Messages

1

RNA structures (DSSR) / Re: Avoiding pairing that cross chains

« on: July 27, 2019, 01:19:34 pm »

Using PyMol worked much better! Thanks for the tip.

2

RNA structures (DSSR) / Re: Avoiding pairing that cross chains

« on: July 27, 2019, 07:12:42 am »

Thank you for the suggestions. I managed to extract a chain in R using bio3d. As an example, I can extract chain A5 of PDB 4V6W:

library(bio3d)
pdb <- read.cif("4V6W.cif")
inds <- atom.select(pdb, chain="A5")
pdb2 <- trim.pdb(pdb, inds)
write.pdb(pdb2, "4V6W.pdb")

When I ran DSSR on the resulting pdb file (attached), I obtained the error:

no ATOM/HETATM records found!

On the original cif file with all chains I obtained the expected result. Could you please help me understand why DSSR is not working on the attached file?

3

RNA structures (DSSR) / Re: Avoiding pairing that cross chains

« on: July 26, 2019, 02:33:17 pm »

Thank you for the quick and informative reply. What is the best way to extract a single chain from a pdb file?

4

RNA structures (DSSR) / Avoiding pairing that cross chains

« on: July 26, 2019, 01:11:05 pm »

I used DSSR to calculate the secondary structure of PDB 4V6W chain A5, which is a eukaryotic LSU rRNA. This resulted in 896 left pairings "(" and 880 right pairings ")". Presumably this imbalance is because some of the pairs are inter-chain. Is there a way to force pairings only within single chains (i.e., intra-chain pairs only)? Ideally, I would like to obtain a balanced structure for each chain by itself.

Thanks,
Erik