Re: [ccp4bb] D-Amino acids to L-Amino acids

Yusuf Akhter wrote: Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change th

Re: [ccp4bb] D-Amino acids to L-Amino acids

onrud Sent: Saturday, August 02, 2008 2:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] D-Amino acids to L-Amino acids First you should look into why your chiral centers flipped. In my experience the most common cause is that the neighboring peptide bond needs to be flipped. If you

Re: [ccp4bb] D-Amino acids to L-Amino acids

First you should look into why your chiral centers flipped. In my experience the most common cause is that the neighboring peptide bond needs to be flipped. If you just want to flip a chiral center in Coot, I think the easiest way is to "real space refine" the residue and before accepting

Re: [ccp4bb] D-Amino acids to L-Amino acids

Did you set the weight (X-ray.vs.Geom.) too high? In principle, at 3A a relatively smaller weight than default (0.3?) may be used. On Aug 2, 2008, at 8:39 AM, Yusuf Akhter wrote: Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After s

Re: [ccp4bb] D-Amino acids to L-Amino acids

: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yusuf Akhter Sent: Saturday, August 02, 2008 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] D-Amino acids to L-Amino acids Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After

[ccp4bb] D-Amino acids to L-Amino acids

Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L

[ccp4bb] D-Amino acids to L-Amino acids

Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L