I have generated a full PDB file from a C-alpha trace using a tool called PD2_ca2main.
Now, I want to compare the two PDB files and find out the accuracy of the newly generated file.
How can I do that?
I used rmsd to compare the two files. But, it says that the files are of different lengths.
TM-align should work for this. The paper in the citation says:
"TM-align only employs the backbone Cα coordinates of the given protein structures; however, the methodology is readily generalized to any type of atom."
And so I suspect it would work where one of the files is just a C-alpha trace.
You aren't supplying details of your actual commands, or input/output, the results of TM-align and so it is hard for anyone here to know & comment.
They talk about the program you used to convert things in Computational reconstruction of atomistic protein structures from coarse-grained models in comparison to related tools. It doesn't look like it is naive as you may expect.
There's several options listed there and maybe they'll make something more sufficient for your needs.
Keep in mind: “All models are wrong, but some are useful”. - George E. P. Box
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version 2.3.6
It seems you've cross-posted this to bioinfo SE as well: https://bioinformatics.stackexchange.com/q/19878/650
Do not do this - it is bad etiquette and annoys users in both communities.
Plus, you have an answer here and did not do the bare minimum of adding a pointer to this post on the other post (and vice versa). Be more thoughtful or neither community will feel appreciated for helping you out.
Please do not delete questions that have received at least one comment/answer. Deleting questions and reposting in a new thread is not appropriate.