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Martinize2: Protein with too many chains
- outihaa
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2 years 1 month ago #9336
by outihaa
Martinize2: Protein with too many chains was created by outihaa
When one has a protein with 200 individual chains, how can one read it into martinize2? There are not enough characters in the alphabet to name the individual chains.
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- xavier
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2 years 1 month ago #9337
by xavier
Replied by xavier on topic Martinize2: Protein with too many chains
Hahahaha more than 200! I would think you can use pairs of characters but I am not sure actually.
But even that wouldn’t cover the 200 chains … You may have to find a different solution.
I would believe that the chains don’t have to be defined, except for specific reasons, which I can’t remember right now. They can in principle be in the box interacting with neighbors using a cutoff without knowing who it is … similar to water-water interactions.
In summary, the chains don’t need to have a name except for specific reasons.
But even that wouldn’t cover the 200 chains … You may have to find a different solution.
I would believe that the chains don’t have to be defined, except for specific reasons, which I can’t remember right now. They can in principle be in the box interacting with neighbors using a cutoff without knowing who it is … similar to water-water interactions.
In summary, the chains don’t need to have a name except for specific reasons.
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- bart
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2 years 1 month ago - 2 years 1 month ago #9339
by bart
Replied by bart on topic Martinize2: Protein with too many chains
I think what you are hinting at here is that you have a giant complex of many proteins which you want to capture in one elastic body, having EN between all the chains (if they fit the distance criterion). Therefore the issue probably lies with Martinize2. Anyway, what I would try first of all is to name all chains to A and try to run Martinize2 as usual. Then you will probably get all kind of errors which we can than start to tackle. I think it is an interesting problem, and one we will start to see more and more.
PS
You can use the B factor in your reference pdb to to put the second chain character (26*26 is enough to uniquely identify your chains). Then at least you can use selections in VMD to get unique residues. Also it could help to renumber all your residues so they are at least unique although this is very software dependent if they will use this number or they base their identity on the line number.
PS
You can use the B factor in your reference pdb to to put the second chain character (26*26 is enough to uniquely identify your chains). Then at least you can use selections in VMD to get unique residues. Also it could help to renumber all your residues so they are at least unique although this is very software dependent if they will use this number or they base their identity on the line number.
Last edit: 2 years 1 month ago by bart.
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