Re: [PyMOL] secondary structure disappears

[Smith L. <smi...@16...>]

I think the secondary structure record (SS) has been lost during your splitting. So just add and edit the SS record in the PDB file to the lost ones.


Smith







At 2015-07-23 22:23:24, "H. Adam Steinberg" <h.a...@gm...> wrote:
Hi All,


If you fetch 3ow9 in PyMOL,
split_states to get all six of the strands,
select all, then copy to object,
You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.


If I open the pdb file for 3ow9 in text edit and remove all the text for the individual models (and the waters), then open that file in PyMOL I get all six strands, but all the cartoon secondary structure is missing except for the two original strands. I tired running the alter command in PyMOL, it changes the secondary structure in the other objects I have open but not in this pdb.


I see the Sheet entry in the pdb file but I don’t know how to duplicate and change the sheet entry so it applies to the other four strands in the file.


Could someone point me to a place on the web that explains how to change the sheet entry (I’d like to learn how to do it)? or tell me how to fix this pdb file?


Thanks!