Hi Adam, You can use iterate to get the secondary structure designation, and then use alter to apply it to the other chains.
secstruc=[] iterate model1 and n. ca, secstruc.append(ss) s1=list(secstruc) alter model2 and n. ca, ss=s1.pop(0) The last two lines need to be repeated, including the copying of the secondary structure list, because the pop will consume the list. Hope it helps, Tsjerk On Thu, Jul 23, 2015 at 5:53 PM, H. Adam Steinberg < h.adam.steinb...@gmail.com> wrote: > The secondary structure is only there for the first set of strands, and > then that is used for the other strands when you split_states, but how do I > change that entry so it applies to the other strands? > > Here is that entry from the file that I attached: > > SHEET 1 A 2 LEU A 2 PHE A 5 0 > > SHEET 2 A 2 LEU B 2 PHE B 5 -1 O VAL B 3 N PHE A 4 > > On Jul 23, 2015, at 10:48 AM, Smith Liu <smith_liu...@163.com> wrote: > > 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.adam.steinb...@gmail.com> > 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! > > > > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Tsjerk A. Wassenaar, Ph.D.
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