Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?
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 Sent At:2019 Jun. 5 (Wed.) 20:43 To:孙业平 ; pymol-users 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 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/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] colored secondary structure of two chains with different colors
Hello all I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg How to do this ? Thank you Stéphane ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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 > 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/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
