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December 12, 2019

Importing a previously created molecu... Log Out | Topics | Search
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WebMO Support Forum » Running WebMO Jobs » Build Molecule » Importing a previously created molecular structure « Previous Next »

Author Message
Chad Jolly
Posted on Monday, June 18, 2001 - 4:51 pm:   

Is it possible to import a molecular structure in .xyz or .pdb format rather than recreating it with the supplied editor?
schmidt
Posted on Monday, June 18, 2001 - 11:13 pm:   

Currently, the editor does not support the direct import of .xyz or .pdb structures due to Java security restrictions. However, a simple workaround is available:

Rather than enter a structure in the editor, simply leave the structure blank. Select to run a single point calculation in either Gaussian or MOPAC, and preview the input file. Paste in the .xyz geometry, and sumbit the job. You can then access the geometry using the "New Job Using this Geometry" in the View Job page, or from the Restart button if the job fails.
Chris Bingham
Posted on Thursday, June 30, 2005 - 2:37 pm:   

When I try to import a molecule created in Gauss View, WebMo distorts aromatic rings and causes it to have to many bonds, and causes hydrogens to bond together. Is there any way to avoid this from happening?
schmidt
Posted on Thursday, June 30, 2005 - 2:58 pm:   

If you would email the file that you are trying to import to schmidt@webmo.net I will take a look.
Chris Earnshaw
Unregistered guest
Posted on Monday, May 09, 2016 - 6:36 am:   

Attempting to read in a file using the Import Molecule button on the Build Molecule page doesn't appear to work in Internet Explorer 11 / Windows 7. Nothing appears in the text area after the file has been selected. It works fine in Firefox under Windows. Could this be a Java security issue, and is there anything we can do to make it work in IE11?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 505
Registered: 11-2006
Posted on Monday, May 09, 2016 - 2:01 pm:   

Chris,

This feature doesn't use Java. Interestingly I just tested this with no issue on IE 11/Win7. You might check the javascript console (F12 in IE) to see if any errors appear.

An alternative workaround is to copy/paste the contents of the text right into the text box -- this works as well.

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