Re: [ccp4bb] Refinement with refmac05 and methionine density
Hi Jeorge, The simplest answer is that you have multiple positions for the Methionine. So you can try adding in an alternate position for it. However, you didn’t mention the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible that your fofc map is just scaled way down and what you are seeing is an exaggeration of what’s barely there. Hope this helps. Cheers! - Greg --- Greg Costakes, Ph.D. Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge, CB2 1GA United Kingdom From: jeorgemarley thomas Sent: Wednesday, November 12, 2014 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with refmac05, and after each refinement the density around this methionine is flipping. and it is difficult to say where this methionine actually have the density. please suggest what I should I do. I am attaching the snap here. Thanks in Advance for your kind suggestions Jeorge --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [ccp4bb] Refinement with refmac05 and methionine density
That looks really odd - the whole MET has a negative/positive ghost Second conformations usually branch at the CB, and dont look like that. Are you sure you havent somehow got two MET residues in the coordinate set ? Turn on cysmmetry display in coot and look for clashes around there. Does the rest of the map look OK? I would set the occupancies of the MET and nearby side chains to 0.00 (you can do that in coot) then refine and look at the maps again. This is very old fashioned but you can do this: distang xyzin coords.pdb dist inter end to get a list of close symmetry clashes contacts Eleanor On 12 November 2014 09:17, Greg Costakes gcost...@purdue.edu wrote: Hi Jeorge, The simplest answer is that you have multiple positions for the Methionine. So you can try adding in an alternate position for it. However, you didn’t mention the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible that your fofc map is just scaled way down and what you are seeing is an exaggeration of what’s barely there. Hope this helps. Cheers! - Greg --- Greg Costakes, Ph.D. Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge, CB2 1GA United Kingdom *From:* jeorgemarley thomas kirtswab...@gmail.com *Sent:* Wednesday, November 12, 2014 8:16 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with refmac05, and after each refinement the density around this methionine is flipping. and it is difficult to say where this methionine actually have the density. please suggest what I should I do. I am attaching the snap here. Thanks in Advance for your kind suggestions Jeorge -- http://www.avast.com/ This email is free from viruses and malware because avast! Antivirus http://www.avast.com/ protection is active.
Re: [ccp4bb] Refinement with refmac05 and methionine density
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jeorge, the 'ghost' could be explained by a shift of an entire section, i.e. you have to split several residues into A+B, not only the MET. The cylR2 structure in 2XJ3 is one example where this was necessary. Best, Tim On 11/12/2014 11:23 AM, Eleanor Dodson wrote: That looks really odd - the whole MET has a negative/positive ghost Second conformations usually branch at the CB, and dont look like that. Are you sure you havent somehow got two MET residues in the coordinate set ? Turn on cysmmetry display in coot and look for clashes around there. Does the rest of the map look OK? I would set the occupancies of the MET and nearby side chains to 0.00 (you can do that in coot) then refine and look at the maps again. This is very old fashioned but you can do this: distang xyzin coords.pdb dist inter end to get a list of close symmetry clashes contacts Eleanor On 12 November 2014 09:17, Greg Costakes gcost...@purdue.edu wrote: Hi Jeorge, The simplest answer is that you have multiple positions for the Methionine. So you can try adding in an alternate position for it. However, you didn’t mention the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible that your fofc map is just scaled way down and what you are seeing is an exaggeration of what’s barely there. Hope this helps. Cheers! - Greg --- Greg Costakes, Ph.D. Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge, CB2 1GA United Kingdom *From:* jeorgemarley thomas kirtswab...@gmail.com *Sent:* Wednesday, November 12, 2014 8:16 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with refmac05, and after each refinement the density around this methionine is flipping. and it is difficult to say where this methionine actually have the density. please suggest what I should I do. I am attaching the snap here. Thanks in Advance for your kind suggestions Jeorge -- http://www.avast.com/ This email is free from viruses and malware because avast! Antivirus http://www.avast.com/ protection is active. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUY0O/UxlJ7aRr7hoRArkIAJsHP6gLpSkRtJPEE7/P/R453uGvJACeMfus jFS3EEDy7g7ss5A6L3D3cco= =uLjH -END PGP SIGNATURE-
