Re: [ccp4bb] Multiple ligand simultaneous docking

[Gary Thompson]

Haddock certainly has support for this



HADDOCK Web Server
science.uu.nl
[favicon.ico]



But I have not run it myself…

regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences,  Division of Natural Sciences
University of Kent,  Canterbury,  Kent,  England,  CT2 7NZ

☎:01227 82 7117
✉️: g.s.thomp...@kent.ac.uk
orchid: orcid.org/-0001-9399-7636

On 6 May 2024, at 17:29, Thripthi Shenoy  wrote:

You don't often get email from thripthishe...@gmail.com. Learn why this is 
important

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Greetings!

I am learning the concept of multiple ligand simultaneous docking and would 
like to know if there is any standard protocol for the same.
Thanking you in advance,

With regards,
Thripthi Shenoy.



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Re: [ccp4bb] Downloading individual chains from the PDB

[Gary Thompson]

I stand corrected and have learnt a new trick, thanks Jose!

Note jose’s reply has a typo it is 
https://models.rcsb.org not 
https://modes.rcsb.org

loading the page https://models.rcsb.org on its own 
gives a nice rather nice listing of the api…

Regards
Gary


Dr Gary S Thompson
NMR Facility Manager
CCPN CoI & Working Group Member

Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Faculty of Natural Sciences
University of Kent, Canterbury,  Kent,
England,  CT2 7NZ


tel: 01227 82 7117
e-mail: g.s.thomp...@kent.ac.uk
orchid: 
orcid.org/-0001-9399-7636



From: CCP4 bulletin board  on behalf of Jose Duarte 

Date: Thursday, 7 September 2023 at 18:03
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Downloading individual chains from the PDB
CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Gary pointed me to a typo in the API reference link (thanks!). This is the 
correct one: https://models.rcsb.org

On Thu, 7 Sept 2023 at 09:34, Jose Duarte 
mailto:jose.dua...@rcsb.org>> wrote:
The ModelServer API is your friend. See the APIs help page at 
https://www.rcsb.org/docs/programmatic-access/web-services-overview and the 
full ModelServer API reference at 
https://modes.rcsb.org

An example that retrieves chain A of 2trx (in CIF format): 
https://models.rcsb.org/v1/2trx/atoms?label_asym_id=A=cif_all_categories=false=false

I'll also take this opportunity to advertise the upcoming RCSB PDB APIs crash 
course: https://iqb.rutgers.edu/node/279 . Though the course will mostly deal 
with other APIs (Data and Search).

Hope this helps

Jose


On Thu, 7 Sept 2023 at 09:17, Whitley, Matthew (NIH/NCI) [C] 
>
 wrote:
Hello all,

I have a script I use from time to time to batch download multiple PDB files 
using curl.

I have certain use cases in which I only need a specific chain from a PDB file 
that contains multiple chains.  At present, I download the complete PDB file 
and then use pdbtools to pull out the specific chain I want.

Does anyone know a way to batch download specific chains from the PDB?   I 
reviewed the “File Download Services” page at the RCSB PDB, but I didn’t find 
anything about downloading specific chains, so I don’t know if this 
functionality exists.

Thanks for your suggestions.
Matthew




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Re: [ccp4bb] Downloading individual chains from the PDB

[Gary Thompson]

The PDB will only provide you with complete deposited files. You can’t download 
individual chains. The only way to do it is as you are doing, grab the 
deposited file and then parse it to get the chains….

Regards
Gary

Dr Gary S Thompson
NMR Facility Manager
CCPN CoI & Working Group Member

Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Faculty of Natural Sciences
University of Kent, Canterbury,  Kent,
England,  CT2 7NZ


tel: 01227 82 7117
e-mail: g.s.thomp...@kent.ac.uk
orchid: 
orcid.org/-0001-9399-7636



From: CCP4 bulletin board  on behalf of Whitley, Matthew 
(NIH/NCI) [C] 
Date: Thursday, 7 September 2023 at 17:17
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Downloading individual chains from the PDB
CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Hello all,

I have a script I use from time to time to batch download multiple PDB files 
using curl.

I have certain use cases in which I only need a specific chain from a PDB file 
that contains multiple chains.  At present, I download the complete PDB file 
and then use pdbtools to pull out the specific chain I want.

Does anyone know a way to batch download specific chains from the PDB?   I 
reviewed the “File Download Services” page at the RCSB PDB, but I didn’t find 
anything about downloading specific chains, so I don’t know if this 
functionality exists.

Thanks for your suggestions.
Matthew




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Re: [ccp4bb] choosing an NMR structure from PDB

[Gary Thompson]

Hi Harry

First off I would look at quality metrics. For the structures from the same 
paper you will need to check what the differences are in the paper and choose 
what’s closest to what you have need (experimental conditions etc) assuming 
they all have similar quality

As a secondary priority you will want to look at number of restraints (and 
especially in the region of interest)

Note I would expect the more modern structures from cyana and aria to better 
due to improved methodologies

Regards
Gary


Dr Gary S Thompson
NMR Facility Manager
CCPN CoI & Working Group Member

Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Faculty of Natural Sciences
University of Kent, Canterbury,  Kent,
England,  CT2 7NZ


tel: 01227 82 7117
e-mail: g.s.thomp...@kent.ac.uk
orchid: 
orcid.org/-0001-9399-7636



From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, 3 May 2023 at 11:45
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] choosing an NMR structure from PDB
CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
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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 need for actually doing experiments), but 
there are only NMR models - how do I choose?

I don’t mean “which model from the ensemble do I choose” - that’s a different 
question.

For P01132, for example, I could choose (from the PDB) 1A3P, 1EGF, 1EPG, 1EPH, 
1EPI, 1EPJ, 1GK5 or 3EGF. Note that some of 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


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Re: [ccp4bb] Is this Spam? This looks like Spam.

[Gary Thompson]

So this was quite real and not spam, here is an update from jisc

---start

https://www.jiscmail.ac.uk/20230111-ServiceDisruption.html

"On Thursday, 05 January 2023, we received notification that one of the email 
servers used by JiscMail was listed on a global spam "blacklist", causing 
recipient mail servers to start rejecting JiscMail posts.
We reported the issue to the operators of that email server, and worked with 
them to ensure that the server was removed from the list. By 09:00hrs on Friday 
(06 January) it was confirmed that the server had been removed from the 
blacklist, and that normal service had resumed.
Unfortunately, later that day, the server was re-added to the blacklist, 
causing recipient servers to start rejecting messages once more.
Due to the way in which the software underpinning the JiscMail service works, 
after several bounced or rejected messages to an individual email address, the 
software assumes that the address no longer exists and removes it from any 
subscribed groups. This had the effect of removing around 50,000 subscriptions 
to just short of 500 JiscMail lists.
We are pleased to inform you that, as of 14:00hrs on Wednesday, 11 January 
2023, we believe the root cause of the issue (the blacklisting) to have been 
resolved, and are in the process of resubscribing all affected users. We expect 
this to be completed by no later than 17:00hrs on Wednesday, 11 January 2023.
Despite these issues having been addressed, subscribers and list owners may 
continue to recieve error messages that have been "queued" by mail servers 
outside of our direct control. These are expected to have fully cleared by 
Friday, 13 January 2023.
---end

Note it contains a link back to the jisc website so you can validate it’s a 
correct message

Regards
Gary


---
Dr Gary S Thompson
NMR Facility Manager
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, University of Kent,
Canterbury,  Kent,  England,  CT2 7NZ


tel: 01227 82 7117
e-mail: g.s.thomp...@kent.ac.uk
orchid: 
orcid.org/-0001-9399-7636
---


From: CCP4 bulletin board  on behalf of Rafael Marques 

Date: Thursday, 12 January 2023 at 09:36
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] RES: [ccp4bb] Is this Spam? This looks like Spam.
CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

The same happened to me. I had to subscribe again cause I was not receiving 
ccp4 mails anymore.

Best


Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"


De: Goldman, Adrian
Enviado:quinta-feira, 12 de janeiro de 2023 06:34
Para: CCP4BB@JISCMAIL.AC.UK
Assunto: Re: [ccp4bb] Is this Spam? This looks like Spam.

Me too. My uni says that a Microsoft set of addresses ended up on a spam 
blacklist, which is why this happened. I suspect your institutions are also 
using office365 outlook (also known as crapmail) as mail server and client

As roberto, I complain all the time to my uni about their mail and it. Probably 
as roberto, it has no effect whatsoever.

Adrian
Sent from my iPhone



On 11 Jan 2023, at 23:13, Becker, Stefan  wrote:
 I also received this kind of message. Is it definitely spam? I waited for 24 
hours and noticed that no messages appeared under CCP4BB. Then I re-registered 
with CCP4BB. From that moment I received messages again.

Best,
Stefan Becker





Am 10.01.2023 um 15:23 schrieb Bernhard Rupp 
mailto:hofkristall...@gmail.com>>:

I got unsubscribed from ccp4em yesterday with a similar message for 
b...@ruppweb.org. That one has a minor certificate 
problem that however does not affect other email recepients.

For some reason, the ssl certificate for 

[ccp4bb] Lectureship Positions University of Kent

[Gary Thompson]

We have two Jobs advertised at the University of Kent that may be of interest 
to structural biologists with expertise in macro molecular crystallography.

https://jobs.kent.ac.uk/Vacancy.aspx?ref=STM-032-19

The School of Biosciences has a long and continuing interest in structural 
biology with several groups exploiting NMR and Macromolecular Crystallography 
to study a wide range of problems. These include infection and drug resistance, 
cancer and age-related diseases, cellular architecture and dynamics and 
reproduction, evolution and genomics and industrial biotechnology.  The School 
of Biosciences consistently has time as a BAG at Diamond and has recently 
invested in a new Mosquito LCP System with humidity control for crystallisation 
drop set up. Other facilities available for structural biologists include a 
well equipped Biomolecular Science Facility  (electrospray and MALDI-TOF mass 
spectrometers, peptide synthesisers, CD etc) an in  house X-Ray source in the 
School of Physical Sciences (Rigaku Oxford Diffraction Supernova)  and a 
dedicated Biological NMR Facility with BAG access at the UK national NMR 
facilities at the Crick and Birmingham. Applications close 23.59 hours BST 19th 
August. See Job Description for further details.

regards
gary

---
Dr Gary S Thompson

School of Biosciences, University of Kent,
Canterbury,  Kent,  England,  CT2 7NZ


tel: 01227 82 7117
e-mail: g.s.thomp...@kent.ac.uk
orchid: orcid.org/-0001-9399-7636
---




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