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...f duplicated connectivity record ([http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT CONECT]) in saved PDB is used to stored ...duplication of the same CONECT records, as specified in, for example, MOL format. See http://wiki.jmol.org/index.php/Support_for_bond_orders

...the input be a '.sdf' or '.sdf.gz' file. If your compounds are not in that format, use the 'babel' tool from OpenBabel to convert them. ...is also a field to enter a PyMOL selection string to compute the hydrogen bonds to. Finally, there is a button to create the clusters and load them into Py

-of rawvideo -mpegopts format=mpeg1 \ # extra N bonds, like in PRO

* Highlight H-bonds, salt bridges, Pi-stacking, Pi-cations, etc. * single-color bonds between nonidentical or any spherical atoms colored specifically

...installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even sa Q: How do I select (especially, iterate through a set of) bonds? The existence of [http://www.pymolwiki.org/index.php/Cycle_Valence cycle

....ucla.edu/~sawaya/uvla/fold/csos3-stereo01.psd labeled figure in photoshop format]. # stick_radius -adjust thickness of atomic bonds