This is a very basic question, but I can't find anything helpful on the internet: I created a molecule on Pymol; is there a way to extract its cartesian coordinate file in xyz-format?
Thank you very much in advance!
XYZ file format from Wikipedia
<number of atoms>
comment line
<element> <X> <Y> <Z>
...
EDITED SORRY JUST REALIZED YOU WERE ASKING ABOUT .xyz format NOT JUST COORDINATES
People suggest using openbabel ( github openbabel ) see here :
Converting a PDB file to XYZ file
From PyMOL old documentation https://pymol.org/dokuwiki/doku.php?id=start seems that it does support loading .xyz format but not saving to it.
Latest PyMOL version shows .xyz format too for export
just select XYZ (*.xyz) as File type when saving exported
molecule , result using file test.pdb below :
27
test
N 32.504002 37.205002 19.346001
C 33.806000 36.685001 19.868999
C 35.000000 37.216000 19.097000
O 34.831001 37.956001 18.112000
C 33.779999 35.136002 19.858000
C 33.676998 34.608002 18.436001
O 34.995998 34.712002 20.476000
N 36.222000 36.900002 19.493000
C 37.466000 37.312000 18.870001
C 37.889999 36.323002 17.771999
O 37.108002 35.425999 17.476999
C 38.573002 37.472000 19.903000
C 38.854000 36.188000 20.687000
N 39.763000 36.310001 21.648001
O 38.219002 35.167999 20.445000
N 39.077999 36.497002 17.205000
C 39.536999 35.640999 16.112000
C 39.734001 34.175999 16.518000
O 39.174000 33.270000 15.869000
C 40.806999 36.208000 15.498000
N 40.123001 33.959999 17.768000
C 40.236000 32.608002 18.357000
C 38.868000 31.997000 18.531000
O 38.570999 30.833000 18.173000
C 40.984001 32.761002 19.690001
C 41.111000 31.396000 20.389999
O 42.296001 33.273998 19.424999
PyMOL API would be :
cmd.save('selection' , 'output.xyz') , but it doesn't work.
output
Traceback (most recent call last):
File "./xxx.py", line 79, in <module>
cmd.save('test' , 'output.xyz')
File "/.../.../.../pymol/exporting.py", line 876, in save
raise pymol.CmdException('File format not supported for export')
pymol.CmdException: Error: File format not supported for export
from PyMOL Wiki! usin PyMOL API:
try : xyz = cmd.get_coords('sele', 1) as explained in
or from PyMOL console as per in :
Thread: [PyMOL] How do you show the coordinates of an atom? :
try : iterate_state 1, <selection_name>, print (x,y,z)
see Iterate and the iterate-family exposed the variables.
More in details using PyMOL console ,
loading file test.pdb in PyMOL :
ATOM 1 N THR A 1 32.504 37.205 19.346 1.00 35.93 N
ATOM 2 CA THR A 1 33.806 36.685 19.869 1.00 33.83 C
ATOM 3 C THR A 1 35.000 37.216 19.097 1.00 34.05 C
ATOM 4 O THR A 1 34.831 37.956 18.112 1.00 37.45 O
ATOM 5 CB THR A 1 33.780 35.136 19.858 1.00 35.93 C
ATOM 6 OG1 THR A 1 34.996 34.712 20.476 1.00 29.78 O
ATOM 7 CG2 THR A 1 33.677 34.608 18.436 1.00 28.68 C
ATOM 8 N ASN A 2 36.222 36.900 19.493 1.00 27.70 N
ATOM 9 CA ASN A 2 37.466 37.312 18.870 1.00 26.38 C
ATOM 10 C ASN A 2 37.890 36.323 17.772 1.00 23.63 C
ATOM 11 O ASN A 2 37.108 35.426 17.477 1.00 26.11 O
ATOM 12 CB ASN A 2 38.573 37.472 19.903 1.00 26.18 C
ATOM 13 CG ASN A 2 38.854 36.188 20.687 1.00 23.57 C
ATOM 14 OD1 ASN A 2 38.219 35.168 20.445 1.00 24.27 O
ATOM 15 ND2 ASN A 2 39.763 36.310 21.648 1.00 25.69 N
ATOM 16 N ALA A 3 39.078 36.497 17.205 1.00 27.65 N
ATOM 17 CA ALA A 3 39.537 35.641 16.112 1.00 27.70 C
ATOM 18 C ALA A 3 39.734 34.176 16.518 1.00 27.15 C
ATOM 19 O ALA A 3 39.174 33.270 15.869 1.00 26.97 O
ATOM 20 CB ALA A 3 40.807 36.208 15.498 1.00 27.00 C
ATOM 21 N THR A 4 40.123 33.960 17.768 1.00 24.83 N
ATOM 22 CA THR A 4 40.236 32.608 18.357 1.00 21.65 C
ATOM 23 C THR A 4 38.868 31.997 18.531 1.00 22.46 C
ATOM 24 O THR A 4 38.571 30.833 18.173 1.00 22.18 O
ATOM 25 CB THR A 4 40.984 32.761 19.690 1.00 19.96 C
ATOM 26 OG1 THR A 4 42.296 33.274 19.425 1.00 28.59 O
ATOM 27 CG2 THR A 4 41.111 31.396 20.390 1.00 23.74 C
using :
select pippo ,resi 1 AND name CA ---> Selector: selection "pippo" defined with 1 atoms.
Then :
iterate_state 1, pippo , print ( x,y,z) ---> 33.805999755859375 36.685001373291016 19.868999481201172 IterateState: iterated over 1 atom coordinate states.
While using PyMOL API on same file test.pdb with code :
import pymol
from pymol import (
cmd ,
stored,
)
print('########## PYMOL VERSION ##########################################')
print(' ', cmd.get_version() )
print('###################################################################')
# pymol.finish_launching() # uncomment to launch PyMOL
cmd.load('test.pdb' , 'test')
cmd.select('pippo' , 'resi 1 AND name CA')
cmd.color('yellow' , 'pippo' , 0)
xyz = cmd.get_coords('pippo', 1)
print('\nxyz : ', xyz , '\n') # ----> xyz : [[33.806 36.685 19.869]]
xyz = cmd.get_coordset('pippo', 1) # Operates on the object-state level, not on selections
print('\nxyz : ', xyz , '\n') # ---> xyz : None
xyz = cmd.get_coordset('test', 1) # Operates on the object-state level, not on selections
print('\nxyz : ', xyz , '\n') # ---> xyz : [[32.504 37.205 19.346] ......... [41.111 31.396 20.39 ]]
xyz = cmd.get_model('pippo', 1).get_coord_list()
print('\nxyz : ', xyz , '\n') # -----> xyz : [[33.805999755859375, 36.685001373291016, 19.868999481201172]]
### OR USING ITERATE :
stored.coords = []
cmd.iterate_state("-1" , "pippo" , "stored.coords.append([x,y,z])")
print('\nstored.coords : ' , stored.coords ,'\n')
#### PRINTS ---> stored.coords : [[33.805999755859375, 36.685001373291016, 19.868999481201172]]
Output :
PyMOL not running, entering library mode (experimental)
Executive: Colored 1 atom.
xyz : [[33.806 36.685 19.869]]
xyz : None
xyz : [[32.504 37.205 19.346]
[33.806 36.685 19.869]
[35. 37.216 19.097]
[34.831 37.956 18.112]
[33.78 35.136 19.858]
[34.996 34.712 20.476]
[33.677 34.608 18.436]
[36.222 36.9 19.493]
[37.466 37.312 18.87 ]
[37.89 36.323 17.772]
[37.108 35.426 17.477]
[38.573 37.472 19.903]
[38.854 36.188 20.687]
[38.219 35.168 20.445]
[39.763 36.31 21.648]
[39.078 36.497 17.205]
[39.537 35.641 16.112]
[39.734 34.176 16.518]
[39.174 33.27 15.869]
[40.807 36.208 15.498]
[40.123 33.96 17.768]
[40.236 32.608 18.357]
[38.868 31.997 18.531]
[38.571 30.833 18.173]
[40.984 32.761 19.69 ]
[42.296 33.274 19.425]
[41.111 31.396 20.39 ]]
xyz : [[33.805999755859375, 36.685001373291016, 19.868999481201172]]
stored.coords : [[33.805999755859375, 36.685001373291016, 19.868999481201172]]
adding this bit of code to the previous one :
stored.xyz_full= []
cmd.iterate_state("-1" , "test" , "stored.xyz_full.append([elem , f'{x:.15f}' , f'{y:.15f}' , f'{z:.15f}'] )")
print('\nstored.xyz_full : ' , stored.xyz_full ,'\n')
print('len(stored.xyz_full) : ', len(stored.xyz_full ))
with open('output_xyz.xyz' , 'w') as handle :
handle.write(str(len(stored.xyz_full ))+'\n')
handle.write('test'+'\n')
for i in stored.xyz_full :
handle.write(str(i[0]) +' ' + str(i[1]) +' ' +str(i[2]) +' ' + str(i[3])+'\n')
##SAVE molecule test in xyz :
# cmd.save('test' , 'output.xyz') # !!!!!!!!!!!!!!!!! pymol.CmdException: Error: File format not supported for export
ouput will have added :
stored.xyz_full : [['N', '32.504001617431641', '37.205001831054688', '19.346000671386719'], ['C', '33.805999755859375', '36.685001373291016', '19.868999481201172'], ['C', '35.000000000000000', '37.215999603271484', '19.097000122070312'], ['O', '34.831001281738281', '37.956001281738281', '18.111999511718750'], ['C', '33.779998779296875', '35.136001586914062', '19.857999801635742'], ['C', '33.676998138427734', '34.608001708984375', '18.436000823974609'], ['O', '34.995998382568359', '34.712001800537109', '20.475999832153320'], ['N', '36.222000122070312', '36.900001525878906', '19.493000030517578'], ['C', '37.465999603271484', '37.312000274658203', '18.870000839233398'], ['C', '37.889999389648438', '36.323001861572266', '17.771999359130859'], ['O', '37.108001708984375', '35.425998687744141', '17.476999282836914'], ['C', '38.573001861572266', '37.472000122070312', '19.902999877929688'], ['C', '38.854000091552734', '36.187999725341797', '20.687000274658203'], ['N', '39.763000488281250', '36.310001373291016', '21.648000717163086'], ['O', '38.219001770019531', '35.167999267578125', '20.444999694824219'], ['N', '39.077999114990234', '36.497001647949219', '17.204999923706055'], ['C', '39.536998748779297', '35.640998840332031', '16.111999511718750'], ['C', '39.734001159667969', '34.175998687744141', '16.517999649047852'], ['O', '39.173999786376953', '33.270000457763672', '15.869000434875488'], ['C', '40.806999206542969', '36.208000183105469', '15.498000144958496'], ['N', '40.123001098632812', '33.959999084472656', '17.767999649047852'], ['C', '40.236000061035156', '32.608001708984375', '18.357000350952148'], ['C', '38.868000030517578', '31.996999740600586', '18.531000137329102'], ['O', '38.570999145507812', '30.833000183105469', '18.173000335693359'], ['C', '40.984001159667969', '32.761001586914062', '19.690000534057617'], ['C', '41.111000061035156', '31.395999908447266', '20.389999389648438'], ['O', '42.296001434326172', '33.273998260498047', '19.424999237060547']]
len(stored.xyz_full) : 27
and the output_xyz.xyz file in .xyz*** format will be written :
27
test
N 32.504001617431641 37.205001831054688 19.346000671386719
C 33.805999755859375 36.685001373291016 19.868999481201172
C 35.000000000000000 37.215999603271484 19.097000122070312
O 34.831001281738281 37.956001281738281 18.111999511718750
..............
this is funny because the original test.pdb had only three decimal places in its cartesian coordinates .
*** still wasnt able to figure out if .xyz format uses space delimited column for the x , y, z values of it there is a fixed column size for them.
EDITED BIS
After a little bit of googling I finally ended up at :
XYZ cartesian coordinates format (xyz) Openbabel
where is written :
On output, the first line written is the number of atoms in the molecule (warning - the number of digits is limited to three for some programs, e.g. Maestro). Line two is the title of the molecule or the filename if no title is defined. Remaining lines define the atoms in the file. The first column is the atomic symbol (right-aligned on the third character), followed by the XYZ coordinates in “10.5” format, in angstroms. This means that all coordinates are printed with five decimal places.
Example :
12
benzene example
C 0.00000 1.40272 0.00000
H 0.00000 2.49029 0.00000
C -1.21479 0.70136 0.00000
H -2.15666 1.24515 0.00000
C -1.21479 -0.70136 0.00000
H -2.15666 -1.24515 0.00000
C 0.00000 -1.40272 0.00000
H 0.00000 -2.49029 0.00000
C 1.21479 -0.70136 0.00000
H 2.15666 -1.24515 0.00000
C 1.21479 0.70136 0.00000
H 2.15666 1.24515 0.00000
So the part of my code writing the output_xyz.xyz file has to be modify accordingly , while the PyMOL exported XYZ (*.xyz) file seems to carry problems too
Use :
cmd.iterate_state("-1" , "test" , "stored.xyz_full.append([elem.rjust(3 , ' ') , f'{x:15.5f}' , f'{y:15.5f}' , f'{z:15.5f}'])")
to get output_xyz.xyz as :
27
test
N 32.50400 37.20500 19.34600
C 33.80600 36.68500 19.86900
C 35.00000 37.21600 19.09700
O 34.83100 37.95600 18.11200
C 33.78000 35.13600 19.85800
........
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