From: Ian Stokes-Rees (
Date: Fri Jul 30 2010 - 13:14:47 CDT

On 7/29/10 11:33 AM, Kirby Vandivort wrote:
> John Stone wrote:
>> Kirby,
>> Can you also check how it behaves for VMD 1.8.7? I'm assuming
>> that's the version that Ian was running.
> Works fine on 1.8.7 for me as well.

Thanks for trying this out. I have started completely from scratch and
I am now able to get this to work properly.

>From having done the VMD tutorial a few weeks ago at Scripps I think the
part I was forgetting was that sometimes VMD or MultiSeq can get
"confused" and it is best to "get out of the car, get back in the car".
I should have tried this before simply deleting all my models and
loading them again, but rather fully exit VMD and restart it.

It would be nice if this wasn't necessary -- if there are no models
loaded, it should be reasonable to assume the system is in a "virgin"
starting state. But being a s/w developer myself, I appreciate how this
isn't always possible.

Anyway, thanks a lot for the quick response and help with this. I look
forward to automating it and using it as a key part of our structure
alignment output.