VMD RNS example


Type: getentry 2rns

Type: vmd

Click 'Display' button in main form

Use pull down menu 'Axes' in display form to turn off the axes

Click middle blue 'Display' button to close display form

Click 'Mol' button in main form

Click 'Load from files button' in mol form

Click 'pdb only'

Type in your PDB filename and click 'Load Molecule' button (here filename was pdb2rns.ent)

Click middle blue 'Molecule' button to close mol form

Use the left mouse button to orient your molecule

Click 'Graphics' button in main form

Click box next to 'Drawing Method' and click 'Off' option

Erase 'all' in 'Selected Atoms' box and type the following:

resid 1 to 15 and not resname HOH and not resname SO4

Click 'Create New' button

Click 'Image Controls' button

Highlight this entry (i.e. your residue selection description) in the blue box

Click box next to 'Drawing Method' and click 'CPK' option

Adjust the S rad and B rad to create tubes (decrease S rad and increase B rad

Erase 'Selected Atoms' box and type the following:

resid 24 to 124 and not resname HOH and not resname SO4

and click 'Create New'

Click box next to 'Drawing Method' and click 'Lines' option

Click box next to 'Coloring Method' and click 'Beta'

Orient your molecule in the graphics window (Use right mouse button in the 'Mouse Mode' menu to turn on 'Translate' and/or 'Scale' options)

Click box next to 'Drawing Method' and click 'Surf' option

For a big surface the render option will crash so snapshot your picture for now.