The fragments file:aat000_03_05.200_v1_3
position: 1 neighbors: 200
1pg4 A 309 W L -108.068 162.569 -178.328 0.102 4.369 116.235 3 0.000 P 1 F 1
1pg4 is the name of protein.But what is the "A 309 W L -108.068 162.569 -178.328 0.102 4.369 116.235 3 0.000 P 1 F 1"?What's the meaning of those?
"{series}{pdb}{chain}{size}_{strategy}.{depth}_{version}" is mentioned in Rosetta user guide.But it is different.
When I used pose=pose_from_pdb("xx.pdb"),there is a warning(core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 3351 in file xx.pdb. Best match rsd_type: ASP).Why?
Post Situation:
Regarding the discarded atoms issue, it's hard to say without seeing the PDB file in question, but that message is usually because there's some naming issue with the residue. Look at that amino acid - does it conform to the standard atom naming conventions? One issue may be if the structure doesn't have a regular aspartate, but instead has some sort of posttranslational modification to the residue. If Rosetta isn't appropriately told about the modification (through patch files), it will simply ignore the extra atoms, and do the best it can with what is left.
Do you know the meaning of the rest string(3 0.000 P 1 F 1)?
Sorry, no. Looking at the code, it looks like those numbers aren't even printed anymore, for more recent versions of the fragment picker. (Though I could be misreading things.)
From what little I can tell, it looks like the P X F Y designation is for "position X fragment Y". The 3 and the 0.000 are still a mystery, though.