Re: [ccp4bb] unidentified density
I think it's MPD. I have also observed in my crystals. Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [e] alut...@uchc.edumailto:alut...@uchc.edu [p] 860/ 679 - 8390 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Vandna Kukshal [vanx...@gmail.com] Sent: Wednesday, October 17, 2012 12:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unidentified density I think it might be PEG. u should try to fit that. On Wed, Oct 17, 2012 at 7:13 AM, RHYS GRINTER r.grinte...@research.gla.ac.ukmailto:r.grinte...@research.gla.ac.uk wrote: Is this density on an 2 fold axis? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir Kumar [sudhir.1...@gmail.commailto:sudhir.1...@gmail.com] Sent: 17 October 2012 12:07 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unidentified density Dear all, I have been working on the crystal structure of an enzyme in which I found the unidentified density (see images in attachments). Crystallization condition has Peg 1000, Peg 1500, Ethylene glycol, Tris and MPD. Does any one has any idea what it could be? Thanks -- best regards Sudhir Kumar Research Scholar C/O Dr. S. Gourinath Structural Biology Laboratory SLS, JNU, New Delhi-110067 -- Vandana kukshal
[ccp4bb] nmr blog
Is any NMR blog available for discussion? Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [e] aut...@uchc.edumailto:aut...@uchc.edu [p] 860/ 679 - 8390 [w] http://spirocheteresearch.uchc.edu/
[ccp4bb] SAXS workshop
Hello If I am not wrong, there was one posting related with SASX workshop where we can also bring own samples. Does someone have that information? Please send me the link. Thanks a lot Amit
[ccp4bb] Hydrophobic interactions
Hi Everyone I have to calculate hydrophobic interactions in pdb files. Is any server available for this type of calculation? Thanks in advance Amit
Re: [ccp4bb] mutation and minimization
Hi If you are familiar with turbo-frodo, you can use it for mutagenesis and refinement . Just go inside the editing menu, replace the residue, save the file and REFINE the residue. You can also select the stretch of residues by picking the first and last residues so you will get the refinement (best rotamer) based on local environment. Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas Förster [docandr...@gmail.com] Sent: Thursday, May 12, 2011 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mutation and minimization Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] B factor
Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu
