Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.0 (DSSR Manual) · Homepage
I have tried using open babel, CIFTr (cif translator), cif2pdb, and have tried reading the cif format using mdtraj in the hopes of being able to translate it to pdb, but all fails for now.That's tough to hear, but quite real, isn't it?
Something very simple such as aligning the bacterial mitocondrial ribosome (4v63.cif) and the human one (3j9m), becomes very difficult.Simple things should not become that difficult. It should be the other way around! When the tools that should serve have become a master?
Once more, having this additional feature in dssr would be great!Will get it done by tomorrow, and report back along this thread.
dssr --select=nt -i=3j9m.cif -o=3j9m_rna.pdbFor the recent structure of the full human mitochondrial ribosome.Is it due to the limitation of the PDB format for such a large structure? Please also play around with some typical small structures to see if it works as expected (it should).
Even though it's quite a large structure it finishes in 31 seconds.
It almost gets it right but it clumps parts of the residues into a column, or at least that is what pymol shows (see attached image at the end).
It would also be useful to get the protein part, sort of like with get_part -p instead of -n.Try --select=protein or --select=aa. Other options are --select=dna or --select=rna. The default is --select=nt which can be shortened to --select. As noted in the User Manual, UPPER or MixED cases are also accepted (e.g., --select=Protein).
It almost gets it right but it clumps parts of the residues into a column, or at least that is what pymol shows (see attached image at the end).I have looked into 3j9m and did not find anything obviously wrong with DSSR-extracted RNA components in PDB format. Did you check the atom ids of the residues clumped into the (right) column as shown in PyMOL? Do they really correspond to any ATOM/HETATM records in the PDB file that DSSR generated?
Note that in the 3j9m_rna.pdb file you produced, the "Atom serial number" in columns 7-11 is a based on CIF "_atom_site.id", and is not necessarily continuous sequentially. You could write a short script to make the "Atom serial number" field consecutive from 1 to n. Please have a try and report back if that does the trick.
Yes, that solves the problem for 3j9m, but for molecules which have a higher content of atoms than 99999, for example the whole 70S ribosome of thermus thermophilus (pdbid=4v63), which has 200836 atoms, then the same problem comes back because it finds repeated atom numbers in the 7-11 columnsI am glad that you confirmed in 3j9m the non-continous atom serial number was what had caused the visualization problem in PyMOL. As for cases with > 99999 atoms, it is yet another story -- here the PDB format is clearly no longer applicable. As I mentioned previously, 3DNA v2.x is not PDBx/mmCIF compatible.
Although much harder and messy to implement I think what would be ideal for users would be to have the same functionality of get_part but producing .cif output.Are you asking for .cif output by the DSSR --select option? That's not a problem. But then you need to still parse the .cif files yourself, and that's not what this thread is about in my understanding.
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University