how to identify selected interface residues

[Anonymous]

Hello everyone,

I am using rosetta scripts (Version 3.5) to redesign a protein-protein interface. I use the following taskoperation to restrict the redesign with 8 ang CB distance cutoff from the interface,

RestrictToInterfaceVector name=vector jump=1 CB_dist_cutoff=10.0 nearby_atom_cutoff=8 vector_angle_cutoff=75.0 vector_dist_cutoff=9.0

I would like to see the residues selected by the program that are within 8 ang cutoff distance. Is this information written somewhere in the outfile?

I could see the list of residues considered by the rotamer building function in the trace outfile, as follows,

core.pack.task: (11) Packer task: initialize from command line()
core.pack.rotamer_set.rotamer_building_functions: (11) water 213 nbrs: 208 207 206 205 204 203 189 188 187 186 185 184 183 182 172 171 170 169 168 167 166 153 152 151 150 149 145 144 142 111 110 106 100 99 98 97 96 95 94 93 92 91 90 89 88 70 69 68 67 66 65 56 55 54 53 42
build_water_rotamers seqpos= 213 found 0 nearby donors, 1 nearby acceptors. Built 0 rotamers.

so is these residue numbers considered for the redesign at the interface? If not please let me know where can I find this information.

Thanks in advance for your kind help.

Regards,
Vijay.

[Anonymous]

You can use the DesignableResidues filter (https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/Filters_%28RosettaScripts%29#DesignableResidues) to report which residues are repackable/redesignable according to your set of task operations.

As a filter it works to count the number of positions which are designable/packable, but it will also print out those residues (in PDB numbering) to the tracer (standard output log file). Just place it as a filter in your PROTOCOLS section just before you’re going to use your RestrictToInterfaceVector operation. (When you do this, though, *don’t* set confidence=0 on the filter. If you do, Rosetta will recognize that running the filter would be pointless, so it won’t run it and thus won’t print the results. The default thresholds on the filter should pass everything, so it won’t actually filter the run.)

[Anonymous]

Yes, it does looks like if you use the PackRotamers mover and some related movers it should place the design and repacking residues in the extra “score” lines in the PDB output. This should be equivalent to what you’d get from the DesignableResidues filter.

[Anonymous]

Thank you very much for your reply.
Before trying your suggestion, I found another information that could be useful. At the end of each output redesigned structure there is some REMARK section which is followed by various scores, as follows,

###at the end of pdb file##
.
.
.
REMARK PackingRes, 2 A, 4 A, 7 A, 31 A, 55 A, 65 A, 172 B, 176 B, 178 B, 179 B, 181 B, 184 B, 207 B, 208 B, 209 B, 210 B, 211 B, 214 D
REMARK DesignRes, 3 A, 28 A, 30 A, 35 A, 36 A, 37 A, 61 A, 64 A, 66 A
bindingenergydensity -0.0215605
complex_normalized -1.89498
dG_cross -63.1939
dG_cross/dSASAx100 -1.55066
dG_separated -95.4104
dG_separated/dSASAx100 -2.34119
dSASA_hphobic 2804.21
dSASA_int 4075.3
dSASA_polar 1271.09
ddg_filter -89.3358
delta_unsatHbonds 8
hbond_E_fraction 0.40121
nres_all 214
nres_int 131
packstat 0.609973
per_residue_energy_int -1.34109
rms 0.732123
sasa_filter 4075.3
sc_value 0
score_filter -405.526
side1_normalized -0.716742
side1_score -55.9059
side2_normalized -1.08265
side2_score -145.075
unsats_filter 8

####

here the list of pdb residue numbers (REMARK DesignRes, 3 A, 28 A, 30 A, 35 A, 36 A, 37 A, 61 A, 64 A, 66 A) matches with the redesign sphere that I have mentioned in the script using DesignAround command. If this information is same as the output that will be produced by DesignableResidues command, then I dont need to redo it. Can you please clarify this out.

Thank you.

[Author]

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