When you use the alter command, then rebuild, and then save the PyMOL session as a .pse file, the changes will be written into the .pse file. They will not be lost when you reopen the .pse file.
The alter command doesn’t do anything to the actual .pdb or .cif file. It’s my understanding that when you open a structure file in PyMOL, it reads the pdb or cif file and then assigns appropriate secondary structure based on the phi and psi angles of the protein backbone. > On Jun 5, 2019, at 11:50 PM, sunyeping <[email protected]> wrote: > > Thank you for the reply. > > Do alter and rebuild commands really change the secondary structure of the > specific residues or they just change the display? I saved the structure > altered bt the alter and rebuild commands, but when I open the structure > agian in pymol, the residues I changes are still displayed as in the original > structure file. > > Best regards > ------------------------------------------------------------------ > From:h. adam steinberg <[email protected]> > Sent At:2019 Jun. 5 (Wed.) 20:43 > To:孙业平 <[email protected]>; pymol-users <[email protected]> > Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol? > > It’s the same command but just change the “S” to an “H”. Or you can use a “L” > if you want a loop (unstructured). > > alter 3-10/, ss=‘H’ > > You also need to enter the command: rebuild, to redraw the structure on your > screen. Use rebuild after you enter the alter command. > > > On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users > <[email protected] > <mailto:[email protected]>> wrote: > > Dear pymol user, > > I wonder why sometimes the secondary structure of a protein can not be > displayed incorrect in pymol. I have a structure, some residues are predicted > to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only > typing "dss" command in pymol doesn't work. I know by using the "alter" > commad the secondary structures can be assigned. The following command: > > alter 61-63/, ss='S' > > can assign residue 61-63 as sheet. However, what is the command to assign > residues as 3-10 helix? > > Thank you in advance. > > Arthur > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/[email protected] > <http://www.mail-archive.com/[email protected]> > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> >
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