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?
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".