Re: [ccp4bb] 2022 MicroED workshop

2022-10-07 Thread Brent Nannenga 
Hi everyone,

This is just a reminder of the 2022 MicroED workshop held UCLA Dec. 11th to the 
14th.

The due date for applying to the workshop is October 11


For more information please see 
https://cryoem.ucla.edu/course-2022



Thanks,



Brent Nannenga


From: CCP4 bulletin board  on behalf of Brent Nannenga 

Date: Wednesday, September 14, 2022 at 10:01 AM
To: CCP4BB@jiscmail.ac.uk 
Subject: [ccp4bb] 2022 MicroED workshop

Dear all,



We are pleased to announce the 7th MicroED workshop to be held the evening of

December 11th to the 14th, 2022, and will be open to both academia and industry.

This workshop will be held at the MicroED Imaging Center at UCLA and will 
contain

both lectures and hands on demonstrations and training. For more information,

tentative schedule, and to apply please see the following website:



   
https://cryoem.ucla.edu/course-2022



Space is limited and historically, the workshop is typically oversubscribed,

therefore we encourage applications to be sent in early.



Topics covered will include all aspects of microcrystal electron

diffraction (MicroED) of diverse samples such as soluble proteins,

membrane proteins, small molecules, natural products, and other materials.



We will cover


* Sample preparation methodologies for proteins and small molecules
* MicroED data collection
* Camera performance
* Cryo-FIB-milling procedures for MicroED
* Data analysis software, structure solution, and refinement



The schedule is available on the registration page.



// Sincerely; on behalf of the organizing committee (Tamir Gonen, Brent 
Nannenga)




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Re: [ccp4bb] ChEBI and SMILES

2022-10-07 Thread Oliver Smart 
On 7 Oct 2022, at 10:12, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:HiProbably 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 ...HarryTo unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/Dear Harry,Although ChEBI has an API this uses SOAP and I am not familiar with ithttps://www.ebi.ac.uk/chebi/webServices.doBut PubChem has a great API system and pubchempy https://github.com/mcs07/PubChemPy provides an easy way to interact with it.Pubchem entries appear to have the CHEBI identifier as one of there synonyms. The attached python script access this information.For instance:$ ./lookup_smiles_in_pubchem.py   "c1c1O"                                                       PubChem_CID:996 ChEBI_ID:15882 (phenol)$./lookup_smiles_in_pubchem.py   "Cn1cnc2n(C)c(=O)n(C)c(=O)c12"PubChem_CID:2519 ChEBI_ID:27732 (caffeine)$./lookup_smiles_in_pubchem.py   "1=NN(C2=C1N=C(NC2=O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)C)OCC)C"PubChem_CID:135398744 ChEBI_ID:9139 (sildenafil)Hope this is usefulOliver

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#!/usr/bin/env python
"""
little script to lookup a SMILES string at PubChem
and print out the CHEBI and ChEMBL identifiers
"""
import pubchempy as pcp
import argparse

# get smiles from command line
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('smiles', metavar='SMILES',
help='SMILES string to lookup')
args = parser.parse_args()
smiles = args.smiles

compound = pcp.get_compounds(smiles, 'smiles')[0]
if compound:
cid = compound.cid
synonyms = compound.synonyms
chebi_ids = [s for s in synonyms if s.startswith('CHEBI:')]
if chebi_ids:
chebi_id = chebi_ids[0].replace('CHEBI:', '')
else:
chebi_id = None
print(f'PubChem_CID:{cid} ChEBI_ID:{chebi_id} ({synonyms[0]})')
else:
print('smiles string not found')



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Re: [ccp4bb] ChEBI and SMILES

2022-10-07 Thread Gerard Kleywegt 

Hi Harry,

On the ChEBI website, if I type a simple SMILES string into the search box 
(c1c1) it takes me to the corresponding entity page. I don't know if they 
have an API that supports this but I'm sure the friendly folks of the ChEBI 
helpdesk (https://www.ebi.ac.uk/chebi/emailChebiForward.do) can tell you.


Another resource that may be of use in this context is UniChem 
(https://www.ebi.ac.uk/unichem/). You provide an InChI (not SMILES 
unfortunately) and it will then return a list of the identifiers of the 
compound in bunch of resources (incl. ChEMBL, ChEBI, PDB, PubChem, Zinc, etc.) 
- if they exist in that resource of course. (It offers an API so is good for 
programmatic access - https://www.ebi.ac.uk/unichem/api/docs )


You can also provide a compound ID from any of those resources to find out 
what it is called in the other resources (if it exists there), e.g. 
https://www.ebi.ac.uk/unichem/compoundsources?type=sourceID=BNZ=3 
searches for the compound we know as BNZ in the PDB.


Hope this helps,

--Gerard




On Fri, 7 Oct 2022, Harry Powell wrote:


Hi Jeet

This is very useful - many thanks.

I was hoping there might be some kind of API for searching the ChEBI database 
online, but there we go…

It looks like downloading the ChEBI database is the first step here, since many 
entries appear to have SMILES information.

But (important to note) ChEBI ≠ ChEMBL, although there is an overlap (a 
considerable ione…).

Harry


On 7 Oct 2022, at 10:29, jeet balraj  wrote:

Hi Harry
To search the ligand of interest in the ChEMBL database, you can follow these 
simple steps:
1. download the ChEMBL database and extract all its SMILES.
2. calculate the MorganFingerprint of each of the SMILES in the database.
3. calculate the MorganFingerprint of your ligand.
4. use the FPSim2 package from ChEMBL for the Tanimoto similarity search.
you can use RDKit to calculate the morgan fingerprints of each 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 13009


On Fri, Oct 7, 2022 at 11:13 AM Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
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


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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] ChEBI and SMILES

2022-10-07 Thread Harry Powell 
Hi Jeet

This is very useful - many thanks. 

I was hoping there might be some kind of API for searching the ChEBI database 
online, but there we go…

It looks like downloading the ChEBI database is the first step here, since many 
entries appear to have SMILES information.

But (important to note) ChEBI ≠ ChEMBL, although there is an overlap (a 
considerable ione…). 

Harry

> On 7 Oct 2022, at 10:29, jeet balraj  wrote:
> 
> Hi Harry
> To search the ligand of interest in the ChEMBL database, you can follow these 
> simple steps:
> 1. download the ChEMBL database and extract all its SMILES.
> 2. calculate the MorganFingerprint of each of the SMILES in the database.
> 3. calculate the MorganFingerprint of your ligand.
> 4. use the FPSim2 package from ChEMBL for the Tanimoto similarity search. 
> you can use RDKit to calculate the morgan fingerprints of each 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 13009
> 
> 
> On Fri, Oct 7, 2022 at 11:13 AM Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 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 following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] ChEBI and SMILES

2022-10-07 Thread jeet balraj 
Hi Harry
To search the ligand of interest in the ChEMBL database, you can follow
these simple steps:
1. download the ChEMBL database and extract all its SMILES.
2. calculate the MorganFingerprint of each of the SMILES in the database.
3. calculate the MorganFingerprint of your ligand.
4. use the FPSim2 package from ChEMBL for the Tanimoto similarity search.
you can use RDKit to calculate the morgan fingerprints of each 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 13009


On Fri, Oct 7, 2022 at 11:13 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> 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 following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] ChEBI and SMILES

2022-10-07 Thread Harry Powell 
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


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