selection by protein chain id?

[Yogesh Sharma]

hi,

I am here with this basic question. I have a protein tetramer with different chain ids but same residue ids within chains. for example resid 6 in all chain refers to same amino acid. so i cant use select_atoms to select residues in a single chain (it will select residues in all chains i guess) how can i select atoms on the basis of chain id A,B,C,D

Achain=u.select_atoms("resid 15-256")               
Achain.write("XXXX.pdb")

[Tamas Hegedus]

Achain=u.select_atoms("resid 15-256 and segid A")
See https://www.mdanalysis.org/docs/documentation_pages/selections.html

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[YAGYA CHAUDHARY]

Hi,

I want to select two chains together to form a group. I am using LID_ca = u.select_atoms('name CA and segid A and segid B'), but this is not working.

Please suggest how to select two chains altogether.

Regards

Yagya

[Kacey Clark]

Hi,

Have you tried u.select_atoms('name CA and (segid A or segid B)')? That way you are selecting things that have segid A or segid B, so you will get both groups.

Best,

Kacey

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[YAGYA CHAUDHARY]

Thank you. This works for me.

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[Lily Wang]

Hi Yagya,

The selection language uses logical conjunctions (https://en.wikipedia.org/wiki/Logical_conjunction). This means that LID_ca = u.select_atoms('name CA and segid A and segid B’) tells MDAnalysis to select all atoms named “CA", in a single chain that is named “A” and “B” at the same time. You can chain segids together, which is an implied “or”:

LID_ca = u.select_atoms('name CA and segid A B’)

Or you can be more explicit:

LID_ca = u.select_atoms('name CA and (segid A or segid B)’)

Hope that helps.

Cheers,

Lily

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