psico.editing

3. 2011 Thomas Holder, MPI for Developmental Biology

License: BSD-2-Clause

Functions

alphatoall([selection, properties, ...])	Expand any given property of the CA atoms to all atoms in the residue
dss_promotif([selection, exe, raw, state, ...])	Secondary structure assignment with PROMOTIF.
dssp([selection, exe, raw, state, quiet, _self])	Secondary structure assignment with DSSP.
mse2met([selection, quiet, _self])	Mutate selenomethionine to methionine
polyala([selection, quiet, _self])	Mutate any residue to Alanine (except Glycines)
remove_alt([selection, keep, quiet, _self])	Remove alternative location atoms.
remove_alt_keep_first([selection, quiet, _self])	Remove alternative location atoms, keep the first observed.
rmsf2b([selection, linearscale, var, quiet, ...])	Determine the root mean square fluctuation (RMSF) per atom for a multi-state object and assign b-factor
set_phipsi(selection[, phi, psi, state, ...])	Set phi/psi angles for all residues in selection.
set_sequence(sequence[, selection, start, _self])	Alters the residue names according to given sequence
split(operator, selection[, prefix, _self])	Create a single object for each entity in selection, defined by operator (e.g. bymolecule, bysegment, ...).
split_chains([selection, prefix, _self])	Create a single object for each chain in selection
split_molecules([selection, prefix, quiet, ...])	Create a single object for each molecule (covalently connected entity) in selection (ignores solvent).
split_segis([selection, prefix, _self])	Create a single object for each segi in selection
sst([selection, raw, state, quiet, _self])	Secondary structure assignment with SST.
stride([selection, exe, raw, state, quiet, ...])	Secondary structure assignment with STRIDE.
stub2ala([selection, quiet, _self])	Mutate stub residues to ALA
update_identifiers(target, source[, ...])	Transfers segi, chain, and resi identifiers from one selection to another.

psico.editing.alphatoall(selection='polymer', properties='b', operator='byca', quiet=1, *, _self=...)

Expand any given property of the CA atoms to all atoms in the residue

Enhanced version of http://pymolwiki.org/index.php/AlphaToAll

Arguments

selection = string: atom selection {default: polymer}

properties = string: space separated list of atom properties {default: b}

psico.editing.dss_promotif(selection='all', exe='', raw='', state=-1, quiet=1, *, _self=...)

Secondary structure assignment with PROMOTIF. http://www.rubic.rdg.ac.uk/~gail/#Software

See Also

dss, dssp, stride

psico.editing.dssp(selection='(all)', exe='', raw='', state=-1, quiet=1, *, _self=...)

Secondary structure assignment with DSSP. http://swift.cmbi.ru.nl/gv/dssp/

Arguments

selection = string: atom selection {default: all}

exe = string: name of dssp executable {default: dsspcmbi}

raw = string: atom property to load raw dssp class into {default: ‘’}

Example

dssp all, /sw/bin/dsspcmbi, raw=text_type color gray color red, text_type H color orange, text_type G color yellow, text_type E color wheat, text_type B color forest, text_type T color green, text_type S set cartoon_discrete_colors, 1

See Also

dss, stride

psico.editing.mse2met(selection='all', quiet=1, *, _self=...)

Mutate selenomethionine to methionine

psico.editing.polyala(selection='all', quiet=1, *, _self=...)

Mutate any residue to Alanine (except Glycines)

See Also

stub2ala

psico.editing.remove_alt(selection='all', keep='first', quiet=1, *, _self=...)

Remove alternative location atoms.

Usage

remove_alt [selection [, keep]]

Arguments

selection = string: atom selection

keep = string: AltLoc to keep, or ‘first’ to keep the first observed AltLoc {default: first}

psico.editing.remove_alt_keep_first(selection='*', *, quiet=1, _self=...)

Remove alternative location atoms, keep the first observed.

psico.editing.rmsf2b(selection='all', linearscale=1.0, var='b', quiet=1, *, _self=...)

Determine the root mean square fluctuation (RMSF) per atom for a multi-state object and assign b-factor

Arguments

selection = string: atom selection {default: name CA}

linearscale = float: if linearscale <= 0, then use real b-factor equation, else use b=(rmsf*linearscale) {default: 1.0}

See Also

spheroid, rmsf_states.py from Robert Campbell

psico.editing.set_phipsi(selection, phi=None, psi=None, state=1, quiet=1, *, _self=...)

Set phi/psi angles for all residues in selection.

See Also

phi_psi, cmd.get_phipsi, set_dihedral, DynoPlot

psico.editing.set_sequence(sequence, selection='all', start=1, *, _self=...)

Alters the residue names according to given sequence

Arguments

sequence = string: amino acid sequence in one-letter code

selection = string: atom selection {default: all}

start = int: residue number to start from {default: 1}

psico.editing.split(operator, selection, prefix='entity', *, _self=...)

Create a single object for each entity in selection, defined by operator (e.g. bymolecule, bysegment, …). Returns the number of created objects.

psico.editing.split_chains(selection='(all)', prefix=None, *, _self=...)

Create a single object for each chain in selection

See Also

split_states

psico.editing.split_molecules(selection='(all)', prefix='mol_', quiet=1, *, _self=...)

Create a single object for each molecule (covalently connected entity) in selection (ignores solvent).

See Also

split_chains, split_states

psico.editing.split_segis(selection='all', prefix=None, *, _self=...)

Create a single object for each segi in selection

See Also

split_chains

psico.editing.sst(selection='(all)', raw='', state=-1, quiet=1, *, _self=...)

Secondary structure assignment with SST. https://lcb.infotech.monash.edu/sst/sst_submission_form.html

See Also

dss, dssp, stride

psico.editing.stride(selection='(all)', exe='stride', raw='', state=-1, quiet=1, *, _self=...)

Secondary structure assignment with STRIDE. http://webclu.bio.wzw.tum.de/stride/

See Also

dss, dssp

psico.editing.stub2ala(selection='all', quiet=1, *, _self=...)

Mutate stub residues to ALA

See Also

polyala

psico.editing.update_identifiers(target, source, identifiers='segi chain resi', match='align', quiet=1, *, _self=...)

Transfers segi, chain, and resi identifiers from one selection to another. This works by mapping old to new identifiers and alters also not aligned atoms (works if any other atom from the same residue got aligned).