[Chimera-users] NOT ABLE TO VIEW SURFACE USING PHYRE MODEL DATA

[Elaine Meng]

Hi Nanette,
Is the problem when you open the file (can you see the atoms), or  
just when you try to show a surface?  Has the problem occurred with  
several different Phyre PDB files?

If the problem is right when you open the file, it may be a problem  
with the format output by Phyre.  If so, it would be great if you  
could send me an example file.

Otherwise, I will assume it is a problem with the molecular surface  
only:
We have been using the MSMS program for making surfaces, but it fails  
on certain structures.  We are developing our own replacement method  
for calculating surfaces, but it is not included in Chimera releases  
yet.

In the meanwhile, because the MSMS method is sensitive to quite small  
changes in coordinates, it is sometimes possible to get it to work by  
simply increasing the VDW radii of all atoms a tiny amount.  For  
example, before trying to show the surface, open the command line  
(Favorites... Command Line) and enter the command:

vdwdefine +.0001

that increases all VDW radii by 0.0001 Angstroms, which is quite  
small considering that PDB atomic coordinates only go to the third  
digit after the decimal anyway.  That or a similar small value may  
allow the surface to be calculated successfully.  Another possibility  
is that if the Phyre structure includes hydrogens, to delete all  
hydrogens before showing the surface  (radii of other atoms are  
automatically adjusted to compensate when hydrogens are not included  
in a structure).

Thanks for your kind words about Chimera - we aim to please!  I hope  
this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 20, 2008, at 4:58 PM, <nyyount at cox.net> <nyyount at cox.net> wrote:

> Hi,
>
> I have not been able to view my Phyre pdb files using Chimera�s  
> surface view.  I get the error code -1073741785 and am immediately  
> shut out of the program.
>
> I am not a computer person � yet.
>
> Are there any quick fixes that I can add to my Phyre generated PDB  
> files to be able to view them in �surface� view?
>
> I�m very pleased with Chimera and have used it for all of the  
> molecular graphics for our next publication.  I would like to be  
> able to view my Phyre models using the same software.
>
> Thank you!
>
> Nannette Y. Yount, Ph.D.
> Harbor-UCLA
>
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