Question re. Yale Morph Server

Q:
I’m having trouble with the multi-chain morph server. My protein includes chains that are designated as an upper case “A” and lower case “a”. When I upload the PDB file and specify all chains including A and a, the resulting Morph PDB file does not contain the lower case chain a. Is there any way to fix this problem?

A:
Thank you for reaching out to us regarding the morph server. It is perhaps the case that the server is internally case-insensitive with regard to the chain. If possible, I would suggest changing chain "a" to a different letter in the PDB input file (ie, by changing "a" to "B" using a simple script). Then, once you get your output from the server, you can again change chain "B" to the original label chain "a".

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