Re: [COOT] DNA structure refining problem
Norman Zhu wrote: This email is a continuation of an inquiry I post last week. The problem I had and still is i can't use the real space refine zone and regularization zone functions on a DNA structure. Whenever i ask the computer to fit the bases into the electron density it would give me a solution that would only satisfies the needs of the purine and pyrimidine bases but at the expense of the sugar and phosphate back bone. The devil's in the detail. Do you atom names in the pdb file match the atom names in the Refmac dictionary? Perhaps you use prime names and the dictionary uses * names. Upgrading to a recent pre-release should help with the diagnostics. Paul.
Re: [COOT] DNA structure refining problem
Hey Norm, What are your sugar atoms named in the pdb? Coot likes to explode them if they have primes (C5') instead of stars (C5*). Tim On Mon, Feb 8, 2010 at 3:23 PM, Norman Zhu zhunor...@gmail.com wrote: hello there This email is a continuation of an inquiry I post last week. The problem I had and still is i can't use the real space refine zone and regularization zone functions on a DNA structure. Whenever i ask the computer to fit the bases into the electron density it would give me a solution that would only satisfies the needs of the purine and pyrimidine bases but at the expense of the sugar and phosphate back bone. The solution would stretch all the atoms on the back bone beyond their bond length and place some other ones out side of the density map. To see if this would also happen to a base that doesn't need to be refined I used the real space refine function on a base that sits comfortably in batch of well defined electron density. The same thing happened. I attached two before and after images to show you what i am talking about. I tries this function again a well defined protein residue and it worked just fine. To fix this problem i tried all kinds of methods but nothing worked. I tried lower the matrix refinement from 60 to 10 to 2, as some people have suggested. I tried anchoring atoms at few key positions. I moved atoms one by one into the density refine it afterward, but nothing worked. It seems as though the program can't recognize the nucleotides as nucleotide. It maybe trying to refine it as a protein and using all the wrong constrains. i don't know, I am not programmer. Has anybody encounter this problem before? Norm P.S. i also included a image of the base i trying to fix. I wanted to show you how a straight forward a problem it should have been. Also that the density of my map is good and should not causing the problem. -- Timothy Silverstein Mount Sinai School of Medicine Structural and Chemical Biology 1425 Madison Avenue Box 1677 New York, NY 10029 212.659.8639
Re: [COOT] [ccp4bb] coot and probe clash
On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote: On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wgsc...@chemistry.ucsc.edu wrote: This is available to install as a binary from here: http://molprobity.biochem.duke.edu/get_molprobity.php Although probe and MolProbity3 are said to be free and open source software distributed under a BSD-style license, I can't find the source code, so I can't make coot depend on it within fink. http://kinemage.biochem.duke.edu/software/probe.php and Reduce (also required for Coot, I think) is here: http://kinemage.biochem.duke.edu/software/reduce.php -Nat OK, I have added both now to fink cvs (unstable branch). Feedback appreciated.
