Open Yago52 opened 1 month ago
the output:
PDB file is found in working directory (6vxx.pdb.gz).
@> 972 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1121 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> DCD file contains 8334 coordinate sets for 1121 atoms.
@> DCD file was parsed in 0.08 seconds.
@> 107.55 MB parsed at input rate 1334.83 MB/s.
@> 8334 coordinate sets parsed at input rate 103434 frame/s.
@> DCD file contains 8334 coordinate sets for 1121 atoms.
@> DCD file was parsed in 0.08 seconds.
@> 107.55 MB parsed at input rate 1327.86 MB/s.
@> 8334 coordinate sets parsed at input rate 102893 frame/s.
@> DCD file contains 8334 coordinate sets for 1121 atoms.
@> DCD file was parsed in 0.10 seconds.
@> 107.55 MB parsed at input rate 1126.91 MB/s.
@> 8334 coordinate sets parsed at input rate 87323 frame/s.
@> DCD file contains 8334 coordinate sets for 1121 atoms.
@> DCD file was parsed in 0.08 seconds.
@> 107.55 MB parsed at input rate 1340.52 MB/s.
@> 8334 coordinate sets parsed at input rate 103875 frame/s.
@> DCD file contains 8334 coordinate sets for 1121 atoms.
@> DCD file was parsed in 0.08 seconds.
@> 107.55 MB parsed at input rate 1331.16 MB/s.
@> 8334 coordinate sets parsed at input rate 103149 frame/s.
@> DCD file contains 8334 coordinate sets for 1121 atoms.
@> DCD file was parsed in 0.08 seconds.
@> 107.55 MB parsed at input rate 1298.62 MB/s.
@> 8334 coordinate sets parsed at input rate 100627 frame/s.
@> WARNING no one-letter mapping found for <Residue: NLM 1148 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1150 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1152 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1154 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1156 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1158 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1160 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1162 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1164 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1166 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1168 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1170 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1172 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1174 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1176 from Chain A from chain_A_aligned (1 atoms)>
@> WARNING no one-letter mapping found for <Residue: NLM 1178 from Chain A from chain_A_aligned (1 atoms)
Hello again,
I think the ref argument in superpose is selecting the atom and not the frame/conformation to superpose the ensemble. So a code like this:
The superpose uses the first atom and not the first frame. prody_version 2.4