Do you know how to change angles in Pymol builder between atoms and where can I find 3d structures of lipids like dgdg (Digalactosyldiacylglycerol) or others lipids?
Normally, you don't change the bond angles. The dihedral angles you can change in PyMOL using
set_dihedral atom1, atom2, atom3, atom4, angle [,state=1] [,quiet=1]
https://pymolwiki.org/index.php/Set_Dihedral
You can find the crystal structures of "small molecules" (from the point of view of somebody working with proteins) in the Cambridge Structural Database (CSD) https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ .
search through: https://www.ccdc.cam.ac.uk/structures/
or https://www.ccdc.cam.ac.uk/structures/WebCSD/StructureSearch
Be aware that the CSD is not as freely accessible as the PDB.
Otherwise, you have to trust the small molecule modeling programs like Chem3D to generate reasonable 3D model, keeping in mind which bonds are freely rotatable and will allow multiple conformations
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