Hi Robert, Unfortunately the MSMS molecular surface calculation code has bugs and so it fails to compute surfaces for most large (>10,000 atom) PDB models. The surface calculation has essentially no chance of working with a model of 110,000 atoms such as your half-virus. That said I used the 64-bit Mac Chimera and split the model by chains and it surfaced fine -- see attached image. The Windows Chimera versions have the most surface calculation failures especially 64-bit Windows Chimera, and Mac and Linux are substantially better. So I made the image bmv.jpg with "split #0; surf; rainbow model". After the split, it is odd that many of the subunits have no atoms shown. I used Actions / Atoms / Show to show them. If you don't require a solvent excluded surface (rolling a ball over the atoms to get the surface), you can use a Gaussian surface. The second image bmv5.jpg was made without splitting the model using a 5 Angstrom density map. molmap #0 5 model #1 volume #1 step 1 color lightblue :.A color lightyellow :.B color pink :.C color red :.D-K scolor #1 zone #0 range 10 Tom
Hi Tom, I am a post doc at Indiana University in the Biochemistry department, and I was at the chimera tutorial you gave to our department through David Morgan. I wasn't sure who to write with this question, so I thought I would start with you but if this is more appropriate for someone else, just let me know.
Forever ago I used Viper to create a 60 subunit (or 1/2) capsid for BMV, and made several models for publications. That .pdb file that I made no longer works within Chimera, and I have literally tried everything to get it to work. Additionally, it seems Viper no longer lets you make those .pdb files anymore. I have tried changing the atomic radii probe radius, the vertex density, set the disjoint surfaces to false, and every combination of those things. Additionally, when I use the split command, it either only shows a weird surface or no surface at all, and almost completely obliterates the original structure. If you know another way to do this, I would really appreciate any advice here as I have spent hours reading through forums. I attached the .pdb to this email. Again I really appreciate your help.
Thanks in advance, Robert
