clean.pdb for cleaning RNA pdb

[Former user]

i am using clean.pdb to clean the protein-RNA complexes as well as few RNA pdb files, clean.pdb works fine with the complexes nut when it comes to cleaning an RNA pbd file it shows up an error like

r = clean.pdb(p) Error in rowSums(apply(xyz, 1, diff)^2) : 'x' must be an array of at least two dimensions

can i use this clean.pdb for rna files, if so how can i resolve this issue for cleaning the RNA PDB files?

[Xinqiu Yao]

Thanks for catching. Should be fixed now (see here).

Please update your bio3d with the latest master or releases branch. Check our wiki page for how to install developmental version bio3d.

Let me know if you have any questions.

[sai_bhavani]

thank you for the response.. the issue has been solved but there is an problem, when i clean my RNA pdb files the columns are being shifted backwards for A,U,G,C . which is not being accepted as input by other softwares. (same goes for RNA in protein-RNA complexes) for example the original file is like

and then on cleaning the columns changes to

the pdb file i used here is 1Q9A.pdb

[Xinqiu Yao]

It is actually a bug in write.pdb(). Should be fixed by the recent commit here.

Let me know if it works. Thanks.

[Xinqiu Yao]

Bug is fixed as said in the commit