Have you tried P2Rank? It is quite fast, and there is a standalone version that has command line options to run against all coordinate files in a directory using batch mode.
https://prankweb.cz/ https://prankweb.cz/about https://github.com/rdk/p2rank You can try the web version to see how it performs with one of your favorites. I like the automatically created pymol scripts as well. It does occasionally split a larger pocket into smaller ones, similar to the fpocket behavior, but perhaps not quite as frequent. -Mike On Wed, Jan 4, 2023 at 6:31 AM Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > THX for the replies - > > > On 3 Jan 2023, at 22:56, Bernhard Rupp <hofkristall...@gmail.com> wrote: > > > > There is also a service from our Polish friends: > > called Spaceball (jokes aside) that calculates the volume of protein > cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/). > > and the services in Hamburg are useful for visualization of binding > pockets and channels > > https://proteins.plus/ > > I really want something that I can put iin a script, not a web-page. These > both appear to be web interfaces > > > James Holton - > > > > PanDDA? > > PanDDA is really for density analysis across putative changed-state > datasets - I have many thousands of models to inspect that have no > associated experimental datasets > > > Andre Godoy - > > > > if you mean predicting binding sites, FT map is quite good > > > > Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php > > I’m really after alternatives to programs like: > > pyKVFinder (but that won’t install easily from PYPI on my Mac > because my OS is too old - if anyone wants to buy me a new big, fast Mac to > replace my old, fast Mac I should be able to install that easily!!) or > > fpocket (which works okay but is splitting up “obvious" > single-site pockets into multiple pockets). > > Plus they need to be able to run from a script (or from the command-line > so it can be scripted) - web interfaces are okay if you have a few > examples, but when you’re analysing 1000 - 1500 models a day, clicking > buttons gets a little boring! > > Sorry my initial post wasn’t clearer > > Harry > ######################################################################## > > 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/ > ######################################################################## 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/
