You are here

Ab initio/relax flag file setup

5 posts / 0 new
Last post
Ab initio/relax flag file setup
#1

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.

Fri, 2009-08-28 11:49
w107kdk

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.

Fri, 2009-08-28 14:30
lshi

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.

Fri, 2009-08-28 14:35
lshi

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).

Mon, 2009-08-31 07:17
smlewis

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

Mon, 2009-08-31 08:26
w107kdk