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I am trying to make a figure in which the protein structures are colored by the distance between the calphas in the overlayed structures.
I am comparing our cryoEM structure to that of a previous crystal structure and trying to show the major distance shifts in an easy to look at manner. I can get the RMSD using some online servers but it doesn't give me a good visual way of looking at the data.
Ok, quite late.... my code stolen from https://pymolwiki.org/index.php/Spectrum as per in my comment:
Not an expert here, but you could try to create a pdb with only c-alpha where B factor column has value according to bond lenght (proportional to it) and then color by b factor spectrum, I am sure there is some command about this : pymolwiki.org/index.php/Spectrum –
code using a fake peptide created with cmd.fab('AFGVAL', 'peptide_1') :
peptide_1.pdb :
ATOM 1 N ALA 1 19.613 5.728 -6.281 1.00 0.00 N
ATOM 2 CA ALA 1 20.289 7.022 -6.281 1.00 0.00 C
ATOM 3 C ALA 1 21.789 6.848 -6.281 1.00 0.00 C
ATOM 4 O ALA 1 22.320 5.731 -6.292 1.00 0.00 O
ATOM 5 CB ALA 1 19.781 7.814 -5.064 1.00 0.00 C
ATOM 6 H ALA 1 20.159 4.796 -6.281 1.00 0.00 H
ATOM 7 HA ALA 1 20.021 7.561 -7.209 1.00 0.00 H
ATOM 8 1HB ALA 1 18.685 7.964 -5.100 1.00 0.00 H
ATOM 9 2HB ALA 1 20.005 7.300 -4.109 1.00 0.00 H
ATOM 10 3HB ALA 1 20.237 8.819 -5.007 1.00 0.00 H
ATOM 11 N PHE 2 22.540 7.897 -6.270 1.00 0.00 N
ATOM 12 CA PHE 2 23.990 7.730 -6.270 1.00 0.00 C
ATOM 13 C PHE 2 24.690 9.068 -6.255 1.00 0.00 C
ATOM 14 O PHE 2 24.050 10.156 -6.244 1.00 0.00 O
ATOM 15 CB PHE 2 24.437 6.942 -7.538 1.00 0.00 C
ATOM 16 CG PHE 2 23.824 5.546 -7.729 1.00 0.00 C
ATOM 17 CD1 PHE 2 22.610 5.411 -8.413 1.00 0.00 C
ATOM 18 CD2 PHE 2 24.430 4.416 -7.174 1.00 0.00 C
ATOM 19 CE1 PHE 2 22.002 4.165 -8.523 1.00 0.00 C
ATOM 20 CE2 PHE 2 23.826 3.167 -7.294 1.00 0.00 C
ATOM 21 CZ PHE 2 22.611 3.043 -7.966 1.00 0.00 C
ATOM 22 H PHE 2 22.130 8.821 -6.260 1.00 0.00 H
ATOM 23 HA PHE 2 24.287 7.177 -5.358 1.00 0.00 H
ATOM 24 2HB PHE 2 25.541 6.842 -7.539 1.00 0.00 H
ATOM 25 3HB PHE 2 24.233 7.549 -8.444 1.00 0.00 H
ATOM 26 1HD PHE 2 22.116 6.283 -8.820 1.00 0.00 H
ATOM 27 2HD PHE 2 25.362 4.509 -6.633 1.00 0.00 H
ATOM 28 1HE PHE 2 21.050 4.077 -9.026 1.00 0.00 H
ATOM 29 2HE PHE 2 24.295 2.298 -6.857 1.00 0.00 H
ATOM 30 HZ PHE 2 22.134 2.079 -8.049 1.00 0.00 H
ATOM 31 N GLY 3 25.980 9.099 -6.253 1.00 0.00 N
ATOM 32 CA GLY 3 26.656 10.393 -6.239 1.00 0.00 C
ATOM 33 C GLY 3 28.155 10.220 -6.239 1.00 0.00 C
ATOM 34 O GLY 3 28.685 9.105 -6.251 1.00 0.00 O
ATOM 35 H GLY 3 26.513 8.242 -6.261 1.00 0.00 H
ATOM 36 3HA GLY 3 26.365 10.908 -5.371 0.00 0.00 H
ATOM 37 HA GLY 3 26.378 10.953 -7.151 1.00 0.00 H
ATOM 38 N VAL 4 28.906 11.269 -6.227 1.00 0.00 N
ATOM 39 CA VAL 4 30.356 11.101 -6.228 1.00 0.00 C
ATOM 40 C VAL 4 31.055 12.440 -6.212 1.00 0.00 C
ATOM 41 O VAL 4 30.429 13.507 -6.201 1.00 0.00 O
ATOM 42 CB VAL 4 30.798 10.251 -7.484 1.00 0.00 C
ATOM 43 CG1 VAL 4 32.326 10.136 -7.737 1.00 0.00 C
ATOM 44 CG2 VAL 4 30.276 8.794 -7.470 1.00 0.00 C
ATOM 45 H VAL 4 28.497 12.192 -6.217 1.00 0.00 H
ATOM 46 HA VAL 4 30.654 10.571 -5.305 1.00 0.00 H
ATOM 47 HB VAL 4 30.366 10.744 -8.381 1.00 0.00 H
ATOM 48 1HG1 VAL 4 32.862 9.673 -6.888 1.00 0.00 H
ATOM 49 2HG1 VAL 4 32.559 9.537 -8.638 1.00 0.00 H
ATOM 50 3HG1 VAL 4 32.799 11.120 -7.921 1.00 0.00 H
ATOM 51 1HG2 VAL 4 29.177 8.752 -7.361 1.00 0.00 H
ATOM 52 2HG2 VAL 4 30.510 8.264 -8.413 1.00 0.00 H
ATOM 53 3HG2 VAL 4 30.710 8.201 -6.643 1.00 0.00 H
ATOM 54 N ALA 5 32.345 12.471 -6.211 1.00 0.00 N
ATOM 55 CA ALA 5 33.021 13.765 -6.196 1.00 0.00 C
ATOM 56 C ALA 5 34.521 13.592 -6.197 1.00 0.00 C
ATOM 57 O ALA 5 35.052 12.475 -6.219 1.00 0.00 O
ATOM 58 CB ALA 5 32.511 14.544 -4.971 1.00 0.00 C
ATOM 59 H ALA 5 32.879 11.614 -6.220 1.00 0.00 H
ATOM 60 HA ALA 5 32.753 14.314 -7.119 1.00 0.00 H
ATOM 61 1HB ALA 5 31.415 14.694 -5.007 1.00 0.00 H
ATOM 62 2HB ALA 5 32.734 14.020 -4.022 1.00 0.00 H
ATOM 63 3HB ALA 5 32.967 15.549 -4.903 1.00 0.00 H
ATOM 64 N LEU 6 35.271 14.641 -6.173 1.00 0.00 N
ATOM 65 CA LEU 6 36.722 14.473 -6.173 1.00 0.00 C
ATOM 66 C LEU 6 37.420 15.811 -6.143 1.00 0.00 C
ATOM 67 O LEU 6 36.792 16.881 -6.122 1.00 0.00 O
ATOM 68 CB LEU 6 37.174 13.638 -7.404 1.00 0.00 C
ATOM 69 CG LEU 6 36.580 12.214 -7.580 1.00 0.00 C
ATOM 70 CD1 LEU 6 37.231 11.514 -8.782 1.00 0.00 C
ATOM 71 CD2 LEU 6 36.743 11.343 -6.323 1.00 0.00 C
ATOM 72 H LEU 6 34.862 15.564 -6.154 1.00 0.00 H
ATOM 73 HA LEU 6 37.013 13.950 -5.245 1.00 0.00 H
ATOM 74 2HB LEU 6 38.279 13.552 -7.384 1.00 0.00 H
ATOM 75 3HB LEU 6 36.958 14.216 -8.325 1.00 0.00 H
ATOM 76 HG LEU 6 35.495 12.316 -7.792 1.00 0.00 H
ATOM 77 1HD1 LEU 6 37.097 12.092 -9.716 1.00 0.00 H
ATOM 78 2HD1 LEU 6 38.318 11.367 -8.642 1.00 0.00 H
ATOM 79 3HD1 LEU 6 36.787 10.518 -8.962 1.00 0.00 H
ATOM 80 1HD2 LEU 6 37.799 11.259 -6.005 1.00 0.00 H
ATOM 81 2HD2 LEU 6 36.175 11.759 -5.470 1.00 0.00 H
ATOM 82 3HD2 LEU 6 36.357 10.318 -6.476 1.00 0.00 H
TER
END
peptide_2_moved.pdb , same pdb with some just carbon alpha moved by hand :
ATOM 1 N ALA 1 19.613 5.728 -6.281 1.00 0.00 N
ATOM 2 CA ALA 1 20.289 7.022 -6.281 1.00 0.00 C
ATOM 3 C ALA 1 21.789 6.848 -6.281 1.00 0.00 C
ATOM 4 O ALA 1 22.320 5.731 -6.292 1.00 0.00 O
ATOM 5 CB ALA 1 19.781 7.814 -5.064 1.00 0.00 C
ATOM 6 H ALA 1 20.159 4.796 -6.281 1.00 0.00 H
ATOM 7 HA ALA 1 20.021 7.561 -7.209 1.00 0.00 H
ATOM 8 1HB ALA 1 18.685 7.964 -5.100 1.00 0.00 H
ATOM 9 2HB ALA 1 20.005 7.300 -4.109 1.00 0.00 H
ATOM 10 3HB ALA 1 20.237 8.819 -5.007 1.00 0.00 H
ATOM 11 N PHE 2 22.540 7.897 -6.270 1.00 0.00 N
ATOM 12 CA PHE 2 24.369 7.337 -6.515 1.00 0.00 C
ATOM 13 C PHE 2 24.690 9.068 -6.255 1.00 0.00 C
ATOM 14 O PHE 2 24.050 10.156 -6.244 1.00 0.00 O
ATOM 15 CB PHE 2 24.437 6.942 -7.538 1.00 0.00 C
ATOM 16 CG PHE 2 23.824 5.546 -7.729 1.00 0.00 C
ATOM 17 CD1 PHE 2 22.610 5.411 -8.413 1.00 0.00 C
ATOM 18 CD2 PHE 2 24.430 4.416 -7.174 1.00 0.00 C
ATOM 19 CE1 PHE 2 22.002 4.165 -8.523 1.00 0.00 C
ATOM 20 CE2 PHE 2 23.826 3.167 -7.294 1.00 0.00 C
ATOM 21 CZ PHE 2 22.611 3.043 -7.966 1.00 0.00 C
ATOM 22 H PHE 2 22.130 8.821 -6.260 1.00 0.00 H
ATOM 23 HA PHE 2 24.287 7.177 -5.358 1.00 0.00 H
ATOM 24 2HB PHE 2 25.541 6.842 -7.539 1.00 0.00 H
ATOM 25 3HB PHE 2 24.233 7.549 -8.444 1.00 0.00 H
ATOM 26 1HD PHE 2 22.116 6.283 -8.820 1.00 0.00 H
ATOM 27 2HD PHE 2 25.362 4.509 -6.633 1.00 0.00 H
ATOM 28 1HE PHE 2 21.050 4.077 -9.026 1.00 0.00 H
ATOM 29 2HE PHE 2 24.295 2.298 -6.857 1.00 0.00 H
ATOM 30 HZ PHE 2 22.134 2.079 -8.049 1.00 0.00 H
ATOM 31 N GLY 3 25.980 9.099 -6.253 1.00 0.00 N
ATOM 32 CA GLY 3 26.656 10.393 -6.239 1.00 0.00 C
ATOM 33 C GLY 3 28.155 10.220 -6.239 1.00 0.00 C
ATOM 34 O GLY 3 28.685 9.105 -6.251 1.00 0.00 O
ATOM 35 H GLY 3 26.513 8.242 -6.261 1.00 0.00 H
ATOM 36 3HA GLY 3 26.365 10.908 -5.371 0.00 0.00 H
ATOM 37 HA GLY 3 26.378 10.953 -7.151 1.00 0.00 H
ATOM 38 N VAL 4 28.906 11.269 -6.227 1.00 0.00 N
ATOM 39 CA VAL 4 30.719 10.841 -6.509 1.00 0.00 C
ATOM 40 C VAL 4 31.055 12.440 -6.212 1.00 0.00 C
ATOM 41 O VAL 4 30.429 13.507 -6.201 1.00 0.00 O
ATOM 42 CB VAL 4 30.798 10.251 -7.484 1.00 0.00 C
ATOM 43 CG1 VAL 4 32.326 10.136 -7.737 1.00 0.00 C
ATOM 44 CG2 VAL 4 30.276 8.794 -7.470 1.00 0.00 C
ATOM 45 H VAL 4 28.497 12.192 -6.217 1.00 0.00 H
ATOM 46 HA VAL 4 30.654 10.571 -5.305 1.00 0.00 H
ATOM 47 HB VAL 4 30.366 10.744 -8.381 1.00 0.00 H
ATOM 48 1HG1 VAL 4 32.862 9.673 -6.888 1.00 0.00 H
ATOM 49 2HG1 VAL 4 32.559 9.537 -8.638 1.00 0.00 H
ATOM 50 3HG1 VAL 4 32.799 11.120 -7.921 1.00 0.00 H
ATOM 51 1HG2 VAL 4 29.177 8.752 -7.361 1.00 0.00 H
ATOM 52 2HG2 VAL 4 30.510 8.264 -8.413 1.00 0.00 H
ATOM 53 3HG2 VAL 4 30.710 8.201 -6.643 1.00 0.00 H
ATOM 54 N ALA 5 32.345 12.471 -6.211 1.00 0.00 N
ATOM 55 CA ALA 5 32.965 13.942 -6.049 1.00 0.00 C
ATOM 56 C ALA 5 34.521 13.592 -6.197 1.00 0.00 C
ATOM 57 O ALA 5 35.052 12.475 -6.219 1.00 0.00 O
ATOM 58 CB ALA 5 32.511 14.544 -4.971 1.00 0.00 C
ATOM 59 H ALA 5 32.879 11.614 -6.220 1.00 0.00 H
ATOM 60 HA ALA 5 32.753 14.314 -7.119 1.00 0.00 H
ATOM 61 1HB ALA 5 31.415 14.694 -5.007 1.00 0.00 H
ATOM 62 2HB ALA 5 32.734 14.020 -4.022 1.00 0.00 H
ATOM 63 3HB ALA 5 32.967 15.549 -4.903 1.00 0.00 H
ATOM 64 N LEU 6 35.271 14.641 -6.173 1.00 0.00 N
ATOM 65 CA LEU 6 37.139 14.337 -6.385 1.00 0.00 C
ATOM 66 C LEU 6 37.420 15.811 -6.143 1.00 0.00 C
ATOM 67 O LEU 6 36.792 16.881 -6.122 1.00 0.00 O
ATOM 68 CB LEU 6 37.174 13.638 -7.404 1.00 0.00 C
ATOM 69 CG LEU 6 36.580 12.214 -7.580 1.00 0.00 C
ATOM 70 CD1 LEU 6 37.231 11.514 -8.782 1.00 0.00 C
ATOM 71 CD2 LEU 6 36.743 11.343 -6.323 1.00 0.00 C
ATOM 72 H LEU 6 34.862 15.564 -6.154 1.00 0.00 H
ATOM 73 HA LEU 6 37.013 13.950 -5.245 1.00 0.00 H
ATOM 74 2HB LEU 6 38.279 13.552 -7.384 1.00 0.00 H
ATOM 75 3HB LEU 6 36.958 14.216 -8.325 1.00 0.00 H
ATOM 76 HG LEU 6 35.495 12.316 -7.792 1.00 0.00 H
ATOM 77 1HD1 LEU 6 37.097 12.092 -9.716 1.00 0.00 H
ATOM 78 2HD1 LEU 6 38.318 11.367 -8.642 1.00 0.00 H
ATOM 79 3HD1 LEU 6 36.787 10.518 -8.962 1.00 0.00 H
ATOM 80 1HD2 LEU 6 37.799 11.259 -6.005 1.00 0.00 H
ATOM 81 2HD2 LEU 6 36.175 11.759 -5.470 1.00 0.00 H
ATOM 82 3HD2 LEU 6 36.357 10.318 -6.476 1.00 0.00 H
TER
END
code :
import pymol
import math
from pymol import (
cmd ,
stored
)
print('########## PYMOL VERSION ##########################################')
print(' ', cmd.get_version() )
print('###################################################################')
pymol.finish_launching()
cmd.set('internal_gui_width' , '500')
cmd.load('peptide_1.pdb' , 'peptide_1')
cmd.load('peptide_2_moved.pdb' , 'peptide_2_moved')
diff_len = lambda x,y : math.sqrt((x[0]-y[0])*(x[0]-y[0]) + (x[1]-y[1])*(x[1]-y[1]) + (x[2]-y[2])*(x[2]-y[2]))
cmd.select('peptide_1_CA' ,'peptide_1 and name CA')
cmd.select('peptide_2_moved_CA' ,'peptide_2_moved and name CA')
stored.peptide_1_CA_coord = []
stored.peptide_2_moved_CA_coord = []
cmd.iterate_state('1' , 'peptide_1_CA' , 'stored.peptide_1_CA_coord.append((x,y,z))')
cmd.iterate_state('1' , 'peptide_2_moved_CA' , 'stored.peptide_2_moved_CA_coord.append((x,y,z))')
print('stored.peptide_1_CA_coord : ' , stored.peptide_1_CA_coord)
print('stored.peptide_2_moved_CA_coord : ' , stored.peptide_2_moved_CA_coord)
stored.newB = list(map(lambda x,y: diff_len(x,y), stored.peptide_2_moved_CA_coord, stored.peptide_1_CA_coord))
print('\nstorednewB to be passed : ', stored.newB , '\n')
cmd.alter('peptide_2_moved_CA', 'b=stored.newB.pop(0)')
cmd.save('peptide_2_moved_CA.pdb' , 'peptide_2_moved_CA')
cmd.spectrum('b', 'rainbow_rev' , 'peptide_2_moved_CA' , '0' , '1')
cmd.color('lightblue' , 'peptide_1' )
cmd.set('cartoon_transparency' , '0.5', 'peptide_1')
cmd.alphatoall('peptide_2_moved')
cmd.save('peptide_2_moved_CA_alphatoall.pdb' , 'peptide_2_moved')
cmd.load('peptide_2_moved_CA_alphatoall.pdb' , 'peptide_2_moved_CA_alphatoall')
cmd.spectrum('b', 'rainbow_rev' , 'peptide_2_moved_CA_alphatoall' , '0' , '1')
output:
########## PYMOL VERSION ##########################################
('2.3.0'
...
stored.peptide_1_CA_coord : [(20.288999557495117, 7.021999835968018, -6.281000137329102), (23.989999771118164, 7.730000019073486, -6.269999980926514), (26.6560001373291, 10.392999649047852, -6.238999843597412), (30.356000900268555, 11.10099983215332, -6.228000164031982), (33.020999908447266, 13.765000343322754, -6.196000099182129), (36.72200012207031, 14.472999572753906, -6.172999858856201)]
stored.peptide_2_moved_CA_coord : [(20.288999557495117, 7.021999835968018, -6.281000137329102), (24.368999481201172, 7.336999893188477, -6.514999866485596), (26.6560001373291, 10.392999649047852, -6.238999843597412), (30.7189998626709, 10.840999603271484, -6.508999824523926), (32.96500015258789, 13.942000389099121, -6.048999786376953), (37.138999938964844, 14.336999893188477, -6.385000228881836)]
storednewB to be passed : [0.0, 0.5984269572074781, 0.0, 0.5275691186189471, 0.23679966390593804, 0.48716415818795433]
showing in pymol window:
that is the CAs trace of moved (rainbow colored) vs original (lightblue [lightgray out of ray to png]) according to Palette https://pymolwiki.org/index.php/Palette_Colorbars rainbow_rev :
that goes from red = 0 to BLUE = 1 as set out in
cmd.spectrum('b', 'rainbow_rev' , 'peptide_2_moved_CA' , '0' , '1')
againg transferred calculated CAs to all atom using AlphaToAll :
cmd.alphatoall('peptide_2_moved') (check it into code) 
To use spectrum from min to max of the actual distance differences use in code above:
.....
stored.min = min(stored.newB)
stored.max = max(stored.newB)
print('\nmin of storednewB : ' , stored.min)
print('\nmax of storednewB : ' , stored.max)
print('\n')
cmd.alter('peptide_2_moved_CA', 'b=stored.newB.pop(0)')
cmd.save('peptide_2_moved_CA.pdb' , 'peptide_2_moved_CA')
cmd.spectrum('b', 'rainbow_rev' , 'peptide_2_moved_CA' , stored.min , stored.max)
....
