| version 1.14 | version 1.15 |
|---|
| |
| \ARGDEF{atomname}{Name of target atom (optional).}} | \ARGDEF{atomname}{Name of target atom (optional).}} |
| {After one or more segments have been built.} | {After one or more segments have been built.} |
| | |
| \item \COMMAND{\IKEY{renameatom} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{newname}} | |
| {Change name of a single atom.} | |
| {\ARGDEF{segid}{Segment ID of target atom.}\\ | |
| \ARGDEF{resid}{Residue ID of target atom.}\\ | |
| \ARGDEF{atomname}{Name of target atom.}\\ | |
| \ARGDEF{newname}{New atom name to be assigned.}} | |
| {After one or more segments have been built.} | |
| | |
| \item \COMMAND{\IKEY{resetpsf}} | \item \COMMAND{\IKEY{resetpsf}} |
| {Delete all segments in the structure. The topology definitions and | {Delete all segments in the structure. The topology definitions and |
| aliases are left intact. If you want to clear the topology and aliases | aliases are left intact. If you want to clear the topology and aliases |
| |
| {After stucture has been generated and known coordinates read in.} | {After stucture has been generated and known coordinates read in.} |
| | |
| \item \COMMAND{\IKEY{coord} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{\{ x y z \}}} | \item \COMMAND{\IKEY{coord} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{\{ x y z \}}} |
| {Set coordinates for a single atom.} | {\textbf{WILL BE DEPRECATED AFTER VERSON 1.6} (use {\tt psfset coord} instead) Set coordinates for a single atom.} |
| {\ARGDEF{segid}{Segment ID of target atom.}\\ | {\ARGDEF{segid}{Segment ID of target atom.}\\ |
| \ARGDEF{resid}{Residue ID of target atom.}\\ | \ARGDEF{resid}{Residue ID of target atom.}\\ |
| \ARGDEF{atomname}{Name of target atom.}\\ | \ARGDEF{atomname}{Name of target atom.}\\ |
| \ARGDEF{\{ x y z \}}{Coordinates to be assigned.}} | \ARGDEF{\{ x y z \}}{Coordinates to be assigned.}} |
| {After structure has been generated.} | {After structure has been generated.} |
| | |
| \item \COMMAND{\IKEY{vel} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{\{ vx vy vz \}}} | \item \COMMAND{\IKEY{psfset} \ARG{attribute} \ARG{segid} \OARG{resid} \OARG{atomname} \ARG{value}} |
| {Set velocities for a single atom.} | {Set an attribute for a given segment, residue, or atom.} |
| {\ARGDEF{segid}{Segment ID of target atom.}\\ | {\ARGDEF{attribute}{ |
| \ARGDEF{resid}{Residue ID of target atom.}\\ | Segment attributes: |
| | \KEYDEF{segid}{the name of the segment} |
| | Residue attributes: |
| | \KEYDEF{resname}{the name of the residue} |
| | Atom attributes: |
| | \KEYDEF{name}{the name of the atom}, |
| | \KEYDEF{mass}{the mass of the atom}, |
| | \KEYDEF{charge}{the charge of the atom}, |
| | \KEYDEF{beta}{the PDB bfactor of the atom}, |
| | \KEYDEF{coord}{the coordinates of the atom as \{x y z\}}, |
| | \KEYDEF{vel}{the velocity of the atom as \{vx vy vz\}} |
| | }\\ |
| | \ARGDEF{segid}{Segment ID of target segment, residue, or atom.}\\ |
| | \ARGDEF{resid}{Residue ID of target residue or atom.}\\ |
| \ARGDEF{atomname}{Name of target atom.}\\ | \ARGDEF{atomname}{Name of target atom.}\\ |
| \ARGDEF{\{ vx vy vz \}}{Velocities to be assigned.}} | \ARGDEF{value}{Value to be assigned.}} |
| {After structure has been generated.} | {After structure has been generated or read from file.} |
| | |
| \item \COMMAND{\IKEY{bfactor} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{b}} | |
| {Set temperature factor (B-factor) for a single atom.} | |
| {\ARGDEF{segid}{Segment ID of target atom.}\\ | |
| \ARGDEF{resid}{Residue ID of target atom.}\\ | |
| \ARGDEF{atomname}{Name of target atom.}\\ | |
| \ARGDEF{b}{Temperature factor to be assigned.}} | |
| {After structure has been generated.} | |
| | |
| \item \COMMAND{\IKEY{writepdb} \ARG{file name}} | \item \COMMAND{\IKEY{writepdb} \ARG{file name}} |
| {Writes PDB file containing coordinates. Atom order is identical to | {Writes PDB file containing coordinates. Atom order is identical to |