Hi Enrico,
I think it's because you are selecting side chains, glycine has no sidechain
and alanine has single carbon atom side chain so this representation won't work
for it. You would need to remove the sidechains from the selection to make it
apply to the backbone atoms, i.e.
Hi Enrico,
You need to use the byres or br. Selection
(https://pymolwiki.org/index.php/Selection_Algebra)
I.e:
cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
Also, consider hiding all protein residues and showing only the ones near the
protein, i.e.:
cmd.show('sticks','br.
Hi Enrico,
This is actually quite simple, see the PyMOL wiki:
https://pymolwiki.org/index.php/Aa_codes
Paste this python dictionary into PyMOL:
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image:
https://pymolwiki.org/index.php/Rebuild
Cheers,
Ali
Ali Kusay |
Hi Enrico,
You can carve the protein surface around the ligand, i.e. show only the surface
behind the ligand, see this guide:
https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
You can also try and made the surface more transparent, but this doesn't always
give the best results,
Hi George,
You can do pairwise alignments, i.e. align 3 of the structures to one structure.
You can also use the "extra_fit" method
(https://pymolwiki.org/index.php/Extra_fit), i.e:
extra_fit name CA, "object", super
Replace object with the structure you want the other 3 to align to, this
Hi Gret,
No worries,
In regards to the selection: “resi 25 and object”
Its more so to ensure that you don’t accidently select “resi 25” from multiple
chains or objects
Like if you load two pdb files into PyMOL (say obj01 and obj02) and both have a
resi 25, then resi 25 from both objects will
Hi Gert,
These selection commands will generate a selection object called "other_waters "
See https://pymolwiki.org/index.php/Selection_Algebra
You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection
in your email
or
select other_waters, br. (resn WAT
