Hi, Sure If someone has a script to share I would be happy to give it a go, I think this would be highly useful. (I actually don’t think I have the resources for this myself) (I don’t I need to look at b-factors right now, just would go with the identified waters at the interface (or networks, ie all water molecules networks that link the two proteins here, resolution is 1.6 Å so they are well established).
Cheers, Tommi From: Rezaul Karim <reza...@yahoo.com> Date: Friday, 8. November 2024 at 10.39 To: Kajander, Tommi A <tommi.kajan...@helsinki.fi> Cc: CCP4BB@jiscmail.ac.uk <CCP4BB@jiscmail.ac.uk> Subject: Re: [ccp4bb] Analysing water molecules at protein interfaces Hi Tommi, From my experience , pymol script might be one of the best options if not the best. Since you might want to consider the relative/normalized b factor for “bridging water” & want to visualize the distances & assess whether all makes sense; pymol script works great for all of those. Unfortunately, not a ready made software but you get tons of ways to customize your script & visualization with the help of command line & pymolwiki. Best, Reza Karim Sent from my iPhone On Nov 6, 2024, at 7:43 AM, Kajander, Tommi A <tommi.kajan...@helsinki.fi> wrote: Dear all, Is there a something available to automatically analyse/identifiy/quantify bound (“bridging”) water molecules at protein-protein interfaces? Could not find anyting right away. Thanks in advance, Best, Tommi ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
