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Commands Which Can Be Run On The Command Line

This document outlines various commands that can be run in the command line to select, label, color, and highlight atoms and residues in molecular structures. Some key commands include using "set picking" to measure distances and angles between selected atoms, "select" to choose specific atoms or residues by number, chain, or proximity to another residue, and "label" to annotate individual atoms.

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108 views2 pages

Commands Which Can Be Run On The Command Line

This document outlines various commands that can be run in the command line to select, label, color, and highlight atoms and residues in molecular structures. Some key commands include using "set picking" to measure distances and angles between selected atoms, "select" to choose specific atoms or residues by number, chain, or proximity to another residue, and "label" to annotate individual atoms.

Uploaded by

brijeshandfamily
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© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Commands which can be run on the command line:

To measure distance/angle/torsion angle: o type "set picking distance", then pick two atoms

o o

type "set picking angle", then pick three atoms type "set picking torsion", then pick four atoms

To trace the chain: 1. select * 2. trace 3. trace off [turn off trace]

To select nucleic acids/proteins only: select [nucleic|protein] To select residues and label, change colors, and highlight them: 0. select mmm,nnn,ooo,ppp,..., then go to the menu and select "Options Labels" 1. color yellow/green/blue/orange/... 2. wireframe/backbone/ribbons 60/80/200/400/...

Example 1) 3. select 500 4. spacefill 400 5. color green

Example 2) 6. select 500 7. wireframe 80 8. color blue

To select atoms within a specific distance from a specific residue(s):

select within(4.5, nnn) Example) select within(8.5, 500) select within(4.5, mmm-nnn) Example) select within(30.0, 500-600)

To select all atoms in the currently loaded structure:

o o

select * select all

To select all atoms in a specific chain (A or B or C or ...):

o o o

select *:a select *:b select *:c

To label a specific atom using the E. coli, T. thermophilus, or H. marismortui numbers (this requires you to select positions manually by going through the PDB file and manually interconvert to type in the numbers)" 0. select atomno=xxx, then 1. label "nnn"

Example) 2. select atomno=1400 3. label "756"

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