From: Mgr. Lubos Vrbka (
Date: Sun Dec 18 2005 - 08:24:02 CST

hi guys,

> I think the best way to accomplish what you have in mind is to write
> a script that analyzes your structure water-by-water, frame-by-frame,
> for the criteria you've specified, and sets the "user" field for each
> atom to 0 or 1 depending on its water/ice status for that frame.
ok, after going through the manual i probably identified the commands i
will need - namely the 'measure commands' and 'measure hbonds' one. i
have some additional questions, though:

firstly, since 'measure hbonds' (or any part of vmd) is not PBC-enabled,
i was thinking about how to solve it.
the easiest way would be to create all 26 copies of the unit cell
surrounding it and then analyze the contacts for the original (central)
image only. is there any description how to do this? it would be
probably necessary to do it separately for each frame and then remove it
again, since the trajectories are quite large.
or, would it be better to re-center the frame for every single water
molecule i will be analyzing? again, any docs? i don't want the original
molecule (in the vmd sense) to be modified. these operations would be
performed only to set the user field...
or, do there exist pbc-enabled 'measure' commands/macros? john, you once
wrote me that some colleague of you wrote something related to this.
however at that time he/she was out of the town and then i forgot about
it. do you have some access to such code? would it be possible to post
it on the vmd page somewhere?
regarding the recent posts about the PBC i think there will be some work
done on this issue, however i need to do the analysis quite soon, so i
cannot wait until it will be fully integrated to vmd (however i'm REALLY
looking forward to it)

also, is it possible to use 'measure hbonds' and the other commands from
the python interface? i found only some required commands in the cmd
manual (e.g., the command to get the PBC parameters or xyz coordinates).
i will use the tcl if necessary, however i'd prefer python. again, any
pointer to the relevant docs / usage examples would be greatly appreciated.

thanks in advance for any hints,

Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic