sel a/*/*/* | Select all atoms from chain A. |
sel * exc m/*/*/ca | Select CA atoms from all chains except chain M. |
sel */*/*/* exc ca,c,n,o | Select all atoms except CA, C, N and O. |
sel a/* exc 72-112/*/ca | Select CA atoms from chain A, but exclude residues from 72 to 112. |
sel 1-100 | Select residues from 1 to 100. |
sel 1-100 exc 20-40 | Select residues 1-100 but exclude 20-40. |
sel 1, 4, 8, 11-48 exc 20-32 | Select residues 1, 4, 8 and 11-48 but exclude 20-32. |
sel ato 1-100 | Select atoms which have serial numbers in the range between 1 and 100. |
sel 1-20 40-50 | Select atoms which have serial numbers between 1 and 20 and between 40 and 50. |
sel phe,tyr,trp | Select PHE, TYR and TRP. |
sel *
sel all |
Select all atoms (select all). |
sel abo
sel above |
Select atoms above the plane. |
sel aci
sel acidic |
Select acidic amino acids (GLU and ASP). |
sel ali
sel aliphatic |
Select aliphatic amino acids (ILE, LEU and VAL). |
sel alt | Select atoms at alternate positions. |
sel bad |
Select bad residues. A residue is treated as bad if the
peptide bond assigned to this residue is non-planar. The peptide bond is non-planar if the omega angle is different for 20 or more degrees from 0 or 180 degrees. |
sel bas
sel basic |
Select basic amino acids (ARG, LYS and HIS). |
sel bel
sel below |
Select atoms below the plane. |
sel cha
sel charged |
Select charged amino acids (ARG, LYS, HIS, GLU and ASP). |
sel cis | Select cis residues. |
sel com
sel complement |
Select atoms which were not selected previously. |
sel het
sel hetero |
Select hetero atoms (heme groups, water etc.). |
sel pho
sel hydrophobic |
Select hydrophobic amino acids
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS). |
sel mai
sel main_chain |
Select main chain atoms (CA, C, N and O). |
sel mod serial_number
sel model serial_number |
Select model specified by serial_number.
NMR structure is a set of models. Example: sel mod 1 |
sel neg
sel negative |
Select negatively charged amino acids (GLU and ASP). |
sel pat
sel pattern |
Select the sequence pattern. The command
PAT (PATTERN) is used to define the sequence pattern. |
sel pol
sel polar |
Select polar amino acids
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR). |
sel pos
sel positive |
Select positively charged amino acids (ARG, LYS and HIS). |
sel seq
sel sequence |
Select sequence fragments which match the sequence stored
to the sequence buffer. The sequence buffer should be initialized before executing this command. |
sel sid
sel side_chains |
Select atoms which belong to side chains (all except CA, C, N and O). |
sel sma
sel small |
Select small amino acids
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN). |
sel sph
sel sphere |
Select atoms inside the sphere. Use the command
RAD (RADIUS) to set the sphere radius. |
sel tm |
Select the transmembrane part
(useful for membrane proteins). |
sel tra
sel trans |
Select trans residues. |
sel tri
sel triplet |
If there are three (or more) positively charged residues in a fragment
of up to five protein residues, select these residues. Detailed explanation may be found in the article: D. Juretic, L. Zoranic and D. Zucic, Basic charge clusters and predictions of membrane protein topology, Journal of Chemical Information and Computer Sciences 42, No. 3, 620-632 (2002). |
sel 2c3 |
If there are two (or more) charged residues in a fragment of three
residues, select these residues. |
sel 2cz3 |
If there are two (or more) charged or zwitterionic residues in a
fragment of three residues, select these residues. |
sel 3c4
sel 3cz4 sel 3c5 sel 3cz5 sel 4c5 sel 4cz5 sel 3c6 sel 3cz6 sel 4c6 sel 4cz6 sel 5c6 sel 5cz6 sel 4c7 sel 4cz7 sel 5c7 sel 5cz7 sel 5c9 sel 5cz9 |
Analogous to sel 2c3 and sel 2cz3.
The same selection criteria may be defined using patterns, but these short keywords are more practical. |
sel 5p7 |
If there are five or more polar residues in a fragment of seven residues,
select there residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP. |
sel 6p7 |
If there are six or more polar residues in a fragment of seven residues,
select there residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP. |