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

Re: [ccp4bb] ContaMiner server down?

Dear Julian I don't know about ContaMiner, but you might also try SIMBAD for contaminant detection https://simbad.readthedocs.io/en/latest/ It's available at the command line, through i2 and Cloud interfaces, and at the CCP4 Online server https://ccp4online.ccp4.ac.uk/ccp4online/ Dan

[ccp4bb] Fully funded PhD studentship: extended deadline

Dear all We have decided to extend the deadline on our new fully-funded PhD studentship. It's co-funded and co-led by Liverpool and CCP-EM and is a really exciting opportunity for the right student. Further details here

Re: [ccp4bb] looking for proteins with no homologues in pdb

One short cut would be to focus on Pfam families that do not yet have a 3D representative. They can be browsed eg https://pfam.xfam.org/family/browse?browse=a or you can also install Pfam locally as MySQL for programmatic access. Choosing Families rather than Domains would make it easier to

[ccp4bb] Fully-funded PhD at the University of Liverpool

Please pass on this information to any plausible candidates you know. Thanks Title: Efficient matching of protein structures to cryo-EM map segments Initial deadline: June 30th This project

Re: [ccp4bb] CCP4BB vs COVID19

Hi James 5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold similar to ORF7 (for which there is a structure; 1xak). https://toolkit.tuebingen.mpg.de/jobs/2717885_1 I must say I got quite excited

Re: [ccp4bb] Searching similar local structural conformations

Dear Lei You can use ASSAM for this http://27.126.156.175/assam/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394286/ In the past I've also used SPASM locally for this http://xray.bmc.uu.se/usf/spasm.html but I think you'll need to generate your own up to date database to search. Best

[ccp4bb] Joint Liverpool/Diamond PhD studentship

Dear all, A fully-funded 4-year PhD studentship, joint between the University of Liverpool and the Diamond Light Source, is now available. Paying an enhanced stipend, it involves application of computational methods to characterise and solve diffraction datasets from crystals of transmembrane