Sunday, November 6, 2016

Some useful PyMol commands

Here some PyMol commands I found useful while writing this paper.

Raytracing (pretty pictures)
ray

Selections
select br. all within 3 of 63/CA
select br. all within 3 of resi 63
select Ala63, br. all within 3 of resi 63
select br. all within 3 of 2kpp///82/
sele tail,  2kzn///142-147/
sele tail,  2KPP///1-7+91-114/

NMR ensembles set all_states, on 
split_states your_object

Superimposing structures # superimpose protA residues 10-25 and 33-46 to protB residues 22-37 and 41-54:
pair_fit protA///10-25+33-46/CA, protB///22-37+41-54/CA

# superimpose ligA atoms C1, C2, and C4 to ligB atoms C8, C4, and C10, respectively:
pair_fit ligA////C1, ligB////C8, ligA////C2, ligB////C4, ligA////C3, ligB////C10

align cluster_lowe///13-25+36-105+111-141/CA,native///13-25+36-105+111-141/CA

Color using numbers in B-factor column
spectrum b, green_red, selection=n. CA,minimum=0.0, maximum=2
spectrum b, blue_white_red, selection=n. CA
spectrum b, blue_white_red, selection=n. CA,minimum=-1.37, maximum=1.37

spectrum b, blue_red, selection=test////CA
spectrum b, green_red, selection=n. CA,minimum=0.0, maximum=3.6

Label atoms 
label n. CA and i. 44, "(%s%s, %s)" % (resn, resi, b)
label n. CA and i. 33+55, "(%s%s, %s)" % (resn, resi, b)
label n. CA and i. 2, "%s%s, %5.2f" % (resn, resi, b)

Get more digits on the distance measurement
set label_distance_digits, 2

Get the orientation data, which you can paste back in to restore orientation
get_view

Change cartoon representation (the first two commands go together)
alter 16:23/, ss='L'
rebuild

set ribbon_width, 8

create new_obj, cluster_lowe_all2
set cartoon_transparency, 0.5,new_obj



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