Hi,
Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won't run.
Thank you for reading this.
same situation here. Have to guess what to do. Not really sounds like doing science(:razz:)
> Hi,
>
> Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
> I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won't run.
>
> Thank you for reading this.
The "-nooutput" in cluster did not work for me, so be careful when you try your LUCK for that part before you fill up your hard disk.
> Hi,
>
> Does anyone know if the the Rosetta 3.0 release structure prediction Flag file requires one of the three types of secondary structure files (i.e Jones . etc) as input in order to run properly? I do not have a native pdb file to provide as input. However, I was able to run the program without any issues with only the FASTA sequence file, and the fragment libraries as input, to generate an ensemble. I am concerned that the decoys generated without a secondary structure file present will not be useful.
> I have attempted to input one of the three secondary structure files into the flag folder but the program fails to recognize it (likely because I am probably not calling it with the correct cmd, etc?) and won't run.
>
> Thank you for reading this.
I can't say for sure but I think you should be safe. The fragment libraries are created from secondary structure prediction, and so the fragments themselves encode the local secondary structure preferences. I don't see an obvious option for including your own ss file either (except for defining where the loops are yourself).
Ok great...and the results I am getting in the output do seem to match the secondary structure provided by the three seperate secondary structure files.
Thank you for your reply