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pFindStudio / pGlyco3

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Converting Glycoworkbench file to gdb file #3

Closed lindaz711 closed 4 months ago

lindaz711 commented 3 years ago

I'm having problems with converting a gwp file to gdb file using pGlyco3. The issue seems to be that the program does not recognize the phosphates ("p", "1P" in gwp) that were used in the gwp file. The phosphate was not defined in the configuration file "glycoworkbench_to_gdb.ini" since it was not a glycan, so I modified the "glyco.ini" to make do. But is there a way to have the program convert gwp files that contain glycan structures with modifications such as phsophorylation, sulfation, nitrosylation, and acetylation?

jalew188 commented 3 years ago

We do not support phosphates for glycoworkbench in current version of pGlyco3. But we can create a GDB based on something like this: image And then replacing X (Xyl) with pH.