hydrogen bond with one end hanging in space

Author	Message
Clif Brown Send message Joined: 15 Feb 14 Posts: 7 Credit: 87,117 RAC: 0	Message 76471 - Posted: 20 Feb 2014, 22:05:32 UTC Working with the Fold-It program, I've come up with a configuration that shows a HB connected to a sidechain on one end with the other hanging in empty space...I assume this is a bug in the program? ID: 76471 · Rating: 0 · rate: / Reply Quote

krypton Volunteer moderator Project developer Project scientist Send message Joined: 16 Nov 11 Posts: 108 Credit: 2,164,309 RAC: 0	Message 76474 - Posted: 21 Feb 2014, 7:12:04 UTC - in response to Message 76471. Working with the Fold-It program, I've come up with a configuration that shows a HB connected to a sidechain on one end with the other hanging in empty space...I assume this is a bug in the program? Hi Clif, Can you send me a screenshot? (my email krypton at uw dot edu) -krypton ID: 76474 · Rating: 0 · rate: / Reply Quote

Clif Brown Send message Joined: 15 Feb 14 Posts: 7 Credit: 87,117 RAC: 0	Message 76478 - Posted: 21 Feb 2014, 20:15:50 UTC - in response to Message 76474. Working with the Fold-It program, I've come up with a configuration that shows a HB connected to a sidechain on one end with the other hanging in empty space...I assume this is a bug in the program? Hi Clif, Can you send me a screenshot? (my email krypton at uw dot edu) -krypton Sent ID: 76478 · Rating: 0 · rate: / Reply Quote

krypton Volunteer moderator Project developer Project scientist Send message Joined: 16 Nov 11 Posts: 108 Credit: 2,164,309 RAC: 0	Message 76480 - Posted: 21 Feb 2014, 20:20:26 UTC Thanks Clif! I forwarded the screenshot to our Foldit people. ID: 76480 · Rating: 0 · rate: / Reply Quote

koepnick Send message Joined: 22 Feb 14 Posts: 1 Credit: 0 RAC: 0	Message 76484 - Posted: 22 Feb 2014, 1:44:07 UTC Hi Clif, I can't be sure just looking at your screenshot, but it looks like that hydrogen bond may involve the N-terminal amine group (which is hidden in the default view settings). You can try changing your "View Protein" setting: In the Menu tab, open "General Options" and make sure the box beside "Show Advanced GUI" is checked. Then go back to the View tab and set the "View Protein" option to something like "Stick+H". These different view settings show different levels of detail in your protein structure. Hopefully, that will reveal a hydrogen atom at the open end of your H-bond! ID: 76484 · Rating: 0 · rate: / Reply Quote

Clif Brown Send message Joined: 15 Feb 14 Posts: 7 Credit: 87,117 RAC: 0	Message 76487 - Posted: 23 Feb 2014, 3:51:14 UTC - in response to Message 76484. Hi Clif, I can't be sure just looking at your screenshot, but it looks like that hydrogen bond may involve the N-terminal amine group (which is hidden in the default view settings). You can try changing your "View Protein" setting: In the Menu tab, open "General Options" and make sure the box beside "Show Advanced GUI" is checked. Then go back to the View tab and set the "View Protein" option to something like "Stick+H". These different view settings show different levels of detail in your protein structure. Hopefully, that will reveal a hydrogen atom at the open end of your H-bond! thanks, I will try that. ID: 76487 · Rating: 0 · rate: / Reply Quote