Attempt2: aanma on selected model from NMR ensemble
I created the issue "aanma on selected model from NMR ensemble" but the format looks very strange, and it makes the index of the lists un-readable.
So, here goes my message again, hopefully with no format issues:
Goal of the calculation:To perform all-atom normal mode analysis on selected models from a number of NMR ensembles deposited in the protein data bank. For example, in the NMR ensemble pdb file of my protein 1 there are 20 models, I want to perform all-atom normal mode analysis only on models 1,3, and 19 of my protein 1. And, repeat for all NMR ensembles I want to study.
My issue: How to get aanma.pdb to read the model that I want to analyze.
Attempts so far:
Read input file, works well:
pdbs_all[[1]] = read.pdb("my.protein1.pdb", multi = TRUE)
I think the following line performs aanma on model 1 only:
aanma.modes <- aanma.pdb(pdbs_all[[1]], outmodes = "calpha", mass = TRUE, rtb = TRUE)
I wish I could do something like the following line if I want to run aanma on model 3 But, I know that the following line does not work (because the indexes access the list of residue names):
aanma.modes <- aanma.pdb(pdbs_all13, outmodes = "calpha", mass = TRUE, rtb = TRUE)
Error message:
Error in aanma.pdb(pdbs_all81, outmodes = "calpha", mass = TRUE, : please provide a 'pdb' object as obtained from 'read.pdb()'.
I have also tried:
aanma.modes <- aanma.pdbs(pdbs_all[[1]]$xyz[3,], outmodes = "calpha", mass = TRUE, rtb = TRUE)
But, of course, I get the following message:
Error in aanma.pdb(pdbs_all1$xyz[3, ], outmodes = "calpha", mass = TRUE, : please provide a 'pdb' object as obtained from 'read.pdb()'.
I have tried aanm.pdbs but it does not work either. And, I do not think I have to go through the route of aligning because all models belong to the same NMR ensemble.
Any suggestion will be greatly appreciated!
sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)
bio3d_2.4-1
Comments (2)
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Issue
#773was marked as a duplicate of this issue. - Log in to comment
Hi,
A quick (but probably “dirty”) way is to create a temporary PDB with the ‘xyz’ taken from the specific row of the original ‘xyz’. For example,