VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 19 2002 - 11:42:08 CDT

Dear VMD-L,
  Just to followup on the previous RMSD discussion, the RMSD
feature is in fact working fine, this problem was a user
error after all.

----- Forwarded message from Vlad Cojocaru <Vlad.Cojocaru_at_mpi-bpc.mpg.de> -----

Date: Fri, 16 Aug 2002 17:33:58 +0200
From: Vlad Cojocaru <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
To: justin_at_ks.uiuc.edu
Subject: Re: the same problem

Hi!
 Thanks for Reply but I realized the problem. I had to fit first and
then to calculate and now it works pretty fine. The problem was that I
tried it this way (fitting first) a while a go but there was an error in
my script by that time. Now I fixed it and so far I managed to calculate
a lots of combinations of rmsd values for different sstructures and
selections and it seems to work.
Thanks a lot and sorry if I have given headaches with otherwise a very
simple thing that became complicated only because of a stupid mistake of
mine.
 Best wishes,
vlad

Justin Gullingsrud wrote:

>Hi Vlad,
>
>Would it be possible for you to send us the two structures you are aligning
>so that we can determine what the problem might be? It wouldn't even have
>to be the entire structure if you'd prefer; just the atoms used to calculate
>the fitting matrix would be sufficient. We've been using rmsd for some time
>now and had figured we'd gotten the code pretty reliable, but this could be
>the test case that uncovers a bug...
>
>Thanks,
>Justin
>
>On Fri, Aug 16, 2002 at 11:33:55AM +0200, Vlad Cojocaru wrote:
>
>>Hi!
>> I am sorry to tell you but when it comes to rmsd fit the VMD 1.8a21
>>gives the same results as 1.7.1. So, for instance for two structures
>>that overlay almost perfectly the rmsd value is something like 3.42
>>....imp[ossible no??
>>Bets regards,
>>vlad
----- End forwarded message ----- 

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