Re: [ccp4bb] cavities volume calculations

Dear nathalie, from the top of my head, I use FLOOD from Upsala software factory: The program fills in water molecules in the cavity; you can specify a radius and start from a point in the pdb, like a side chain atom or you can put a dummy water molecule in the middle of your cavity and start

Re: [ccp4bb] cavities volume calculations

Dear Nathalie, try CASTp ( http://sts.bioe.uic.edu/castp/index.html?2cpk ) Cheers, Flavio. Il giorno lun 6 lug 2020 alle ore 15:41 Nathalie Colloc'h < coll...@cyceron.fr> ha scritto: > Hi everybody, > > I am aware of programs which compute the volume of cavities and pockets. > > However, I am

Re: [ccp4bb] cavities volume calculations

thanks joana, it is true that you can give a set of coordinates to Caver, but to my knowledge, Caver look for tunnels only. It does not seem to compute the volume of surface pockets or internal cavities. best nathalie Le 06/07/2020 à 15:46, Joana Pereira a écrit : Hi Nathalie, I

Re: [ccp4bb] cavities volume calculations

Hi Nathalie, I think Caver tools can do that: https://caver.cz/index.php?sid=133 Best wishes Joana > On 6. Jul 2020, at 15:39, Nathalie Colloc'h wrote: > > Hi everybody, > > I am aware of programs which compute the volume of cavities and pockets. > >

[ccp4bb] cavities volume calculations

Hi everybody, I am aware of programs which compute the volume of cavities and pockets. However, I am looking for a program which can compute the volume around a given point (given by its coordinates), and return also the information about if it is an open surface pocket or an internal cavity.