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pymol.pml
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pymol.pml
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##load structures
#load 6whs.pdb
/cmd.set('bg_rgb',0,u'',0)
#/cmd.set('cartoon_cylindrical_helices','1',u'',0)
set orthoscopic, on
show cartoon
hide lines
set cartoon_fancy_helices, on
set cartoon_transparency, 0.6
remove hydro
set cartoon_side_chain_helper, on
dss
set ray_shadows, 0
#chain selection
select a, r1_prot_p2_lig_fit and resi 1-133
select a_residues, r1_prot_p2_lig_fit and resi 52 or resi 80 or resi 81 or resi 84
show sticks, a_residues
select b1, r1_prot_p2_lig_fit and resi 134-264
select b1_residues, r1_prot_p2_lig_fit and resi 187 or resi 215 or resi 216 or resi 219
show sticks, b1_residues
select c, r1_prot_p2_lig_fit and resi 265-397
select c_residues, r1_prot_p2_lig_fit and resi 316 or resi 344 or resi 345 or resi 348
show sticks, c_residues
select d, r1_prot_p2_lig_fit and resi 398-528
select d_residues, r1_prot_p2_lig_fit and resi 451 or resi 479 or resi 480 or resi 483
show sticks, d_residues
util.cba(154,"a",_self=cmd)
util.cba(154,"a_residues",_self=cmd)
util.cba(154,"c",_self=cmd)
util.cba(154, "c_residues",_self=cmd)
util.cba(5262,"d",_self=cmd)
util.cba(5262,"d_residues",_self=cmd)
util.cba(5262,"b1",_self=cmd)
util.cba(5262,"b1_residues",_self=cmd)
select lig, resname LIG
util.cbao("lig")
show sticks, lig
set_view (\
0.682371795, -0.201983318, 0.702540338,\
0.730940223, 0.177055061, -0.659061849,\
0.008731524, 0.963244915, 0.268455654,\
0.000000000, 0.000000000, -84.048927307,\
89.642494202, 53.960002899, 42.555000305,\
68.992706299, 99.105148315, -20.000000000 )
pseudoatom asn_cog
show spheres, asn_cog
util.cbag("asn_cog")
color green, asn_cog
set sphere_scale, 1
set_view (\
0.531912148, -0.197172478, 0.823518991,\
0.846782565, 0.120272219, -0.518149078,\
0.003118854, 0.972956538, 0.230936944,\
0.000000000, 0.000000000, -84.048927307,\
89.630561829, 54.242778778, 50.001667023,\
68.992706299, 99.105148315, -20.000000000 )
pseudoatom pcp_cog
show spheres, pcp_cog
distance asn-pcp-dist, asn_cog, pcp_cog
set_view (\
0.448698521, 0.168899506, 0.877572179,\
0.877385914, 0.103356838, -0.468502671,\
-0.169833109, 0.980189800, -0.101814464,\
0.000000000, 0.000000000, -84.048927307,\
89.877510071, 54.032501221, 56.196784973,\
68.992706299, 99.105148315, -20.000000000 )
pseudoatom thr_cog
show spheres, thr_cog
color salmon, thr_cog
set sphere_scale, 0.7
distance asn-pcp-dist, thr_cog, pcp_cog
set label_size, 0
set_view (\
-0.533606172, 0.078780286, -0.842056334,\
-0.845733643, -0.048940945, 0.531357527,\
0.000649818, 0.995689809, 0.092741944,\
0.000000000, 0.000000000, -58.297489166,\
89.919548035, 54.411819458, 50.131591797,\
8.442249298, 108.152732849, 20.000000000 )
ray 1280,960
#png PCP_COG_analysis.png, dpi=300
png PCP_COG_analysis.png