add a/*/*/* | Add all atoms from chain A to current selection. |
add * exc m/*/*/ca | Add CA atoms from all chains except chain M. |
add */*/*/* exc ca,c,n,o | Add all atoms except CA, C, N and O. |
add a/* exc 72-112/*/ca | Add CA atoms from chain A, but exclude residues from 72 to 112. |
add 1-100 | Add residues from 1 to 100 to current selection. |
add 1-100 exc 20-40 | Add residues 1-100 but exclude 20-40. |
add 1, 4, 8, 11-48 exc 20-32 | Add residues 1, 4, 8 and 11-48 but exclude 20-32. |
add ato 1-100 | Add atoms which have serial numbers in the range between 1 and 100. |
add 1-20 40-50 | Add atoms which have serial numbers between 1 and 20 and between 40 and 50. |
add phe,tyr,trp | Add PHE, TYR and TRP to current selection. |
add *
add all |
Add all atoms to current selection, i.e. select all. |
add abo
add above |
Add atoms above the plane. |
add aci
add acidic |
Add acidic amino acids (GLU and ASP). |
add ali
add aliphatic |
Add aliphatic amino acids (ILE, LEU and VAL). |
add alt | Add atoms at alternate positions. |
add bad |
Add 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. |
add bas
add basic |
Add basic amino acids (ARG, LYS and HIS). |
add bel
add below |
Add atoms below the plane. |
add cha
add charged |
Add charged amino acids (ARG, LYS, HIS, GLU and ASP). |
add cis | Add cis residues. |
add com
add complement |
Add atoms which were not select previously. |
add het
add hetero |
Add hetero atoms (heme groups, water etc.). |
add pho
add hydrophobic |
Add hydrophobic amino acids
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS). |
add mai
add main_chain |
Add main chain atoms (CA, C, N and O). |
add mod serial_number
add model serial_number |
Add model specified by serial_number.
NMR structure is a set of models. Example: add mod 1 |
add neg
add negative |
Add negatively charged amino acids (GLU and ASP). |
add pat
add pattern |
Add the sequence pattern. The command
PAT (PATTERN) is used to define the sequence pattern. |
add pol
add polar |
Add polar amino acids
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR). |
add pos
add positive |
Add positively charged amino acids (ARG, LYS and HIS). |
add seq
add sequence |
Add sequence fragments which match the sequence stored
to the sequence buffer. The sequence buffer should be initialized before executing this command. |
add sid
add side_chains |
Add atoms which belong to side chains (all except CA, C, N and O). |
add sma
add small |
Add small amino acids
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN). |
add sph
add sphere |
Add atoms inside the sphere. Use the command
RAD (RADIUS) to set the sphere radius. |
add tin
add tiny |
Add tiny amino acids (GLY,ALA and SER). |
add tm |
Add the transmembrane part
(useful for membrane proteins). |
add tra
add trans |
Add trans residues. |
add tri
add triplet |
If there are three (or more) positively charged residues in a fragment
of up to five protein residues, add these residues to the current set of selected atoms. Detailed explanation may 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). |
add 2c3 |
If there are two (or more) charged residues in a fragment of
three residues, add these residues to the current selection. |
add 2cz3 |
If there are two (or more) charged or zwitterionic residues in
a fragment of three residues, add these residues to the current selection. |
add 3c4
add 3cz4 add 3c5 add 3cz5 add 4c5 add 4cz5 add 3c6 add 3cz6 add 4c6 add 4cz6 add 5c6 add 5cz6 add 4c7 add 4cz7 add 5c7 add 5cz7 add 5c9 add 5cz9 |
Analogous to add 2c3 and add 2cz3.
The same selection criteria may be defined using patterns, but these short keywords are more practical. |
add 5p7 |
If there are five or more polar residues in a fragment of five residues,
add these residues to the current selection. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP. |
add 6p7 |
If there are six or more polar residues in a fragment of five residues,
add these residues to the current selection. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP. |