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', \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
The one letter codes can be accessed with one_letter[resn]
To do something like Y-119:
label sele, '{}-{}'.format(one_letter[resn], resi) # front end command
cmd.label('sele', "'{}-{}'.format(one_letter[resn], resi)") # backend command
Cheers,
Ali
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
On 12/1/22, 11:26 pm, "Enrico Martinez" <jmsstarli...@gmail.com> wrote:
exactly we may do it in the context meny for the particular selection
(we do not need to select a particular residues, so ..)
but may we create the same label using label command as well ??
cmd.label('sele', 'resn')
I think something should be used instead of 'resn'. there is also
option 'resi' which shows only the number of the amino acid. So I need
to combine "resn" and "resi"
:-)
вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com>:
>
> For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
>
>
>
> Vaheh
>
>
>
> From: Enrico Martinez <jmsstarli...@gmail.com>
> Sent: Tuesday, January 11, 2022 12:34 PM
> To: pymol-users <pymol-users@lists.sourceforge.net>
> Subject: [PyMOL] Set label for visible amino acids
>
>
>
> Dear Pymol users!
> Here is the chain of the pymol commands that I am using to label the
> visible amino-acids shown as lines in the current pymol session.
> cmd.select('name CA and rep lines')
> cmd.label('sele', 'resn')
> cmd.set('label_font_id', '14')
> cmd.set('label_color', 'indigo')
> cmd.set('label_position', '3,0,0')
> It produces nice labeling according to the amino acid name (example
> Tyr). How it would be possible to indicate additionally the number of
> the amino acid like Tyr-119 or simply using one letter code + the
> number?
> Many thanks in advance
> Enrico
>
>
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