jamesmkrieger
commented
2 years ago This is a known problem with the normal mode wizard and .nmd files, which we plan to fix at some point. For now, the main suggestion is to just hide the connecting residues. There are some other work-arounds I've used in the ProDy Python API itself though I don't exactly remember what they were right now. I think it had to do with which PDB file was used as a reference.
Perhaps one thing to do could be to add chain IDs into your PDB file, which you can do in PyMOL.
Another thing that I think helped was to use the extend model feature, which exists in the normal mode wizard as well as the Python API.
I can look in the app code and see if there's anything in there that could be causing the problem too, but probably there isn't.
Hi,
I'm using prody to do PCA analysis on a dimer. I aligned my trajectory (.dcd) file first on VMD with the PDB. The PDB I used for aligning also has 2 segments named in a separate column. But once I do the analysis the .nmd file shows that the 2 segments/chains are connected to each other. How do I solve this issue? I read in the manual that through hierarchical view different segments can be accessed but I'm not sure how to use it for PCA analysis.
command I used ,
prody pca -a -A --select calpha --pdb CA_nowater.pdb aligned5-13.dcd --aligned
Thank you !