Fragment files

[Anonymous]

Hello everybody,

I have been getting the fragment files using Robetta Server. Sometimes, it takes so long time to generate because of large number of queues. Therefore, could anybody have an idea that how we generate fragment file locally?

[Anonymous]

> Hello everybody,
>
> I have been getting the fragment files using Robetta Server. Sometimes, it takes so long time to generate because of large number of queues. Therefore, could anybody have an idea that how we generate fragment file locally?

You can do it with make_fragments.pl. We are having problems getting it to work properly with all the programs it calls. If you figure it out, please let me know!!

Thanks,
Christy

[Anonymous]

This older thread describes a way to run make_fragments.pl in a simpler way. The quality might suffer but it’s fine for most purposes.

http://www.rosettacommons.org/node/1565

[Anonymous]

Hello,
I have a question about the robetta fragment-file. what does the numbers mean?!

1ofd A 1068 S L -163.692 159.068 168.636 -0.177 4.773 84.262 3 0.000 P 1 F 1
1ofd A 1069 P L -59.041 138.502 179.354 -0.177 4.773 84.262 3 0.000 P 1 F 1
1ofd A 1070 L L -65.398 -35.892 176.967 -0.177 4.773 84.262 3 0.000 P 1 F 1
Are the first free values angles?!

I have the same understanding problems with the silent.out file.

1 L 0.000 115.760 -11.712 1.458 0.000 0.000 174.910 -16.319 0.000 0.000 S_00000001
2 L -66.362 -101.587 -182.586 2.717 0.969 2.285 30.184 -36.782 28.708 0.000 S_00000001
3 E -174.094 75.957 170.068 -0.100 1.839 4.685 177.349 164.795 179.226 -178.826 S_00000001
4 E -59.667 160.921 168.430 -0.296 5.284 6.266 -64.416 0.000 0.000 0.000 S_00000001
What mean the values?!

[Anonymous]

Generally it’s best to start a new thread for new questions. Only post your questions to other threads if it’s more-or-less the same question as the one in the previous thread.

[Author]

Posts