VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 06 2009 - 19:48:47 CST

Hi Haosheng,
when you say the protein has been moved, do you mean it has been
translated as a whole, or that it has also undergone some internal
changes? You might want to check the secondary structure assignments
(color by secondary structure or use $sel get structure) to verify that
you're not just seeing stretches that are flagged by stride as coil or turn.

On windows, do you only get the error for your modified structure, or
any time you try to use the cartoon rep?
Peter

haosheng_at_hec.utah.edu wrote:
> Hi All:
>
> I met a problem which is probably common as I read the threads in the
> mailing list. But I couldn't find a solution.
>
> I loaded two exactly same .pdb file in VMD 1.8.6 and change the
> representation to Cartoon or NewCartoon. The only difference is that
> one protein has been moved. The result is that one shows up normally
> but another has a 'partial' Cartoon structure and a 'partial' ribbon
> structure. Some time it just shows up a ribbon-like representation.
> Every other conditions are the same, only one of the protein has been
> moved.
>
> This happens in many Linux machines I've tried and also Windows
> system. I seems it always works perfectly with ribbons representation.
>
> On Windows, there shows up a error message:
> "stride_WIN32.exe has encountered a problem and needs to close. We are
> sorry for the inconvenience."
> and also an error messege on vmd console:
> "Stride::read_stride_record: unable to read output file from Stride"
>
> Graphic card is Nvidia 8400GS.
>
> On Linux, there shows no error message, simply shows a wrong
> representation with 'half ribbon half cartoon'. And where it is a
> ribbon or a cartoon is almost random. The GPU is Nvidia 8600GT.
>
>
> THANKs,
> Haosheng