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@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@cox.net> <nyyount@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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