VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Wed Apr 20 2005 - 16:34:14 CDT

Wei,

   It's telling that the problems are with the backbone-dependent representations. It looks like it's related to the presence of an disulfide bond between the two Cys 229 residues. Perhaps VMD is treating the entirety of chain B as part of the CysA229 side chain, at least on some level? Anyway, if I decrease the x coordinate of the chain A Cys229 sulfur atom by 1 (thereby moving it out of the distance for which VMD finds a bond), then chain B displays normally.
   Perhaps the developers can shed further insight...

Chris

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> Of Wei Chen
> Sent: Wednesday, April 20, 2005 1:21 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: representation_problem
>
>
> Hi,
>
> I met a problem with VMD. When I loaded 1E4K.pdb in VMD and
> chose Cartoon or
> Tube representation, chain B could not be shown. Only when I
> deleted Cys229 of
> chain A, chain B could be shown in Tube. I checked this in
> detail. And I found
> this probably is due to a large turn from Pro230 of chain A
> to Cys229 of chain
> A.
>
> Does anybody have this situation?
>
> Wei Chen
>
> --
>
>
>