Hi Amber users,
Just thought to let you know that I just figured out what happened.
It seems that the spaces between columns and the alignment of the columns
is made to look good but really impractical: if I respect the number of
spaces between columns and align in the coordinate columns the dots that
separate the digits then everything is working fine.
So if you ever get into such a problem this is what you should pay
attention to.
Sorry for the two messages.
Thanks,
Ioana
****************************************************************************
* Ioana Cozmuta, PhD * *
* NASA-AMES Research Center * "Gravitation can not be held responsible*
* Mail Stop 230-3 * for people falling in love" *
* Moffet Field * *
* phone: (650) 604-0993 * Albert Einstein*
* fax: (650) 604-0350 * (1879-1955) *
****************************************************************************
On Fri, 22 Nov 2002, Ioana Cozmuta wrote:
> Hi Amber users,
>
> I hope that someone can help me with this, I am not sure what is causing
> me the problem.
>
> I have a pdb file with a protein channel. In its own system of coordinates
> the channel is not align on the OZ axis and I want to reorient the channel
> with the axis channel to be parallel to OZ.
> What I did is I plot the original coordinates in matlab and it seems that
> the channel is parallel with the bisector of the (XOZ) plane so then I
> apply the coordinate transformation
> xnew(i)=(x_init(i)-z_init(i))/sqrt(2);
> znew(i)=(x_init(i)+z_init(i))/sqrt(2);
> If I replot the new coordinates in matlab the protein is indeed reoriented
> and parallel to OZ.
> Then I make a new pdb file with the new coordinates and load the pdb
> file in leap. However in xleap my structure is completely gone.
>
> Does anyone have an idea what could cause this? I would appreciate your
> help
>
> Thanks,
> Ioana
>
>
> ****************************************************************************
> * Ioana Cozmuta, PhD * *
> * NASA-AMES Research Center * "Gravitation can not be held responsible*
> * Mail Stop 230-3 * for people falling in love" *
> * Moffet Field * *
> * phone: (650) 604-0993 * Albert Einstein*
> * fax: (650) 604-0350 * (1879-1955) *
> ****************************************************************************
>
>
Received on Fri Nov 22 2002 - 17:44:22 PST
