Re: [Jmol-users] Fwd: Re: Chain order changes: a problem for Proteopedia

2009-03-30 Thread Eran Hodis
Bob, Thank you for the clarification. Everything makes sense. Eran On Tue, Mar 31, 2009 at 1:39 AM, Robert Hanson wrote: > Let's clear up the atom serial number business. > > PDB file contain atom serial numbers. These are in the ATOM and HETATM > records. Behind the scenes, in the Jmol code,

Re: [Jmol-users] Fwd: Re: Chain order changes: a problem for Proteopedia

2009-03-30 Thread Robert Hanson
Let's clear up the atom serial number business. PDB file contain atom serial numbers. These are in the ATOM and HETATM records. Behind the scenes, in the Jmol code, we call these "atom serial numbers" as opposed to "atom index numbers", which start at 0 and go consecutively through ALL models load

Re: [Jmol-users] Fwd: Re: Chain order changes: a problem for Proteopedia

2009-03-30 Thread Robert Hanson
On Mon, Mar 30, 2009 at 4:16 PM, Eric Martz wrote: > Dear Bob, > > How difficult would it be to change the state script generator in Jmol to > avoid using atom serial numbers? > impossible. It has to use atom index numbers (what you are calling "serial numbers"). That I know. > > I'm sure none

Re: [Jmol-users] Fwd: Re: Chain order changes: a problem for Proteopedia

2009-03-30 Thread Eran Hodis
Dear Eric, Your email mentioned atom serial numbers but Bob said in a previous email "Eric, Jmol does not use atom serial numbers in state scripts. It uses atom indexes, but maybe that's what you were referring to." However, Bob, if atom indexes are the same as atom serial numbers, then I too woul

[Jmol-users] Fwd: Re: Chain order changes: a problem for Proteopedia

2009-03-30 Thread Eric Martz
Dear Bob, How difficult would it be to change the state script generator in Jmol to avoid using atom serial numbers? I'm sure none of us ever envisioned the current state of affairs. We have who knows how many state scripts saved in Proteopedia, and now an unknown number of March-17-remediated PD