Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Ab initio/relax flag file setup
- This topic has 4 replies, 3 voices, and was last updated 15 years ago by
Anonymous.
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August 28, 2009 at 6:49 pm #355
Anonymous
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.
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August 28, 2009 at 9:30 pm #4161
Anonymous
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. -
August 28, 2009 at 9:35 pm #4162
Anonymous
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. -
August 31, 2009 at 2:17 pm #4164
Anonymous
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).
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August 31, 2009 at 3:26 pm #4165
Anonymous
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
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