[PyMOL] secondary structure disappears

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

Re: [PyMOL] secondary structure disappears

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: SHEET1 A 2 LEU A 2 PHE A 5 0

Re: [PyMOL] secondary structure disappears

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" wrote: Hi All, If you fetch 3ow9 in PyMOL, split_states to get all six of the strands,

Re: [PyMOL] secondary structure disappears

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 cop

Re: [PyMOL] secondary structure disappears

Hi Adam, I think you also want to make sure that each strand as a distinct chain ID if you want the cartoon representation to work correctly. Unfortunately that means you have to use "alter" but to change the chain IDs on the objects created by the split_states command before merging them all int

Re: [PyMOL] secondary structure disappears

I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.net email address is currently down due to SF server issues), to ensure it is added to this thread in the archive: This is due to chain identifier conflict. He's merging 6 models with identic

Re: [PyMOL] secondary structure disappears

Big thank you to all of you! I really need to find some time to better learn code. :/ > On Jul 23, 2015, at 4:36 PM, Sampson, Jared wrote: > > I'm posting the following solution on behalf of Thomas Holder (whose > sourceforge.net email address is currently down due