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December 12, 2019

A problem while adding hydrogens Log Out | Topics | Search
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WebMO Support Forum » Bug Reports » WebMO Version 4.X » A problem while adding hydrogens « Previous Next »

Author Message
Olli Lehtonen
Posted on Wednesday, December 21, 2005 - 10:47 am:   

I recently installed the version 6.0.003. After I add hydrogens (importing the molecule first from a file) also some non-hydrogen atoms in the original structure are displaced.

Additionally, while exporting the structure in xyz format, the last line seems to miss y and z coordinates, e.g.

...
H 6.79547077 -3.95035870 4.55788089
H 5.63895920 -
schmidt
Posted on Wednesday, December 21, 2005 - 10:56 am:   

I need to ask for a few clarifications regarding your post.

Regarding the first item: Let me make sure I understand the problem. You import a molecule which does not contain any hydrogen atoms (from a PDB?), and then use the 'Add hydrogens' menu item to add them in. You are saying that the problem is that some of the backbone atoms have been moved?

Regarding the second item: I can't seem to reproduce this. Are you exporting the structure from the 'View Results' page or the 'Build Molecule' page? Does this only occur when importing a structure that you just built, or perhaps when exporting very large structures?

Thanks for the clarifications.

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