On Mon, 2006-01-30 at 16:04 -0600, Wu, Bainan wrote: > Hi, all > > > > I am a newer of xplor-nih, so I hope this is not a stupid question. I > am trying to incorporate a MTSL into the structure of my protein. > Adding ligands into a structure was tricky for me. But it is doable.
> Luckily, I found xplor-nih had the topology file of the MTSL and also > included a protocol in PSF_generation folder of xplor-nih-2.12 talking > about how to incorporate it into protein. I test the demo, run > addAtoms.py and it looks work pretty good. However, after I change the > script with the sequence and pdb file of my protein, it shows the > warning of ?atom not found in structure? for every atom in pdb file. > It seems that PDBTool in the > > Python file does not read my pdb file at all. Can anybody tell me why? > Is that because of the format of pdb file? If yes, could you give me > some hints about how to fix it? > One problem that I ran into had to do with segment identifiers. If the seg ID's in your input PDB don't match the chain ID's in the PSF file, then XPLOR-NIH won't find the atoms. Does your PDB file have segment ID's in it? (They're in something like rows 70-74) - past the x, y, z, occupancy, and B-factor columns. I notice that the example in eginput/PSF_generation uses no segment ID. If you do need a segment ID, there's an option to seqToPSF() called segName that should help. See http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/psfGen.html I hope this helps. -Greg Zornetzer [email protected] --
