Re: [ccp4bb] D-Amino acids to L-Amino acids
I would assume that the wrong chiralities were introduced during building. It is not very hard to change chiral centers around if you're dragging atoms around in and out of density... Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Dale Tronrud 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 just want to flip a chiral center in Coot, I think the easiest way is to "real space refine" the residue and before accepting the result, drag the CA to the side you want. You may have over-drag to get it to stay. It only takes a moment. But don't assume that your refinement program is just doing something stupid. Look for the primal cause. Dale Tronrud 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 these D-amino acids to L-amino acids?? > > Is there any option in Coot for that?? > > > Thanks in advance, > yusuf >
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 the result, drag the CA to the side you want. You may have over-drag to get it to stay. It only takes a moment. But don't assume that your refinement program is just doing something stupid. Look for the primal cause. Dale Tronrud 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 these D-amino acids to L-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf
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 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-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/ Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
Re: [ccp4bb] D-Amino acids to L-Amino acids
The easiest (albeit by far not the simplest!) option is to mutate the offending amino acid to Gly, then back to what it should be. Alternatively you could use a script to accomplish the same, but if you only messed up 1 or 2 residues, the above is easier. Artem -Original Message- From: 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 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-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/
[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-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/
[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-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/
