U Sam wrote:
Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into "difference Density", we can select a specific "rotamer" conformation and refine. For fitting ligand of above kind, how does it work out.
For amino acids there are tens of thousands of examples from which one can derive rotomer libraries. There is no such luck with most other compounds. This is why Coot has special case code for handling amino acids that does not understand your (or my) favorite molecules. Fortunately, Coot does not require such information to run its real space refinement. You do need a cif definition that includes, amongst other things, the ideal bond lengths and bond angles. You can work with Coot to build the conformation of your molecule that fits your density. All conformations will be consistent with the same bonds and angles, unless you have a very strange molecule.
Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature.
SHELXL will take whatever conformation you build and come up with a model that is consistent with the values on the DFIX and DANG statements. It should never produce a model that deviates from the literature values, if you put those values on your DFIX and DANG statements. The final model will have a configuration similar to what you built in Coot. Use Coot to make the big changes and SHELXL to fine tune. I have been refining some long chain hydrocarbons along with my protein and have had no problems, once I was able to create the proper definitions for Coot and SHELXL. SHELXL is certainly easier to create a library for, but you need both if you want to model build and refine. Building a cif with ideal geometry for Coot/Refmac is not an easy task. You need to understand your chemistry and the file format, which is not well documented. You have several options: 1) You can sit down and figure out how to create a cif definition. This is hard to do but a valuable skill to acquire. 2) You can find a compound similar to yours for which there is a definition built into Coot and modify it for your needs. You still need to understand the file format, but you can get away with less understanding because you are starting with something that works. 3) You can use web resources to find/create a file for you. A number of options are available, none of which I would trust completely. The HIC-UP website is perhaps the most popular, but the values are quite unreliable. These files can be used as a starting point but always verify... The Elbow builder in Phenix is quite reasonable, but takes a bit of study to understand, and again, don't trust it. Remember the quote from the Harry Potter books: "Never trust anything you can't see where it keeps its brains."
I appreciate suggestion and comments. Many Thanks Sam _________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607
