Dear All,
I was trying to upload a refmac-generated deposit file to PDB Autdep but
it says the format is invalid. So I opened the file and have a look.
In it I saw a number of lines with <nul><nul>... which I suspect was the
cause of error. It looks like it is corrupted. Does anyone know why it
happened? It seems the numeric values in these lines are all there and
it is just the data labels that are corrupted/missing. Is there an easy
way I can find out the missing data field names (and the correct order)
that I can edit them into the deposit file without re-running refmac?
The affected lines (section) are the following:
+++++++++++++++++++++++++++++
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
r_bond_refined_d 670 0.029 0.022
r_bond_other_d 467 0.001 0.020
r_angle_refined_deg 905 2.288 2.000
r_angle_other_deg 1158 3.113 3.000
r_dihedral_angle_1_deg 80 6.351 5.000
r_dihedral_angle_2_deg 27 33.598 24.815
r_dihedral_angle_3_deg 141 14.992 15.000
r_dihedral_angle_4_deg 4 22.156 15.000
r_chiral_restr 111 0.276 0.200
r_gen_planes_refined 688 0.010 0.021
r_gen_planes_other 120 0.002 0.020
115 0.299 0.200
411 0.189 0.200
292 0.168 0.200
306 0.095 0.200
67 0.269 0.200
7 0.218 0.200
r_symmetry_vdw_other 11 0.147 0.200
13 0.273 0.200
r_mcbond_it 402 2.576 1.500
r_mcbond_other 158 1.171 1.500
r_mcangle_it 670 3.553 2.000
r_mcangle_other 532 1.745 2.000
r_scbond_it 268 5.423 3.000
r_scbond_other 309 1.932 3.000
r_scangle_it 235 7.410 4.500
r_scangle_other 626 3.770 4.500
r_sphericity_free 108 20.126 5.000
r_sphericity_bonded 1130 5.566 5.000
r_rigid_bond_restr 1137 2.479 3.000
+++++++++++++++++++++++++++++++++++++
I am running refmac ver. 5.5.0072. Thanks in advance.
Wai
