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...|right|Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19]] supercell 2,1,1, 2x19, green

* 1: Curved helices (since PyMOL 2.5) set cartoon_cylindrical_helices, 1

# the default value is 1 Larger values of <integer> result in higher quality sphere rendering. Values >1 may result in poor [[:Category:Performance|performance]] during real-time r

#Matte 1 #Swirl 1

...e (float) number between 0 and 1 (with 0 meaning the object is opaque, and 1 == invisible).

cmd.get_fastastr(string selection='all', int state=-1, int quiet=1)

cap1, cap2 # should the ends be solid (1) or open (0)? plain_sphere = [cgo.SPHERE, 0, 0, 0, 1]

Image:PHE_valence_1_mode_1.png|set valence, 1<br>set valence_mode, 1<br>#bonds inside Image:PHE_valence_1_mode_0.png|set valence, 1<br>set valence_mode, 0<br>#bonds centered

attach O, 1, 1 # adds an Oxygen atom to picked atom.

util.cbc(selection='(all)',first_color=7,quiet=1,legacy=0,_self=cmd) * quiet defaults to 1

aa_3l = {'ALA':0, 'ARG':1, 'ASN':2, 'ASP':3, 'CYS':4, 'GLN':5, 'GLU':6, 'GLY':7, 'HIS':8, 'ILE':9, 'L ..., -1, -1, -1, 0, -2, -2, -2, -1, -2, -3, -1, 1, 0, -4, -3, -1, -2, -1, -1, -6],

cmd.get_view(output=1, quiet=1) *1 = don't output matrix to screen

set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide set cartoon_ring_finder, 1 # ribose and base rings (not displayed since ring mode 0)

* level = the contour level. (default=1.0) * state = the state into which the object should be loaded (default=1) (set state=-2 to append new surface as a new state)

|align="center" | 1 || simple plane for ribose and base rings covering area between ring bonds ...ose and base rings covering area inside sticks (slightly smaller than mode 1)

== Example 1: Same interpreter, same thread == cmd.png('/tmp/foo.png', ray=1)

''Version: 1.0'' Currently supports '''Kabat, Chothia, Contact, IMGT'''¹

color_cbcobj selection, [first_color=0..n, [quiet=0/1 ]] PyMOL>color_cbcobj all and elem C,2,1

...SuperSymExample.png|300px|thumb|right|Symmetry partners for 1hpv showing 6-1 screw axis]] This plugin was developed in 2010 for PyMOL version 1.2r1 and has not been updated since.

print cmd.intra_fit("1i8e////CA", 1) [-1.0, 1.1934459209442139, 1.2950557470321655, 0.71329855918884277,

cmd.redo(int steps=1)

* '''state''' = int: object state {default: 1} * '''load_b''' = 0/1: Load the surface area per atom into the b-factor {default: 0}

*mode 1: return a list of tuples of the object name and the identifier

rms = cmd.intra_rms("(name ca)",1)

*level = float: the contour level (in sigma units) {default: 1.0} ...aded (default=1) (set state=0 to append new mesh as a new state) {default: 1}

rms = cmd.intra_rms_cur("(name ca)",1)

center = cpv.scale(center, 1./len(centeratoms)) atom.index = model.nAtom + 1

cmd.iterate(selection, "stored.atomnumber = stored.atomnumber + 1")

int state=0, int updates=1, int log=0 )

| 1 |rowspan="1"| Affects [[cartoon]]

1. Download cctbx from http://cci.lbl.gov/cctbx_build

<source lang="python">cmd.ray(int width,int height,int renderer=-1,float shift=0)</source> set ray_trace_mode, 1

png base.png, ray=1 png overlay.png, ray=1

...i/10.1111/mmi.12494/abstract ''Molecular Microbiology'', Volume 91, Number 1, January 2014]. Image:Science 2011 16.jpg|'''Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing''', [[ht

1. Download the [https://github.com/pymodproject/pymod/releases/download/v3.0 Janson G, Zhang C, Prado MG, Paiardini A. Bioinformatics. 2017 Feb 1;33(3):444-446. doi: 10.1093/bioinformatics/btw638. PMID: 28158668

...r (t). This parameter represents the relative time within the range of [0, 1] that describes any change of animation or property over time. Programs are

|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B2 |+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000

'''DockingPie''': a Molecular Docking plugin for PyMOL [1]. DockingPie is installed, as any other PyMOL [1] plugin, via the PyMOL plugin manager:

cmd.undo(int steps=1)

It superseedes the [[apbsplugin|APBS Tool2.1]] plugin. set assembly, 1

...lation factor from [0, 1] (0 represents the beginning of the animation and 1 represents the end). Visually, they are represented as clips with a keyfram def timeline_add_keyframe(track: Track, frame_num: int, obj_state: int = -1) -> Keyframe

# Performing hierarchical clustering on the results from 1) The results of 1 and 2 are saved to python pickle files so you do not have to recompute them

* '''quiet''' = 0/1: suppress output {default: 0 in command mode, 1 in API} * '''transform''' = 0/1: do superposition {default: 1}

*# fix cartoonize for 1-6 and 6-1 bonds * 2015-08-31 (Version 0.8.1)

...distance_digits or label_dihedral_digits or label_angle_digits are set to -1. #1.