VMD-L Mailing List

From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Sat Dec 08 2007 - 16:53:51 CST

Alex,

First of all, thank you for your attention.

The case looks like to the second scenario much more. I load the same configuration and trajectory files; however, I assign the new cartoon representation to the structure at different frames while the trajectory is being loaded to VMD. If I assign the new cartoon representation to the peptide before loading the trajectory, I got the same secondary structure representation. However, if I assign the representation at different frames, I got different structures and it continued till the end of the last frame of the trajectory file.

I had performed a replica-exchange simulation in vacuum, so my peptide moves a lot indeed.

So, how can I get information about the secondary structure of my peptide exactly?

Thank you

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 17:08:22 -0500 (EST)
Subject: Re: Re: vmd-l: problem with the new cartoon representation mode

On Sat, 8 Dec 2007, OZGE ENGIN wrote:

OE> Alex,
OE>

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

let me get this straight. you are loading the _exact_ same file
and you get different secondary structure assignments?

or are you loading different portions of a trajectory?

if it is the first case, please upload the file and some
snapshot images to the VMD biofs on the VMD public biocore
project, so that we can have a look at it and verify it.
this sounds very strange indeed. do you get any warnings
and/or error message in the VMD console window?

if it is the second case, it depends a lot on your protein
and the simulation. if it moves a lot the structure assignment
can change, too.

thanks,
   axel.

OE>
OE> I am using the 1.8.6 version of VMD. The problem was the same for both Windows and Linux.
OE>
OE> Thanks
OE>
OE> Ozge.
OE>
OE> -----Original Message-----
OE> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
OE> To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
OE> Date: Sat, 8 Dec 2007 15:37:00 -0500 (EST)
OE> Subject: Re: vmd-l: problem with the new cartoon representation mode
OE>
OE> On Sat, 8 Dec 2007, OZGE ENGIN wrote:
OE>
OE> OE> Hi all,
OE>
OE> ozge,
OE>
OE> OE> I have a problem with the new cartoon/structure mode of
OE>
OE> whenever you have a problem with VMD, please state the version
OE> of VMD you are using and the platform that you are running on.
OE>
OE> OE> representation. Each time, it assigns a different secondary
OE>
OE> what do you mean by "each time"? please describe in more detail
OE> what you are doing and what you expect (and don't see). none of
OE> us can see your computer screen or what you do.
OE>
OE> OE> structural pattern to my peptide. So, I could not get a clear
OE> OE> picture of the structure of my peptide.
OE>
OE> OE> Why is it the case? What may be the problem?
OE>
OE> with so little information, one can only speculate.
OE>
OE> since computers and software are (usually) deterministic,
OE> it is quite possible, that VMD is simply reflecting an
OE> inconsistency in what you are doing. PEBCAC?
OE>
OE>
OE> cheers,
OE> axel.
OE>
OE>
OE> OE>
OE> OE>
OE> OE>
OE> OE>
OE> OE>
OE>
OE> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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