Problem with ClashCountCalculator

[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.

[Anonymous]

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

[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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