Aa codes - Revision history

Cchem: 1 revision

2017-09-18T02:46:08Z

1 revision

Speleo3: Bio.Data.SCOPData.protein_letters_3to1

2017-09-06T17:48:05Z

Bio.Data.SCOPData.protein_letters_3to1

Pyadmin: 7 revisions

2014-03-28T01:48:50Z

7 revisions

Tlinnet: /* Simple */

2013-02-01T15:04:55Z

Simple

New page

Just a quick little script to allow you to convert from 1-to-3 letter codes and 3-to-1 letter codes in PyMOL. Copy the code below and drop it into your .pymolrc file. Then, each time you load PyMOL, "one_letter" and "three_letter" will be defined.

= The Code =
== Simple ==
<source lang="python" enclose="pre">
# one_letter["SER"] will now return "S"
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'}

# three_letter["S"] will now return "SER"
three_letter = dict([[v,k] for k,v in one_letter.items()])

three_letter ={'V':'VAL', 'I':'ILE', 'L':'LEU', 'E':'GLU', 'Q':'GLN', \
'D':'ASP', 'N':'ASN', 'H':'HIS', 'W':'TRP', 'F':'PHE', 'Y':'TYR', \
'R':'ARG', 'K':'LYS', 'S':'SER', 'T':'THR', 'M':'MET', 'A':'ALA', \
'G':'GLY', 'P':'PRO', 'C':'CYS'}
</source>

== Simple and Clever ==
Here's another way to accomplish this
<source lang="python">
# The real convenience in there is that you can easily construct any
# kind of hash by just adding a matching list, and zipping.
aa1 = list("ACDEFGHIKLMNPQRSTVWY")
aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split()
aa123 = dict(zip(aa1,aa3))
aa321 = dict(zip(aa3,aa1))

# Then to extract a sequence, I tend to go for a construction like:
sequence = [ aa321[i.resn] for i in cmd.get_model(selection + " and n. ca").atom ]
</source>

== Using BioPython ==
If you have BioPython you can use the following, which includes also many three-letter codes of modified amino acids:
<source lang="python">
from Bio.PDB import to_one_letter_code as one_letter
</source>

== Using PyMOL ==
<source lang="python">
from pymol.exporting import _resn_to_aa as one_letter
</source>

= Example Usage =
<source lang="python">
# we used to have to do the following to get the amino acid name
from pymol import stored
stored.aa = ""
cmd.iterate("myselection", "stored.aa=resn")

# now we can just call
three_letter[string.split(cmd.get_fastastr("myselection"),'\n')[1]]
</source>

[[Category:UI_Scripts]]

Speleo3: LEU missing in aa3

2011-07-05T12:34:20Z

LEU missing in aa3

New page

Just a quick little script to allow you to convert from 1-to-3 letter codes and 3-to-1 letter codes in PyMOL. Copy the code below and drop it into your .pymolrc file. Then, each time you load PyMOL, "one_letter" and "three_letter" will be defined.

= The Code =
== Simple ==
<source lang="python">
# one_letter["SER"] will now return "S"
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'}

# three_letter["S"] will now return "SER"
three_letter = dict([[v,k] for k,v in one_letter.items()])
</source>

== Simple and Clever ==
Here's another way to accomplish this
<source lang="python">
# The real convenience in there is that you can easily construct any
# kind of hash by just adding a matching list, and zipping.
aa1 = list("ACDEFGHIKLMNPQRSTVWY")
aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split()
aa123 = dict(zip(aa1,aa3))
aa321 = dict(zip(aa3,aa1))

# Then to extract a sequence, I tend to go for a construction like:
sequence = [ aa321[i.resn] for i in cmd.get_model(selection + " and n. ca").atom ]
</source>

== Using BioPython ==
If you have BioPython you can use the following, which includes also many three-letter codes of modified amino acids:
<source lang="python">
from Bio.PDB import to_one_letter_code as one_letter
</source>

== Using PyMOL ==
<source lang="python">
from pymol.exporting import _resn_to_aa as one_letter
</source>

= Example Usage =
<source lang="python">
# we used to have to do the following to get the amino acid name
from pymol import stored
stored.aa = ""
cmd.iterate("myselection", "stored.aa=resn")

# now we can just call
three_letter[string.split(cmd.get_fastastr("myselection"),'\n')[1]]
</source>

[[Category:UI_Scripts]]

← Older revision	Revision as of 02:46, 18 September 2017
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@@ Line 37: / Line 37: @@
 <source lang="python">
 from Bio.PDB import to_one_letter_code as one_letter
 </source>

← Older revision	Revision as of 01:48, 28 March 2014
(No difference)