Dear pymol users,
I would like to know if there is a way to change pymol2 settings in order
to fit older version.
My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same
results.
I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7:
cmd.fetch('1atp')
cmd.select('lig','organic')
Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of ATP
molecule but pymol2 does not.
Using the command below, I compare the differences between the two versions
in sdf file format.
cmd.save('atp.sdf',selection='lig')
diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf
2c2
< PyMOL186 3D 0
---
> PyMOL2.0 3D 0
18,19c18,19
< 11.1000 9.8800 -1.4300 O 0 5 0 0 0 0 0 0 0 0 0 0
< 13.9290 9.9200 -2.7000 O 0 5 0 0 0 0 0 0 0 0 0 0
---
> 11.1000 9.8800 -1.4300 O 0 0 0 0 0 0 0 0 0 0 0 0
> 13.9290 9.9200 -2.7000 O 0 0 0 0 0 0 0 0 0 0 0 0
24c24
< 15.7480 6.8350 -0.4270 O 0 5 0 0 0 0 0 0 0 0 0 0
---
> 15.7480 6.8350 -0.4270 O 0 0 0 0 0 0 0 0 0 0 0 0
38c38
< 1 18 2 0 0 0 0
---
> 1 18 1 0 0 0 0
41c41
< 2 19 2 0 0 0 0
---
> 2 19 1 0 0 0 0
47c47
< 3 24 2 0 0 0 0
---
> 3 24 1 0 0 0 0
How can I force pymol2 to write exactly the same sdf as before ?
Is there new defaults settings in pymol2 that I can override ?
Thanks,
Fabrice
Fabrice Carles - PhD student
Structural Bioinformatics & Chemoinformatics,
Institut de Chimie Organique et Analytique (ICOA)
University of Orleans - France
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