[Chimera-users] Non-ASCII error

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 6 09:02:12 PDT 2017


Hi Armin,
That means you made some mistake when editing the file.  Maybe you did not save the edited file as plain text.

It is easy to delete HOH after opening the original PDB file in Chimera.  Maybe show all atoms first so you can see what is happening, for example with menu: Presets… Interactive 2 (all atoms).  Then to delete the HOH you could just use command (after showing Command Line from Favorites menu):

delete :HOH

(the “:” means residue).  Probably also the following would work too:

delete solvent

Then if you want, you can save the result to file with menu: File… Save PDB.  

Deleting solvent is done in several of the Chimera tutorials, for example
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

There is also a “Dock Prep” tool (menu: Tools… Structure Editing… Dock Prep) that has an option to delete solvent.  It has lots of other options too, although you could turn off all of the ones you didn’t want.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 6, 2017, at 5:15 AM, ARMIN HODAEI <ahodaei15 at ku.edu.tr> wrote:
> 
> 
> Dear Chimera users,
>      My PDBhas some extra HOH water molecules in it. when I delete them manually from the pdb I could not open the PDB with Chimera, it gives the error Non-ASCII file. What can I do to fix it? Or is there any way to delete extra HOH atoms from the PDBfile inside the Chimera software?




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