I have one protein eg: 1R9M, like that. Now I want to delete a complete chain to do the superimposition, please let me know how to do it in PyMol.
Thanks in advance
Using the graphical interface:
select the selection mode to "chain" (bottom left panel) and click on the chain you wish to delete. For the selection object (sele), choose A: remove atoms
Using the command line, use the "remove" command (https://pymolwiki.org/index.php/Remove)
e.g.
remove chain A
Dear Ajay Sharma you can delete the in pymol..simply open your protein in pymol then show sequences..and then select all the sequences of one particular chain and simply delete it, that's it.
best of luck
You can do superimposition without deleting anything at all. You can select the target (a chain or part of a chain) and rename that selection (say 'target') and then select the mobile atoms (some chain that you want to align) and then align the current selection to the named selection ('target').
In addition to what Uttam Pal said about aligning just a selection without removing other chains, in PyMOL you can define whether you load the asymmetric unit of the crystal or the biological unit using the "set assembly" command: https://pymolwiki.org/index.php/Assembly . This can help you to load just one instance of your molecule or complex in those cases where the asymmetric unit of the crystal contains many instances.
How to know target protein by its chain? For example i have target protein 2W3L with two chain (A and B) Crystal Structure of Chimaric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex, my target is Phenyl Tetrahydroisoquinoline Amide Complex, how to know that target in which chain? Please help
How to know target protein by its chain? For example i have target protein 2W3L with two chain (A and B) Crystal Structure of Chimaric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex, my target is Phenyl Tetrahydroisoquinoline Amide Complex, how to know that target in which chain? Please help
How to know target protein by its chain? For example i have target protein 2W3L with two chain (A and B) Crystal Structure of Chimaric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex, my target is Phenyl Tetrahydroisoquinoline Amide Complex, how to know that target in which chain? Please help
How to know target protein by its chain? For example i have target protein 2W3L with two chain (A and B) Crystal Structure of Chimaric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex, my target is Phenyl Tetrahydroisoquinoline Amide Complex, how to know that target in which chain? Please help
How to know target protein by its chain? For example i have target protein 2W3L with two chain (A and B) Crystal Structure of Chimaric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex, my target is Phenyl Tetrahydroisoquinoline Amide Complex, how to know that target in which chain? Please help
How to know target protein by its chain? For example i have target protein 2W3L with two chain (A and B) Crystal Structure of Chimaric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex, my target is Phenyl Tetrahydroisoquinoline Amide Complex, how to know that target in which chain? Please help
@Hasriatun Padmi , Check out the corresponding record on www.rcsb.org
This is a case where you have two copies of the protein in the asymmetric unit - you can either download biological assembly 1 or 2 instead of the whole asymmetric unit of the crystal to have just a single complex, including the corresponding ligand(s)
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