VMD-L Mailing List

From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Sat Dec 08 2007 - 15:36:37 CST

Alex,

I loaded the trajectory to VMD more than one and after each loading step, I saw a different representation for the peptide although I loaded the same conformation and the trajectory file.
For instance, in one attempt of loading, I saw some of the portions of the peptide as beta strands, however, in other cases, these structures were displayed as coil regions.

I am using the 1.8.6 version of VMD. The problem was the same for both Windows and Linux.

Thanks

Ozge.

-----Original Message-----
From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
Date: Sat, 8 Dec 2007 15:37:00 -0500 (EST)
Subject: Re: vmd-l: problem with the new cartoon representation mode

On Sat, 8 Dec 2007, OZGE ENGIN wrote:

OE> Hi all,

ozge,
 
OE> I have a problem with the new cartoon/structure mode of

whenever you have a problem with VMD, please state the version
of VMD you are using and the platform that you are running on.

OE> representation. Each time, it assigns a different secondary

what do you mean by "each time"? please describe in more detail
what you are doing and what you expect (and don't see). none of
us can see your computer screen or what you do.

OE> structural pattern to my peptide. So, I could not get a clear
OE> picture of the structure of my peptide.

OE> Why is it the case? What may be the problem?

with so little information, one can only speculate.

since computers and software are (usually) deterministic,
it is quite possible, that VMD is simply reflecting an
inconsistency in what you are doing. PEBCAC?

cheers,
   axel.

OE>
OE>
OE>
OE>
OE> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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