Ccg-chemistry-faq/Protein Structure Import Problems

From Earlham Cluster Department

Jump to: navigation, search

WebMO may not properly import your molecule from a .pdb file, depending on how the .pdb was created. For example, for NMR structure determination, sometimes hydrogens are not listed as H but as Q (for reasons we need not get into here). Although visualization programs like PyMOL will work fine, WebMO's import feature doesn't like this very much.

If your file looks like this, you're OK:

Workingpdb.png


However, if your file looks more like this:

Brokenpdb.png

you'll need to make several corrections before proceeding.

1) Replace any Qs, as circled above, with H.

2) Delete any numbers PRECEEDING an H (any annotation afterwards, like HAX, is fine).

This should solve basic import problems.

Personal tools
Namespaces
Variants
Actions
websites
wiki
this semester
Toolbox