CODEWITHSUNDEEP
pymol
Overwatchgamer
Overwatchgamer

Reputation: 29

print or output the selected residues in pymol

I am following this step to print the residues that I selected in pymol, and I found that some of the residues got iterated more than 1 time. Does anyone know what the problem is?

ls = [] 

iterate selected, ls.append((resi, resn))

print ls

The selected residues are 29 amino acids in total, and here is the result of the output.

[('1', 'MET'), ('2', 'PHE'), ('3', 'ILE'), ('4', 'PHE'), ('5', 'LEU'), ('6', 'LEU'), ('7', 'PHE'), ('8', 'LEU'), ('9', 'THR'), ('10', 'LEU'), ('11', 'THR'), ('12', 'SER'), ('13', 'GLY'), ('14', 'SER'), ('15', 'ASP'), ('16', 'LEU'), ('17', 'ASP'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('18', 'ARG'), ('19', 'CYS'), ('19', 'CYS'), ('19', 'CYS'), ('19', 'CYS'), ('19', 'CYS'), ('19', 'CYS'), ('20', 'THR'), ('20', 'THR'), ('20', 'THR'), ('20', 'THR'), ('20', 'THR'), ('20', 'THR'), ('20', 'THR'), ('21', 'THR'), ('21', 'THR'), ('21', 'THR'), ('21', 'THR'), ('21', 'THR'), ('21', 'THR'), ('21', 'THR'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('22', 'PHE'), ('23', 'ASP'), ('23', 'ASP'), ('23', 'ASP'), ('23', 'ASP'), ('23', 'ASP'), ('23', 'ASP'), ('23', 'ASP'), ('23', 'ASP'), ('24', 'ASP'), ('24'
, 'ASP'), ('24', 'ASP'), ('24', 'ASP'), ('24', 'ASP'), ('24', 'ASP'), ('24', 'ASP'), ('24', 'ASP'), ('25', 'VAL'), ('25', 'VAL'), ('25', 'VAL'), ('25', 'VAL'), ('25', 'VAL'), ('25', 'VAL'), ('25', 'VAL'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('26', 'GLN'), ('27', 'ALA'), ('27', 'ALA'), ('27', 'ALA'), ('27', 'ALA'), ('27', 'ALA'), ('28', 'PRO'), ('28', 'PRO'), ('28', 'PRO'), ('28', 'PRO'), ('28', 'PRO'), ('28', 'PRO'), ('28', 'PRO'), ('29', 'ASN'), ('29', 'ASN'), ('29', 'ASN'), ('29', 'ASN'), ('29', 'ASN'), ('29', 'ASN'), ('29', 'ASN'), ('29', 'ASN')]

Upvotes: 2

Views: 9194

Answers (1)

István Lőrincz
István Lőrincz

Reputation: 21

Pymol iterates over every atom. Restrict search to one atom per residue like this:

iterate selected and name CA, ls.append((resi, resn))

Or, better yet, have the whole seqeunce in one line like this:

iterate selected and name CA, print (resi, resn)

Upvotes: 2

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