Problem with ClashCountCalculator

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    • #2114
      Anonymous

        Hello everybody,

        i have done structure calculation of a protein with four zinc atoms. I have a native structure and i want to refine this structure. In every calculation I found the following error:

        protocols.metrics.ClashCountCalculator: BB BUMP: 2 41 O CA 2.63836 2.02792
        protocols.metrics.ClashCountCalculator: BUMP: 3 40 C CB 3.52878 3.21062
        protocols.metrics.ClashCountCalculator: BUMP: 3 40 O CB 2.10652 2.42369
        protocols.metrics.ClashCountCalculator: BUMP: 4 27 CEN CEN 4.80461 1.63026
        protocols.metrics.ClashCountCalculator: BUMP: 4 40 N CB 2.02192 4.35951
        protocols.metrics.ClashCountCalculator: BUMP: 6 17 C CB 4.29415 2.53333
        protocols.metrics.ClashCountCalculator: BUMP: 6 17 C CEN 5.51913 1.37911
        protocols.metrics.ClashCountCalculator: BUMP: 6 17 O CB 4.79319 0.305857
        protocols.metrics.ClashCountCalculator: BUMP: 6 17 O CEN 4.46378 0.0161593
        protocols.metrics.ClashCountCalculator: BUMP: 27 39 CA CB 2.77987 3.96237
        protocols.metrics.ClashCountCalculator: BUMP: 27 39 C CB 2.34127 4.4286
        protocols.metrics.ClashCountCalculator: BUMP: 27 39 CB CB 2.8558 3.78283
        protocols.metrics.ClashCountCalculator: BB BUMP: 31 54 C O 2.05849 2.47902
        protocols.metrics.ClashCountCalculator: BB BUMP: 32 54 N C 2.35804 2.80373
        protocols.metrics.ClashCountCalculator: BB BUMP: 32 54 C CA 2.35734 1.71169
        protocols.metrics.ClashCountCalculator: BUMP: 37 52 CB CB 4.97762 1.90308
        protocols.metrics.ClashCountCalculator: BUMP: 66 88 CB CB 2.68598 3.96005
        protocols.metrics.ClashCountCalculator: BUMP: 66 88 CB CEN 3.73272 2.47377
        protocols.metrics.ClashCountCalculator: BUMP: 66 88 CEN CEN 3.9286 3.16115
        protocols.metrics.ClashCountCalculator: BB BUMP: 69 86 C C 2.61565 2.13715
        protocols.metrics.ClashCountCalculator: BB BUMP: 69 86 C O 3.73767 1.04701
        protocols.metrics.ClashCountCalculator: BB BUMP: 69 86 O C 2.14885 2.38954
        protocols.metrics.ClashCountCalculator: BB BUMP: 69 86 O O 2.88076 0.69316
        protocols.metrics.ClashCountCalculator: BUMP: 69 86 CB C 4.18167 2.62884
        protocols.metrics.ClashCountCalculator: BUMP: 69 86 CEN C 2.69094 2.62617
        protocols.metrics.ClashCountCalculator: BB BUMP: 69 87 N C 3.11897 2.09768
        protocols.metrics.ClashCountCalculator: BUMP: 69 87 CB N 6.76035 0.369732
        protocols.metrics.ClashCountCalculator: BUMP: 69 87 CB CA 5.01025 1.96394
        protocols.metrics.ClashCountCalculator: BUMP: 69 87 CB C 2.44207 4.31465
        protocols.metrics.ClashCountCalculator: BUMP: 69 87 CEN N 4.73765 0.369762
        protocols.metrics.ClashCountCalculator: BUMP: 69 87 CEN CA 5.17823 1.9648
        protocols.metrics.ClashCountCalculator: BB BUMP: 71 85 N C 2.3085 2.8534
        protocols.metrics.ClashCountCalculator: BUMP: 71 85 CA CB 6.46644 0.898144
        protocols.metrics.ClashCountCalculator: BUMP: 71 85 C CB 4.87706 2.05726
        protocols.metrics.ClashCountCalculator: BB BUMP: 71 85 O N 2.54714 0.763648
        protocols.metrics.ClashCountCalculator: BB BUMP: 71 85 O CA 2.92802 1.77578
        protocols.metrics.ClashCountCalculator: BUMP: 71 85 CB CB 5.96378 1.17005
        protocols.metrics.ClashCountCalculator: BUMP: 71 85 CEN CEN 2.71327 1.44473

        I have do align this with 1dsv (has 1 zinc atom). In this protocol I also find this error, but in the end of the protocol the error disappear. In my protocol it doesn`t disappear. What can I do against it?! maybe be that an error for false zinc-constraints?!

        Thanks for help.

      • #10750
        Anonymous

          Please post your command line +/or xml you are using to run the protocol.

        • #10757
          Anonymous

            The lines you’re posting aren’t errors per se – they’re simply informative messages from the ClashCountCalculator that it’s finding clashes, and what the clashes that it finds are.

            Depending on the protocol you’re running, you may expect to find clashes early on, but as you relax/refine the structure, the clashes go away. Depending on how you constrain the structure, they may never go away, as the constraints enforce a geometry that is counted as a “clash”. (Note that the last number printed on the line is the distance squared, and the second to last value is the clash “score”, which is related to how much the atoms are overlapping as compared to their minimal distance. So in “BUMP: 71 85 CB CB 5.96378 1.17005”, the two Cbeta atoms are about 1.08 Ang apart.)

            I’d pay more attention to the geometry of the output structures, rather than the intermediate info lines. (Though you can use the tracer output as a guide to see which regions you need to examine more closely.)

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