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get_raw_distances [ names [, state [, selection ]]] select_distances [ names [, name [, state [, selection [, cutoff ]]]]]

set internal_gui, 0 set internal_gui, 1

* '''settings''' = str: space separated list of setting names or empty string for all settings {default: } set cartoon_color, blue, 1rx1

...the Pymol color names and corresponding internal color indices. The Pymol names can be used to designate color for objects, see [[Color]]. To retrieve a s set the RGBs, and then click Apply.

# names with dots are treated special set group_auto_mode, 2

* selection = the set of objects to include in the flattening. The selection will be expanded to * quiet = If set to 0, print some additional information about progress and chain renaming {

For RNA, the residue names might need adjustment, see [[#RNA|troubleshooting RNA]]. For '''pdb2pqr''', RNA resdiue names must be RA, RC, RG, and RU.

# simple example: label residue 22's atoms with their names ...object/selection you want to label and '''expression''' is some string (or set of strings) which PyMOL is to use to label the given selection.

...r multi-model structures, a value of 0 indicates that models have the same set of atoms (e.g. trajectory files or NMR structures), allowing memory savings * '''object_props : string''' = Space delimited list of property names (or * wildcard) to load from .sdf or .mae files {default: use [[load_object

...rly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b * For pdb2pqr, '''RNA''' resdiue names must be RA, RC, RG, and RU.<source lang="python">alter polymer & resn A+C+G

'''PyTMs''' is a PyMOL plugin that enables to easily introduce a set of common post-translational modifications (PTMs) into protein models.<br> ...ids have altered names, and altered/added atoms are identifyable by unique names.<br>

Additionally, the residue names can be changed for bonded cysteines: ...the chemical structure, an object must be loaded with the "discrete" flag set to zero.

...med have are distinguished from objects by having parentheses around their names. For example, ''foo'' would be an object and ''(foo)'' would be some selec :: A state is a particular conformation (set of coordinates) for a given object. For example an NMR ensemble could cont

PyMOL has a predefined set of colors that can be edited in the ''Settings->Colors'' menu. set cartoon_discrete_colors, 1

cmd.set("dot_solvent", 1) # set some string names for temporary objects/selections

* names and keywords are case-insensitive unless [[ignore_case]] is set * names and keywords can be abbreviated to non-ambiguous prefixes

1) If you are modifying this script to illustrate a different set of coordinates, it is best to have the secondary structure assignments in t set antialias = 1

* [[select_sites]] can set author/paper selections according to SITE annotation in pdb file * [[b2transparency]] can set surface transparency based on atom b-factor