| version 1.13 | version 1.14 |
|---|
| |
| \KEYDEF{coordinates}{Return x, y, z coordinates for the given atom.}\\ | \KEYDEF{coordinates}{Return x, y, z coordinates for the given atom.}\\ |
| \KEYDEF{velocities}{Return x, y, z velocities for the given atom.}\\ | \KEYDEF{velocities}{Return x, y, z velocities for the given atom.}\\ |
| \KEYDEF{mass}{Return the mass of the given atom.}\\ | \KEYDEF{mass}{Return the mass of the given atom.}\\ |
| \KEYDEF{atomid}{Return the atomid of the given atom. These are only assigned during/after writing a PDB file. If {\tt writepdb} has not been called, this will just return zero for all atoms.}\\ | \KEYDEF{atomid}{Return the one-based atomid of the given atom. These are only assigned/updated when writing a file. Therefore {\tt writepsf}, {\tt writepdb}, or {\tt writemol} must be called to avoid returning old atomid values or zero.}\\ |
| \KEYDEF{first}{Returns the name of the patch that was applied | \KEYDEF{first}{Returns the name of the patch that was applied |
| to the beginning of the specified segment.}\\ | to the beginning of the specified segment.}\\ |
| \KEYDEF{last}{Returns the name of the patch that was applied | \KEYDEF{last}{Returns the name of the patch that was applied |
| |
| {\tt resid} are specified, all atoms from just that residue will be removed. | {\tt resid} are specified, all atoms from just that residue will be removed. |
| If {\tt segid}, {\tt resid}, and {\tt atom name} are all specified, just a | If {\tt segid}, {\tt resid}, and {\tt atom name} are all specified, just a |
| single atom will be removed.} | single atom will be removed.} |
| {\ARGDEF{segid}{Name of segment.}\\ | {\ARGDEF{segid}{Segment ID of target atom.}\\ |
| \ARGDEF{resid}{Name of residue (optional).}\\ | \ARGDEF{resid}{Residue ID of target atom (optional).}\\ |
| \ARGDEF{atom name}{Name of atom (optional).}} | \ARGDEF{atomname}{Name of target atom (optional).}} |
| {After all segments have been built and patched.} | {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 |
| |
| {} | {} |
| {At any time.} | {At any time.} |
| | |
| \item \COMMAND{\IKEY{writepsf} \OKEY{charmm} \OKEY{x-plor} \OKEY{cmap} \OKEY{nocmap} \ARG{file name}} | \item \COMMAND{\IKEY{writepsf} \OKEY{charmm} \OKEY{x-plor} \OKEY{cmap} \OKEY{nocmap} \OKEY{nopatches} \ARG{file name}} |
| {Write out structure information as PSF file. A simplified session log is listed in the REMARKS | {Write out structure information as PSF file. A simplified session log is listed in the REMARKS |
| section of the PSF file.} | section of the PSF file.} |
| { \KEYDEF{charmm}{Use CHARMM format (numbers for atom types).}\\ | { \KEYDEF{charmm}{Use CHARMM format (numbers for atom types).}\\ |
| \KEYDEF{x-plor}{Use X-PLOR format (names for atom types), the default format required by NAMD.}\\ | \KEYDEF{x-plor}{Use X-PLOR format (names for atom types), the default format required by NAMD.}\\ |
| \KEYDEF{cmap}{Write cross-term entries to PSF file if present, the default.}\\ | \KEYDEF{cmap}{Write cross-term entries to PSF file if present, the default.}\\ |
| \KEYDEF{nocmap}{Do not write cross-term entries to PSF file, even if present.}\\ | \KEYDEF{nocmap}{Do not write cross-term entries to PSF file, even if present.}\\ |
| | \KEYDEF{nopatches}{Do not write list of applied patches to PSF file header.}\\ |
| \ARGDEF{file name}{PSF file to be generated.}} | \ARGDEF{file name}{PSF file to be generated.}} |
| {After all segments have been built and patched.} | {After all segments have been built and patched.} |
| | |
| |
| \ARGDEF{real name}{Atom name found in topology file.}} | \ARGDEF{real name}{Atom name found in topology file.}} |
| {Before reading coordinates with coordpdb. May call multiple times.} | {Before reading coordinates with coordpdb. May call multiple times.} |
| | |
| \item \COMMAND{\IKEY{coord} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{\{ x y z \}}} | |
| {Set coordinates 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{\{ x y z \}}{Coordinates to be assigned.}} | |
| {After structure has been generated.} | |
| | |
| \item \COMMAND{\IKEY{coordpdb} \ARG{file name} \OARG{segid} \OKEY{namdbin} \OARG{namdbin file name}} | \item \COMMAND{\IKEY{coordpdb} \ARG{file name} \OARG{segid} \OKEY{namdbin} \OARG{namdbin file name}} |
| {Read coordinates from PDB file, matching segment, residue and atom names.} | {Read coordinates from PDB file, matching segment, residue and atom names.} |
| {\ARGDEF{file name}{PDB file containing known or aliased residues and atoms.}\\ | {\ARGDEF{file name}{PDB file containing known or aliased residues and atoms.}\\ |
| |
| {None.} | {None.} |
| {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 \}}} |
| | {Set coordinates 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{\{ x y z \}}{Coordinates to be assigned.}} |
| | {After structure has been generated.} |
| | |
| | \item \COMMAND{\IKEY{vel} \ARG{segid} \ARG{resid} \ARG{atomname} \ARG{\{ vx vy vz \}}} |
| | {Set velocities 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{\{ vx vy vz \}}{Velocities to be assigned.}} |
| | {After structure has been generated.} |
| | |
| | \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 |
| PSF file generated by writepsf (unless structure has been changed). | PSF file generated by writepsf (unless structure has been changed). |