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

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 structu

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

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 st

[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 To unsubscribe from the CCP4BB list

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

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)

Re: [ccp4bb] 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

[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 model

Re: [ccp4bb] Downloading trouble of SITCOM software

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

[ccp4bb] Downloading trouble of SITCOM software

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 installa

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

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 (m