Error when running cluster

[Anonymous]

I’m getting the following error:
ERROR: No values of the appropriate type specified for multi-valued option -cluster:exclude_res

for the following flag:
-cluster:exclude_res 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240

If I take out the exclude_res flag, cluster runs fine. I need to exclude residues though, so I need to figure out where that error is coming from.
I used this format from the cluster documentation:
-cluster:exclude_res int [int int ..] #Exclude residue numbers

Here are my other flags
“-l %s” % sys.argv[1],
“-in:file:fullatom”,
“-cluster”,
“-cluster:radius 2”,
“-sort_groups_by_energy”,

[Anonymous]

The issue is that Rosetta somehow thinks that the values you’re feeding to the -cluster:exclude_res flag aren’t integers.

My best guess is that there is some non-printing character in that big list of numbers which is causing Rosetta to choke. If you have the list in a flags file, it might be at the very end of the list. (Line-endings cause issues when working between multiple operating systems, or even when working in the same operating system for Macs)

Recreate your flags by *retyping* the options (don’t copy and paste, as you may copy and paste the non-printing character). You may want to try it with a few excluded residues first, and then gradually build up to the full list, to see if a particular one is giving you problems. If it fails, it should fail rather quickly, so if you get past the point where it would normally fail, you can just cancel the run and quickly extend the options list.

By the way, I’ve never taken advantage of it myself, but reading the code, it looks like you can use range notation in integer vector options lists. So you could possibly use “-cluster:exclude_res 1-240” instead of writing out the whole list. (This is untested, though, so if it’s giving you issues, try debugging with the explicit list.)

[Anonymous]

Aren’t non-printing characters visible in emacs?

It runs fine if i use this:
“-cluster:exclude_res 241”,

But if I try to exclude more than one res (typed by hand):
“-cluster:exclude_res 241 242”,
or
“-cluster:exclude_res 241 242 243 244 245 246”,
give this exit:
“ERROR: No values of the appropriate type specified for multi-valued option -cluster:exclude_res”

I also tried this:
“-cluster:exclude_res 241-252”,
and it runs, but it gives the exact same clusters as not excluding any residues… since the structures are all very different by 30 or more Angstrom distance at residue 253 (the only one included according to this flag) I would think it would produce different clusters if it was only considering residue 253, so it doesn’t seem like this flag is working.

I’m not sure I understand the similarity metric. Are C alpha distances being compared between two pdbs? Say I use an radius of 2 Angstroms, should I expect every structure in one cluster to have backbones within 2A of the structure at the cluster center? I’m clustering peptides (12aa long) with radius=2A and I’m getting clusters of structures where the termini are 15A from the center. I thought using a 2A radius would give me structures that were no more than 2A different across the entire backbone, but maybe I just don’t understand how the algorithm works.

Maybe there is something wrong with my PDB format?
ATOM 3754 N THR B 241 0.559 33.275 48.092 1.00 0.00
ATOM 3755 CA THR B 241 1.620 33.051 47.071 1.00 0.00
ATOM 3756 C THR B 241 2.527 34.276 46.942 1.00 0.00
ATOM 3757 O THR B 241 2.124 35.305 46.400 1.00 0.00
ATOM 3758 CB THR B 241 1.028 32.727 45.687 1.00 0.00
ATOM 3759 OG1 THR B 241 0.223 31.544 45.773 1.00 0.00
ATOM 3760 CG2 THR B 241 2.137 32.509 44.670 1.00 0.00
ATOM 3761 1H THR B 241 -0.405 33.232 47.828 1.00 0.00
ATOM 3762 2H THR B 241 0.497 32.676 48.890 1.00 0.00
ATOM 3763 3H THR B 241 0.515 34.144 48.585 1.00 0.00
ATOM 3764 HA THR B 241 2.255 32.222 47.381 1.00 0.00
ATOM 3765 HB THR B 241 0.401 33.559 45.366 1.00 0.00
ATOM 3766 HG1 THR B 241 -0.145 31.344 44.909 1.00 0.00
ATOM 3767 1HG2 THR B 241 1.699 32.282 43.698 1.00 0.00
ATOM 3768 2HG2 THR B 241 2.743 33.411 44.594 1.00 0.00
ATOM 3769 3HG2 THR B 241 2.763 31.677 44.989 1.00 0.00
ATOM 3770 N ASP B 242 3.752 34.155 47.442 1.00 0.00
ATOM 3771 CA ASP B 242 4.742 35.216 47.311 1.00 0.00
ATOM 3772 C ASP B 242 5.866 34.807 46.367 1.00 0.00
ATOM 3773 O ASP B 242 6.853 34.202 46.787 1.00 0.00
ATOM 3774 CB ASP B 242 5.314 35.587 48.681 1.00 0.00
ATOM 3775 CG ASP B 242 6.312 36.737 48.655 1.00 0.00
ATOM 3776 OD1 ASP B 242 6.635 37.194 47.584 1.00 0.00
ATOM 3777 OD2 ASP B 242 6.622 37.252 49.703 1.00 0.00
ATOM 3778 H ASP B 242 4.003 33.304 47.927 1.00 0.00
ATOM 3779 HA ASP B 242 4.278 36.101 46.876 1.00 0.00
ATOM 3780 1HB ASP B 242 4.550 35.787 49.432 1.00 0.00
ATOM 3781 2HB ASP B 242 5.834 34.661 48.929 1.00 0.00
ATOM 3782 N SER B 243 5.725 35.160 45.076 1.00 0.00
ATOM 3783 CA SER B 243 6.769 34.961 44.077 1.00 0.00
ATOM 3784 C SER B 243 8.011 35.779 44.408 1.00 0.00
ATOM 3785 O SER B 243 7.912 36.919 44.862 1.00 0.00
ATOM 3786 CB SER B 243 6.249 35.324 42.699 1.00 0.00
ATOM 3787 OG SER B 243 7.254 35.262 41.725 1.00 0.00
ATOM 3788 H SER B 243 4.857 35.596 44.800 1.00 0.00
ATOM 3789 HA SER B 243 7.039 33.914 43.937 1.00 0.00
ATOM 3790 1HB SER B 243 5.454 34.628 42.433 1.00 0.00
ATOM 3791 2HB SER B 243 5.849 36.336 42.732 1.00 0.00
ATOM 3792 HG SER B 243 7.578 34.361 41.656 1.00 0.00
ATOM 3793 N ARG B 244 9.179 35.190 44.178 1.00 0.00
ATOM 3794 CA ARG B 244 10.462 35.874 44.451 1.00 0.00
ATOM 3795 C ARG B 244 10.795 37.188 43.687 1.00 0.00
ATOM 3796 O ARG B 244 11.646 37.979 44.079 1.00 0.00
ATOM 3797 CB ARG B 244 11.608 34.887 44.287 1.00 0.00
ATOM 3798 CG ARG B 244 11.557 33.687 45.220 1.00 0.00
ATOM 3799 CD ARG B 244 11.871 34.001 46.638 1.00 0.00
ATOM 3800 NE ARG B 244 11.961 32.838 47.507 1.00 0.00
ATOM 3801 CZ ARG B 244 11.636 32.833 48.814 1.00 0.00
ATOM 3802 NH1 ARG B 244 11.236 33.930 49.417 1.00 0.00
ATOM 3803 NH2 ARG B 244 11.753 31.698 49.482 1.00 0.00
ATOM 3804 H ARG B 244 9.192 34.251 43.807 1.00 0.00
ATOM 3805 HA ARG B 244 10.486 36.213 45.487 1.00 0.00
ATOM 3806 1HB ARG B 244 11.585 34.540 43.255 1.00 0.00
ATOM 3807 2HB ARG B 244 12.531 35.439 44.464 1.00 0.00
ATOM 3808 1HG ARG B 244 10.554 33.262 45.185 1.00 0.00
ATOM 3809 2HG ARG B 244 12.279 32.947 44.872 1.00 0.00
ATOM 3810 1HD ARG B 244 12.830 34.517 46.683 1.00 0.00
ATOM 3811 2HD ARG B 244 11.091 34.648 47.038 1.00 0.00
ATOM 3812 HE ARG B 244 12.263 31.897 47.294 1.00 0.00
ATOM 3813 1HH1 ARG B 244 11.168 34.794 48.897 1.00 0.00
ATOM 3814 2HH1 ARG B 244 10.997 33.905 50.398 1.00 0.00
ATOM 3815 1HH2 ARG B 244 12.080 30.868 49.007 1.00 0.00
ATOM 3816 2HH2 ARG B 244 11.517 31.667 50.462 1.00 0.00
ATOM 3817 N SER B 245 10.042 37.557 42.677 1.00 0.00
ATOM 3818 CA SER B 245 10.478 38.919 42.290 1.00 0.00
ATOM 3819 C SER B 245 9.605 39.992 41.607 1.00 0.00
ATOM 3820 O SER B 245 8.807 39.686 40.721 1.00 0.00
ATOM 3821 CB SER B 245 11.695 38.726 41.406 1.00 0.00
ATOM 3822 OG SER B 245 12.199 39.944 40.932 1.00 0.00
ATOM 3823 H SER B 245 9.290 37.117 42.167 1.00 0.00
ATOM 3824 HA SER B 245 10.858 39.506 43.128 1.00 0.00
ATOM 3825 1HB SER B 245 12.469 38.223 41.985 1.00 0.00
ATOM 3826 2HB SER B 245 11.415 38.104 40.557 1.00 0.00
ATOM 3827 HG SER B 245 13.111 39.826 40.654 1.00 0.00
ATOM 3828 N THR B 246 9.772 41.240 42.031 1.00 0.00
ATOM 3829 CA THR B 246 9.066 42.358 41.417 1.00 0.00
ATOM 3830 C THR B 246 10.040 43.412 40.907 1.00 0.00
ATOM 3831 O THR B 246 11.249 43.307 41.118 1.00 0.00
ATOM 3832 CB THR B 246 8.083 43.017 42.403 1.00 0.00
ATOM 3833 OG1 THR B 246 8.812 43.599 43.490 1.00 0.00
ATOM 3834 CG2 THR B 246 7.104 41.988 42.947 1.00 0.00
ATOM 3835 H THR B 246 10.403 41.419 42.799 1.00 0.00
ATOM 3836 HA THR B 246 8.507 42.010 40.548 1.00 0.00
ATOM 3837 HB THR B 246 7.533 43.802 41.884 1.00 0.00
ATOM 3838 HG1 THR B 246 9.480 42.979 43.796 1.00 0.00
ATOM 3839 1HG2 THR B 246 6.417 42.472 43.642 1.00 0.00
ATOM 3840 2HG2 THR B 246 6.540 41.551 42.123 1.00 0.00
ATOM 3841 3HG2 THR B 246 7.653 41.204 43.467 1.00 0.00
ATOM 3842 N GLY B 247 9.508 44.428 40.236 1.00 0.00
ATOM 3843 CA GLY B 247 10.328 45.517 39.718 1.00 0.00
ATOM 3844 C GLY B 247 10.964 46.314 40.849 1.00 0.00
ATOM 3845 O GLY B 247 10.329 46.575 41.871 1.00 0.00
ATOM 3846 H GLY B 247 8.510 44.446 40.083 1.00 0.00
ATOM 3847 1HA GLY B 247 11.115 45.102 39.090 1.00 0.00
ATOM 3848 2HA GLY B 247 9.702 46.182 39.123 1.00 0.00
ATOM 3849 N ASP B 248 12.221 46.700 40.660 1.00 0.00
ATOM 3850 CA ASP B 248 12.941 47.482 41.658 1.00 0.00
ATOM 3851 C ASP B 248 13.742 48.602 41.007 1.00 0.00
ATOM 3852 O ASP B 248 14.780 48.360 40.390 1.00 0.00
ATOM 3853 CB ASP B 248 13.868 46.582 42.479 1.00 0.00
ATOM 3854 CG ASP B 248 14.612 47.298 43.597 1.00 0.00
ATOM 3855 OD1 ASP B 248 14.509 48.500 43.679 1.00 0.00
ATOM 3856 OD2 ASP B 248 15.147 46.631 44.450 1.00 0.00
ATOM 3857 H ASP B 248 12.691 46.444 39.804 1.00 0.00
ATOM 3858 HA ASP B 248 12.232 47.961 42.335 1.00 0.00
ATOM 3859 1HB ASP B 248 13.371 45.699 42.882 1.00 0.00
ATOM 3860 2HB ASP B 248 14.576 46.281 41.706 1.00 0.00
ATOM 3861 N PHE B 249 13.253 49.830 41.146 1.00 0.00
ATOM 3862 CA PHE B 249 13.863 50.977 40.483 1.00 0.00
ATOM 3863 C PHE B 249 14.528 51.906 41.491 1.00 0.00
ATOM 3864 O PHE B 249 13.931 52.266 42.505 1.00 0.00
ATOM 3865 CB PHE B 249 12.818 51.744 39.670 1.00 0.00
ATOM 3866 CG PHE B 249 12.233 50.953 38.535 1.00 0.00
ATOM 3867 CD1 PHE B 249 11.223 50.030 38.762 1.00 0.00
ATOM 3868 CD2 PHE B 249 12.691 51.129 37.239 1.00 0.00
ATOM 3869 CE1 PHE B 249 10.684 49.301 37.718 1.00 0.00
ATOM 3870 CE2 PHE B 249 12.154 50.404 36.193 1.00 0.00
ATOM 3871 CZ PHE B 249 11.149 49.488 36.434 1.00 0.00
ATOM 3872 H PHE B 249 12.439 49.973 41.726 1.00 0.00
ATOM 3873 HA PHE B 249 14.649 50.638 39.807 1.00 0.00
ATOM 3874 1HB PHE B 249 11.985 52.034 40.310 1.00 0.00
ATOM 3875 2HB PHE B 249 13.265 52.634 39.231 1.00 0.00
ATOM 3876 HD1 PHE B 249 10.854 49.882 39.778 1.00 0.00
ATOM 3877 HD2 PHE B 249 13.485 51.852 37.048 1.00 0.00
ATOM 3878 HE1 PHE B 249 9.891 48.579 37.911 1.00 0.00
ATOM 3879 HE2 PHE B 249 12.523 50.553 35.179 1.00 0.00
ATOM 3880 HZ PHE B 249 10.726 48.914 35.611 1.00 0.00
ATOM 3881 N GLY B 250 15.767 52.291 41.204 1.00 0.00
ATOM 3882 CA GLY B 250 16.535 53.137 42.110 1.00 0.00
ATOM 3883 C GLY B 250 16.008 54.567 42.108 1.00 0.00
ATOM 3884 O GLY B 250 15.826 55.172 43.164 1.00 0.00
ATOM 3885 H GLY B 250 16.188 51.990 40.337 1.00 0.00
ATOM 3886 1HA GLY B 250 16.464 52.734 43.121 1.00 0.00
ATOM 3887 2HA GLY B 250 17.577 53.143 41.795 1.00 0.00
ATOM 3888 N ASN B 251 15.766 55.100 40.915 1.00 0.00
ATOM 3889 CA ASN B 251 15.266 56.462 40.773 1.00 0.00
ATOM 3890 C ASN B 251 13.877 56.477 40.149 1.00 0.00
ATOM 3891 O ASN B 251 13.325 57.541 39.863 1.00 0.00
ATOM 3892 CB ASN B 251 16.217 57.319 39.958 1.00 0.00
ATOM 3893 CG ASN B 251 17.556 57.525 40.609 1.00 0.00
ATOM 3894 OD1 ASN B 251 17.668 58.185 41.649 1.00 0.00
ATOM 3895 ND2 ASN B 251 18.581 57.035 39.960 1.00 0.00
ATOM 3896 H ASN B 251 15.932 54.549 40.086 1.00 0.00
ATOM 3897 HA ASN B 251 15.167 56.925 41.757 1.00 0.00
ATOM 3898 1HB ASN B 251 16.362 57.133 38.893 1.00 0.00
ATOM 3899 2HB ASN B 251 15.619 58.221 40.091 1.00 0.00
ATOM 3900 1HD2 ASN B 251 19.503 57.135 40.335 1.00 0.00
ATOM 3901 2HD2 ASN B 251 18.442 56.561 39.091 1.00 0.00
ATOM 3902 N GLY B 252 13.315 55.291 39.938 1.00 0.00
ATOM 3903 CA GLY B 252 11.983 55.166 39.359 1.00 0.00
ATOM 3904 C GLY B 252 10.927 54.981 40.441 1.00 0.00
ATOM 3905 O GLY B 252 9.738 54.860 40.147 1.00 0.00
ATOM 3906 H GLY B 252 13.824 54.455 40.187 1.00 0.00
ATOM 3907 1HA GLY B 252 11.756 56.068 38.791 1.00 0.00
ATOM 3908 2HA GLY B 252 11.964 54.305 38.692 1.00 0.00
ATOM 3909 N PHE B 253 11.368 54.958 41.694 1.00 0.00
ATOM 3910 CA PHE B 253 10.457 54.832 42.825 1.00 0.00
ATOM 3911 C PHE B 253 10.381 56.129 43.619 1.00 0.00
ATOM 3912 O PHE B 253 11.346 56.891 43.675 1.00 0.00
ATOM 3913 OXT PHE B 253 9.371 56.418 44.200 1.00 0.00
ATOM 3914 CB PHE B 253 10.892 53.682 43.736 1.00 0.00
ATOM 3915 CG PHE B 253 10.460 52.328 43.251 1.00 0.00
ATOM 3916 CD1 PHE B 253 9.574 52.205 42.190 1.00 0.00
ATOM 3917 CD2 PHE B 253 10.936 51.174 43.854 1.00 0.00
ATOM 3918 CE1 PHE B 253 9.176 50.959 41.743 1.00 0.00
ATOM 3919 CE2 PHE B 253 10.541 49.928 43.409 1.00 0.00
ATOM 3920 CZ PHE B 253 9.659 49.821 42.352 1.00 0.00
ATOM 3921 H PHE B 253 12.360 55.031 41.868 1.00 0.00
ATOM 3922 HA PHE B 253 9.447 54.628 42.466 1.00 0.00
ATOM 3923 1HB PHE B 253 11.978 53.654 43.811 1.00 0.00
ATOM 3924 2HB PHE B 253 10.463 53.808 44.729 1.00 0.00
ATOM 3925 HD1 PHE B 253 9.193 53.106 41.708 1.00 0.00
ATOM 3926 HD2 PHE B 253 11.633 51.258 44.689 1.00 0.00
ATOM 3927 HE1 PHE B 253 8.479 50.878 40.909 1.00 0.00
ATOM 3928 HE2 PHE B 253 10.923 49.028 43.891 1.00 0.00
ATOM 3929 HZ PHE B 253 9.344 48.839 42.001 1.00 0.00
#END_POSE_ENERGIES_TABLE 1AUT_PAR1_renum_ppk_0053_0002_0006_0001.pdb
TER

I don’t see in the documentation…. What is the meaning of the last column in the output?
protocols.cluster: Cluster: 0 N: 77GN: 78 c.0.*.pdb
protocols.cluster: 1AUT_PAR1_renum_ppk_0006_0001_0001_0001_peptide.pdb -1.28232
protocols.cluster: 1AUT_PAR1_renum_ppk_0006_0001_0003_0001_peptide.pdb 2.47879

[Anonymous]

I just noticed the %sys.argv[1] — Are you running this through Python? If that’s the case, you have to be careful how you’re passing the parameters around. Rosetta is expecting all the elements of the option to be passed through separately, not as a single space-separated unit. So the parameter list would be something like [“path/to/cluster.linuxgccrelease”,”-s”,”test.pdb”,”-cluster:exclude_res”,”1″,”2″,”3″] and NOT [“path/to/cluster.linuxgccrelease”,”-s”,”test.pdb”,”-cluster:exclude_res”,”1 2 3″] If the list of residues are being passed as a single option (e.g. like you surrounded the list in quotes in the bash shell), then you’ll see the error you’re seeing.

Regarding the similarity metric, unless you use the options to change it to GDT (-cluster::gdtmm) the default is to use Calpha rmsd. The cluster radius is the largest radius of the cluster permitted. If you’re doing rmsd clustering it’s in Angstroms (for GDT clustering it’s “inverse GDT_TS”). So for a radius of 2, all structures will be within 2 Ang rmsd of each other. However, that’s only for those residues which are being calculated under the rmsd. Keep in mind that there’s a superposition step. So if you simply translate a peptide, the rmsd will still be zero – only internal degrees of freedom will change it.

The last column in the output is the “silent_score” – which as I understand it should be the Rosetta energy for that particular structure.

[Author]

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