search

akohlmey / topotools

VMD plugin for manipulating topology information
Other
28 stars 16 forks source link

Update residues #8

Closed jonas-feldt closed 7 years ago

jonas-feldt commented 7 years ago

Dear Developers,

I'm using the TopoTools commands clearbonds and addbonds to correctly set the bonds for my system which works like a charm. However the definition of residues is not updated based on the new bonds.

I would like to use the residue information for atomselections or subsequent calls to PBCTools wrap function with the compound option.

I tried to set the residue information manually with the set command of atomselections. However I just get the message data not modifiable. Is there any possibility to update the residues with TopoTools?

Thank you for time, Jonas

jvermaas commented 7 years ago

Are the resids the same? My recollection is that VMD checks for things to have the same resid in addition to being bonded. It might also require the atoms being consecutive. In any event, "mol reanalyze top" is the VMD command you want, since it reevaulates residue definitions.

jonas-feldt commented 7 years ago

Thanks a lot @jvermaas ! 'mol reanalyze' is exactly what I was looking for.

I had a number of molecules merged into a single residue because the distance based bond detection connected them all. So I set the correct bonds (= disconnected them) and hoped that it will also redefine the residues.