Hi Moritz, There are several different ways... I'll mention a few. You could select the two atoms from the Chimera window (Ctrl-click one, Shift-Ctrl-click the other) and then use command: bond sel <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html> The Command Line can be shown using the Favorites menu. If the Cys atoms are not already displayed, try command: disp :cys Or instead of selecting, you could specify atoms by name, something like: bond :25.a@sg :45.a@sg ... if the Cys were residue 25 and 45 in chain A. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Or, instead of commands you could use Build Structure (in menu under Tools... Structure Editing), the Adjust Bonds tab. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond> 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 Dec 4, 2012, at 7:12 AM, Moritz Bitzhenner wrote:
Dear Chimera Users
I am fairly new to the program and I have a particular problem with the display of disulfide bonds. I have an amino acid sequence, I created a pdb-file with Expasys Swiss Model Workspace. I opened the pdb file with Chimera and coloured the ribbon structue (it looks amazing), I even did a movie of my rotating protein. But I cannot display the three disulfide bonds. Is my pdb file lacking the CONECT information? How can I include them? With Swiss PDB Viewer (Deepviewer) I can show the bonds, but somehow I cannot transfer the information to the pdb file and Chimera. I also tried manually bonding the closest cysteins by selecting Cystein residues and "bond" in the command line. How do I select the two single atoms that I want to connect? I read through former similar questions in the list server but nothing helped so far. If you can find any time helping my case, it would be greatly appreciated. With best regards from Germany, Moritz
Here is the AA sequence: GEIDNNQCQICELLVKDIIEGLTANQSVEVIEHGLNLICDHIPLHVRVCKQFVDSNFQKIVQFIENHDDPQEICEKCGVC