute 
provides access to world-class research facilities, including X-ray 
crystallography, biological NMR spectroscopy, single molecule microscopy and 
the state-of-the-art Midlands Regional Cryo-EM facility.

About you
Successful candidate should have a background in structural studies by single 
particle cryoEM. They must have a track record in conducting internationally 
competitive research. We are looking for a creative and ambitious person with 
good communication skills and keen to work on challenging projects.

LISCB is one of five flagship research institutes recently established by the 
University of Leicester, UK. We have excellent access to state-of-the-art 
structural biology technologies including a Krios cryo-EM microscope equipped 
with K3/BioQuantum and in house GPU cluster for data processing.

For further information and to apply please see the link below:

Research Associate (Structural Biology of Genome 
Regulation)

Closing date is August 31st 2022.

All the best,

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk




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Re: [ccp4bb] Regarding the correct space group identification

2022-08-02 Thread Andrew Leslie - MRC LMB 
Dear Sayan,

   For interest, the only other example I know of where 
diffraction images show two different space groups is presented in a paper by 
Zbyszek Dauter et al, Acta Cryst D61, 967-975, 2005, where crystals of the 
proteolytic domain of Lon contained superimposed orthorhombic and monoclinic 
lattices. At the time (2005) this was the first reported example for proteins 
and I have not come across another since then.

Best wishes,

Andrew

> On 28 Jul 2022, at 07:15, Sayan Saha  wrote:
> 
> Dear All,
> 
> We have collected home-source X-ray intensity data for a protein at 2.6 
> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and 
> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained in 
> both the space groups. However, the solution can be refined with an Rw/Rf of 
> 29/32% only. The protein is bound to a ligand (co-crystallization) for which 
> a clear density can be observed.
> 
> Any help and suggestion in this regard would be very helpful.
> 
> With best regards,
> Sayan Saha.
> 
> 
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Re: [ccp4bb] scitbx issue....

2022-08-02 Thread Harry Powell 
Hi Billy

Many thanks for this - unfortunately, there are other dependencies that appear 
not to be included in

> conda create -n new_environment -c conda-forge cctbx-base python=3.9

e.g. 

> [MacPro:~] harry% conda activate phenix_env
> (phenix_env) [MacPro:~] harry% python
> Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:52) 
> [Clang 13.0.1 ] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scitbx
> Traceback (most recent call last):
>   File "", line 1, in 
>   File 
> "/Volumes/Users/harry/.local/lib/python3.9/site-packages/scitbx/__init__.py", 
> line 1, in 
> from .manage_yaml import Yaml
>   File 
> "/Volumes/Users/harry/.local/lib/python3.9/site-packages/scitbx/manage_yaml.py",
>  line 1, in 
> import yaml
> ModuleNotFoundError: No module named 'yaml'
> >>> 

(WHAT? No YAML?).

I’ll continue this discussion off-BB…

Regarding the PAE matrix reader, I wrote my own since I need to read them for 
other applications. But it’s good to know that (once I get 
process_predicted_model working) you guys are on the case.

Best wishes

Harry

> On 2 Aug 2022, at 06:52, Billy Poon  wrote:
> 
> Hi Harry,
> 
> Can you try creating a new environment with cctbx-base?
> 
> conda create -n new_environment -c conda-forge cctbx-base python=3.9
> 
> Then activate the environment to test
> 
> [bkpoon@eeyore:~] conda activate new_environment
> (new_environment) [bkpoon@eeyore:~] python
> Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:33) 
> [Clang 13.0.1 ] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scitbx
> >>> import scitbx.array_family
> >>> 
> 
> It looks like you are installing cctbx-base into the Anaconda version of 
> python which is from the defaults channel. Mixing packages from different 
> channels does not always work, even though newer packages in the defaults 
> channel tend to be compatible with packages from conda-forge.
> 
> Also, if you do not need all the packages that come with the standard 
> Anaconda installation, I would recommend the miniconda or miniforge 
> installers for getting the conda tool.
> 
> As for the PAE format, some updates have just been committed 
> (https://github.com/cctbx/cctbx_project/pull/775). The latest nightly builds 
> for the cctbx-base conda package will have those. To get them, prepend the 
> "cctbx-nightly" channel to your conda command.
> 
> conda create -n new_environment -c cctbx-nightly -c conda-forge cctbx-base 
> python=3.9
> 
> You should see that the version for cctbx-base is 2022.8a2. I just made an 
> update for conda-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 Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Fax: (510) 486-5909
> Web: https://phenix-online.org
> 
> 
> On Mon, Aug 1, 2022 at 7:06 AM Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 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).
> 
> (2) Does process_predicted_model.py (when I get it working) read the 
> new-style PAE matrices that Sameer told us about last week?
> 
> Since “upgrading” my conda env so that I am using Python 3.9, I’m getting an 
> error with “process_predicted_model”, which is used for splitting up 
> AlphaFold models into (cough, cough) “domains”, based on the PAE matrix. It 
> ran before I did the move from Python 3.7.something…
> 
> I had to remove and reinstall conda to upgrade because I managed to screw up 
> the environment (and didn’t notice that the Python I was using wasnot 
> actually the conda one…). So this is on a freshly installed conda...
> 
> The error I get when trying to run process_predicted_model.py is - 
> 
> > [MacPro:~/icl/test] harry% python3 process_predicted_model.py 
> > pae/AF-Q8W3K0-F1-predicted_aligned_error_v2.json
> > Traceback (most recent call last):
> >   File "/Volumes/Users/harry/icl/test/process_predicted_model.py", line 14, 
> > in 
> > from scitbx.array_family import flex
> > ModuleNotFoundError: No module named ‘scitbx.array_family'
> 
> I’ve tried things like - 
> 
> conda install -c conda-forge cctbx-base
> 
> which installs a load of useful stuff, but not, apparently, 
> scitbx.array_family - 
> 
> > Python 3.9.12 (main, Jun  1 2022, 06:36:29) 
> > [Clang 12.0.0 ] :: Anaconda, Inc. on darwin
> > Type "help", "copyright", "credits" or "license" for more information.
> > >>> import scitbx