Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Irwin Selvam]

Hi,

Have you tried GESAMT? See 
https://www.ccp4.ac.uk/html/gesamt.html#command-line-options

All the best,

Irwin

From: CCP4 bulletin board  on behalf of Manoj N 

Sent: Thursday, March 2, 2023 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Tools for structure-based multiple sequence alignment


Dear all,

We want to generate a structure-based multiple sequence 
alignment for a large number of homologous structures (>100).


What are the available programs (stand-alone or webserver) to do this?


Thank you,

Best wishes,

Manoj



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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Rigden, Dan]

Dear Manoj

I would recommend CCP4's own GESAMT for this.

Dan

Sent from Outlook for Android

From: CCP4 bulletin board  on behalf of Manoj N 

Sent: Thursday, March 2, 2023 7:45:39 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Tools for structure-based multiple sequence alignment


Dear all,

We want to generate a structure-based multiple sequence 
alignment for a large number of homologous structures (>100).


What are the available programs (stand-alone or webserver) to do this?


Thank you,

Best wishes,

Manoj



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[ccp4bb] Tools for structure-based multiple sequence alignment

[Manoj N]

Dear all,
                We want to generate a structure-based multiple sequence alignment for a large number of homologous structures (>100).




What are the available programs (stand-alone or webserver) to do this? 



Thank you,
Best wishes,
Manoj








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Re: [ccp4bb] Protein models with Cofactors, metal clusters and heme

[Joel Tyndall]

Thanks for the recommendations.

From: Dias, Joao M. 
Sent: Thursday, 2 March 2023 10:17 AM
To: Joel Tyndall ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: Protein models with Cofactors, metal clusters and heme

Hi Joel,
Have you tried Alphafill:
AlphaFold Filled 
(alphafill.eu)
https://alphafill.eu/


AlphaFill: enriching AlphaFold models with ligands and cofactors
Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten & Anastassis Perrakis
Nature Methods volume 20, pages205–213 (2023)
https://www.nature.com/articles/s41592-022-01685-y

Good luck,
Joao


Joao M. Dias, Ph.D.
Principal Scientist
Pfizer
Structural and Molecular Sciences
Building 220/ room 3263, MS-8220-3224
445 Eastern Point Rd.
Groton, CT 06340




From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Joel Tyndall
Sent: Wednesday, March 1, 2023 4:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Protein models with Cofactors, metal clusters and 
heme

Hi,

I have a slightly off topic question around structure models, e.g. Homology 
modelling. It may appear that Alpha fold etc could make homology modelling 
somewhat redundant. However I have noticed that in at least two structures, 
either a cofactor or heme are not present on the Alphafold models (that I am 
aware of).

Is anyone aware of any webserver/package that will model these cofactors 
reliably (outside of modeller)?

Many thanks

J

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | 
pharmacy.otago.ac.nz





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Re: [ccp4bb] Protein models with Cofactors, metal clusters and heme

[Dias, Joao M.]

Hi Joel,
Have you tried Alphafill:
AlphaFold Filled (alphafill.eu)
https://alphafill.eu/


AlphaFill: enriching AlphaFold models with ligands and cofactors
Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten & Anastassis Perrakis
Nature Methods volume 20, pages205–213 (2023)
https://www.nature.com/articles/s41592-022-01685-y

Good luck,
Joao


Joao M. Dias, Ph.D.
Principal Scientist
Pfizer
Structural and Molecular Sciences
Building 220/ room 3263, MS-8220-3224
445 Eastern Point Rd.
Groton, CT 06340




From: CCP4 bulletin board  On Behalf Of Joel Tyndall
Sent: Wednesday, March 1, 2023 4:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Protein models with Cofactors, metal clusters and 
heme

Hi,

I have a slightly off topic question around structure models, e.g. Homology 
modelling. It may appear that Alpha fold etc could make homology modelling 
somewhat redundant. However I have noticed that in at least two structures, 
either a cofactor or heme are not present on the Alphafold models (that I am 
aware of).

Is anyone aware of any webserver/package that will model these cofactors 
reliably (outside of modeller)?

Many thanks

J

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | 
pharmacy.otago.ac.nz





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[ccp4bb] Protein models with Cofactors, metal clusters and heme

[Joel Tyndall]

Hi,

I have a slightly off topic question around structure models, e.g. Homology 
modelling. It may appear that Alpha fold etc could make homology modelling 
somewhat redundant. However I have noticed that in at least two structures, 
either a cofactor or heme are not present on the Alphafold models (that I am 
aware of).

Is anyone aware of any webserver/package that will model these cofactors 
reliably (outside of modeller)?

Many thanks

J

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | pharmacy.otago.ac.nz





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Re: [ccp4bb] Downloading trouble of SITCOM software

[Tim Gruene]

Dear Fu Xingke,

the new URL http://webapps.embl-hamburg.de/sitcom/ should work.

Best regards,
Tim

On Wed, 1 Mar 2023 20:13:48 +0800
fuxingke  wrote:

> Dear Colleagues,
>  I found SITCOM is useful, but I find the websites can't be
> opened. The old from paper is
> http://schneider.group.ifom-ieo-campus.it/sitcom. So I can't download
> the package to install for using.
> 
> 
> So, I wuould be really appreciate it if you can provide the
> SITCOM installation packages for linux or MacOS.
> 
> 
> I'm looking forward to your reply.
> 
> 
> Regards
> 
> 
> 
> 
> 
> 
> 
> Best wishes,
> 
> Fu Xingke
> 
> Institute of Physics CAS
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpl8kjutd1CK.pgp
Description: OpenPGP digital signature

[ccp4bb] Downloading trouble of SITCOM software

[fuxingke]

Dear Colleagues,
 I found SITCOM is useful, but I find the websites can't be opened. The old 
from paper is http://schneider.group.ifom-ieo-campus.it/sitcom. So I can't 
download the package to install for using.


So, I wuould be really appreciate it if you can provide the SITCOM 
installation packages for linux or MacOS.


I'm looking forward to your reply.


Regards







Best wishes,

Fu Xingke

Institute of Physics CAS





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[ccp4bb] SFX at SwissFEL Alvra - call for proposals open until 15.03.2023

[Beale Emma Victoria]

Dear all,

I would like to draw your attention to the latest call for proposals for serial 
femtosecond crystallography (SFX) experiments at the SwissFEL Alvra Endstation 
at the Paul Scherrer Institute, Switzerland: 
https://www.psi.ch/en/swissfel/calls

Proposal submission deadline: 15.03.2023 (midnight CEST time)

Proposals evaluated: 15.03.2023 – 30.04.2023

Beamtimes scheduled: 01.08.2023 – 17.12.2023

New or inexperienced users are welcome to contact the Alvra group leader Camila 
Bacellar (camila.bacel...@psi.ch) to discuss 
their proposals ahead of submission.

Users must submit their proposals via the DUO system (https://duo.psi.ch/duo/). 
Details of the available experimental parameters at Alvra are shown here: 
https://www.psi.ch/en/swissfel/alvra.

Sample delivery with in-house support is predominantly achieved using a 
high-viscosity extruder, suitable for both membrane and soluble protein 
crystals. Laboratory space onsite is available for sample preparation, 
including a dark room with an anaerobic chamber.

A pipeline for pre-characterising sample prior to applying for beamtime, in 
collaboration with the beamline staff, is available and strongly encouraged. 
Please contact me directly for details 
(emma.be...@psi.ch).

Best wishes,

Emma Beale


Paul Scherrer Institut
Emma V. Beale
OVGA/414
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

email: emma.be...@psi.ch
phone: +41 56 310 53 69

Office hours: Tuesday, Wednesday and Thursday
Bürozeiten: Dienstag, Mittwoch und Donnerstag








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