Hello, Using Chimera, I positioned the ligand where it should be, used the "copy/combine" function in the Model Panel, and saved the combination in both PDB format and Mol2 format. However, when I open the PDB again (using Chimera, as well as other viewers), there are several errors (particularly, incorrect bonds between nearby atoms). The Mol2 file, however, does not seem to have such errors. Additonally, I am not sure if the combination PDB file has correct differentiation for ligand atoms and protein atoms. Would a file format converter (e.g. OpenBabel) help? Please advise. Thanks, Nancy On Fri, Oct 2, 2009 at 10:41 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nancy, Different programs have different rules for interpreting PDB format. If you open the file you wrote from Chimera back into Chimera, I expect it will show both structures. I cannot be sure about the other program, but probably it only shows the first set of coordinates because there is an ENDMDL line between the two sets.
If you want the two models written into one file as one model, you need to generate a combined model (after positioning the ligand as you wish relative to the protein) and then write that out. You can generate a combined model with the "combine" command or the "copy/combine" function in the Model Panel.
"structural errors" is not enough information for us to work with -- we would need to know much more, including what version of Chimera you are using -- please use "Help... Report a Bug" in the Chimera menu and attach the file you wrote, plus include an explanation of why you think there are structural errors, and your email address if you want a reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 2, 2009, at 7:24 PM, Nancy wrote:
Hello,
I am planning to run a docking simulation in a different program, and I need to have a "reference ligand" included in the PDB file. The particular PDB I am working on does not have a ligand included. So I am trying to position one using Chimera.
I started with the protein file and a ligand file (ligand is in .mol2 format). I loaded both into Chimera, and I correctly positioned the ligand relative to the PDB. I then saved both using File -> Save PDB... I choose to save the file relative to the protein, and I select "save multiple models: in a single file". However, when I load the file into the docking program, it does not show the ligand. Additionally, there are a few structural errors in the output PDB file. Please advise. Thanks, Nancy