Unsolved

Hi,

I want to use fixbb on a pdb file that contains ions (the ions are classified as HETATM in the pdb file) in addition to the protein chain (whose atoms are classified as ATOM in the pdb file). My question is: If I use fixxb on the pdb file for repacking, will the algorithm consider the presence of the ions or will it ignore them?

Hi,
I used the rosetta3.4_membrane_homology_modeling to build a pdb file. but when I extract them from the silent file, my target pdb didn't looks like a normal protein, even like a jumble of segments.

Did I make a mistake?

the silent file was created by this command line: ~/rosetta3.4/rosetta_source/bin/minirosetta.linuxgccrelease @flags, and the flag file was attached.

to extract the pdb file from silent file by: ~/rosetta3.4/rosetta_source/bin/extract_pdbs.linuxgccrelease @convert.flags,and the convert.flag was also attached.

Dear everyone.

I used the rosetta membrane homology modeling, recently, when I tried to create the template pdb file by the script createTemplate.pl, the error of "attempt to assign missing density from parent[86] as a takeoff for query[167]" occurred. it righet that the parent pdb file do have 86 residues.

my zone file is :
zone 17-29 : 1-13
zone 41-46 : 14-19
zone 80-82 : 20-22
zone 88-92 : 23-27
zone 110-167 : 29-86

the aligment file is:
>quary
SVKKLADVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTALNGTNGSVE
ADGLVWESLDLYLSDPENYLLKNGTSDVLLCGNSSDAGTCPEGYRCLKAG

Hi,
I am trying to fix the clashes in a homology model structure I have created of a membrane protein. I tried fixbb to fix only the sidechains, yet I still get clashes ):. Therefore, I want to try to use the relax application in rosetta3.1 to remove clashes. My questions are:
1. Is it O.K to use relax for a membrane protein? If so, what flags should I use to indicate in relax that I want the calculations done on a membrane protein (for instance, would adding -score:patch no_solvation be enough?)