Thanks for everybody, especially for Greg. I go back to check my pdb file and then find possible mistakes. The initial structure uses two long linkers to connect three chains. When I prepare my pdb file, I delete these linkers without giving the different chain number. This may be the point.
Here, I have another question. If there is a jump on residue number due to the chain break, can addAtom.py read through sequence file to match the corresponding atoms in pdb file? Best Regards! bwu -----Original Message----- From: Greg Zornetzer [mailto:[email protected]] Sent: Monday, January 30, 2006 4:29 PM To: Wu, Bainan Subject: Re: [Xplor-nih] how to incorporate into MTSL into a protein? 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]
