missing atoms in PDB input (2hol)

[amir-tagh]

Hello,

Thank you for developing such a useful tool. I have some issues with some PDB entries (like 2hol). The pdb file has some missing atoms for example in U46 there is no base and the U residue is just sugar+backbone. Do you have any suggestions how to handle such cases.

Thanks for your help.

error:
[ Info ] Converting PDB file to the SimRNA representation ...
[ Info ] Checking RNA structure ...
[ Fail ] In residue G 9 there are no atoms: P
[ Fail ] In residue U 36 there are no atoms: N1,C2,C4
[ Fail ] In residue C 54 there are no atoms: N1,C2,C4
[ Fail ] In residue U 55 there are no atoms: N1,C2,C4
[ Fail ] In residue U 63 there are no atoms: N1,C2,C4
[ Fail ] There are 5 errors in the given RNA structure. Please fix it and resubmit.

[filipsPL]

Hi,

Thanks for reporting the problem. Actually, AnnapuRNA cannot handle structures with missing atoms (due to the nature of the method).

The workaround would be:

• either remove the whole residue (easy)
• or remodel the residue and add missing atoms (difficult)

I would start with the first one. U46 does not seem to be very close to the ligand, so hopefully the contribution is not very large.

[amir-tagh]

Hello,

Thank you for your help. I will try the first approach, seems easier to implement regarding the large number of structures I need to study.

Best,