Hi Friends,
I was wondering if you know how to generate only and only 6 moleculaes around one molecule in Pymol.
I do this: Action--> Generate --> symmetry mates --> 6a
but 12 molecuales appear! what should I do?
Thank you in advance!
If you want to see only six symmetry mates. Select one chain at a time and delete it.
Each symmetry mate is a separate object. You can either undisplay it by clicking on its name, or delete it using Action->delete object. You may also try to remove the solvent before generating the symmetry mates (if you don't need it for future analysis) and try a slightly lower distance cutoff of 4Å to get only symmetry mates that are in actual VdW contact. Using the command line, you can use the symexp command https://pymolwiki.org/index.php/Symexp for better command, or the SuperSym script https://pymolwiki.org/index.php/SuperSym to generate symmetry mates based on the unit cell rather than based on contact criteria.
Dear Ramin,
Thank you.
Would you please tell me how?
Can yu write me the script?
You have to define more clearly what you want to do:
Pymol Action--> Generate --> symmetry mates --> 6a
or the equivalent Pymol command-line command:
symexp name_for_new_objects, asymmetric_name,(asymmetric_name),distance
will generate all symmetry-related copies of the asymmetric unit that have at least one atom which is no farther away than 6 Å from an atom in your original molecule. In your case, there are twelve symmetry-related objects that fulfill that criterion. This method is used if you want to analyze all crystal contacts your protein is involved in.
No script can know automatically which six of the twelve copies that fulfill the criterium you want to see!
On the other hand, the pymol SuperSym Plugin will fill the unit cell of the crystal (or the specified array of unit cells) with replicates of the asymmetric unit. This method is used if you want to analyze how the unit cell of your crystal is packed. The number of replicates generated by this method is defined by the space group of the crystal. Again, arbitrarily omitting replicates might invalidate your analysis.
This server will do the same: http://dicsoft2.physics.iisc.ernet.in/sem/
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