no nucleotide in some structures

[shuxiang]

Hi Xiang-Jun,

I'm using DSSR to analyze some structures and it showed there is no nucleotide was found. When I visualized these structures using pymol. I indeed saw nucleotides are there. For example (6CEV):

x3dna-dssr -i=6cev.pdb

Thanks.

Best,
Shuxiang

[xiangjun]

By default, DSSR checked for ATOM/HETATM records with the alternative location (altloc) set either as space (most common) or 'A'. In PDB entry 6CEV, the DNA atoms have altloc as 'B'. That's why you do not see any results from a default DSSR run.

Try: x3dna-dssr -i=6cev.pdb --altloc=B

Best regards,

Xiang-Jun

[shuxiang]

Thank you so much for the explanation and an option to solve my problem.

Best,
Shuxiang