| 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). |