Hi Hari, You're welcome! There is no way to change the chain ID in Chimera. The only way I know is to just text-edit the PDB file. However, the two chains are already distinguishable by their model ID numbers #0.1 and #0.2, so there is no reason to give them different chain IDs. FindHBond ignores interactions between models with the same first number and different second numbers, so now you are only getting the H-bonds within each chain anyway. In the PDB, multi-model files like that are only used to describe multiple conformations of the same structure that are on top of each other (such as from NMR), where you wouldn't want them to "see" each other. So there are two issues, (1) how to find H-bonds between them and (2) how to separate the results for H-bonds between the structures and within each structure. (1) You cannot find H-bonds between #0.1 and #0.2 with the FindHBond graphical interface (GUI) and your current file. However, the "findhbond" command has an option "interSubmodels true" to include those interactions: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html Alternatively, you can edit your file into two separate files; then you could use either the GUI or the command. (2) You can do separate calculations of inter-model and intra-model H- bonds, so you do not have to postprocess the combined results. Both the GUI and the command have options to do those calculations separately: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html If you did not edit the file, you have to use the command to calculate the H-bonds between the structures, as mentioned above. For example, these keywords would give only the H-bonds between the structures: hb intersub true intermod false You could use either GUI or command to calculate H-bonds within each structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 10, 2008, at 10:27 AM, Harinathachari Bahudhanapati wrote:
Hi Elaine, Thanks for all the answers you give to our questions. They are very helpful as I learn more everyday. I have a question.
Is there anyway to rename a chain in a PDB file through the GUI? I have a few PATCHDOCK generated PDB files with two different chains named under Chain 'A' as #0.1 and #0.2. When I try to get the list of hydrogen bonds between these two chains, the chain name 'A' appears for all of the h-bonding pairs. So, I want to have them named Chain A and Chain B for easier analysis than scratching my head figuring out which h-bond pair is between the chains or with in the chain. I am attaching the pdb file. Please help me.
(I thought of renaming the chains in the PDB file going through the PDB header (text file) and manually changing the name. But I am not a expert if anything goes wrong.)
Sincerely Hari