[ccp4bb] Real space refinement of alternative conformations

then required (but coot cleverly remembers the B factors for the alt conf when you add it back in, which is neat). I'd be extremely grateful for any help to resolve this! Thanks in advance Isaac Westwood

Re: [ccp4bb] Protein-Ligand Crystallization

In addition to the previous suggestions, if you have a metal-binding protein, beware of acidic compounds chelating the metal and stripping it out of the protein, as this often lead to the effect you observed as well. Isaac On 5 Feb 2015 13:45, "Monica Mittal" wrote: > Hi all, > I am working to c

Re: [ccp4bb] Superposition of select residues

I find that the superposition in CCP4MG is the most flexible and easy to use implementation of any program I've used. There are multiple superposition methods each with the ability to select residues or atoms. It's very powerful. CCP4MG also happens to produce very pretty pictures! Isaac On 5 Feb

Re: [ccp4bb] water at the same exactly position

Dear Lu Zuokun, There are several methods you can use to locate these problem residues. Here are 3: a) manually step through your PDB file in coot (good practice anyway, this is fundamentally what we as crystallographers should be doing when we are model building) b) identify waters with close co

Re: [ccp4bb] Unidentified density in coot

Dear Shanti Pal, did you use ethylene glycol as cryoprotectant? It may even be there in small amounts in your PEG400 solution. As Nicholas and Tony have said, this could be noise (or could be distorted due to noise) as it's on a 2-fold axis. From those pictures, it looks to me like one molecule of

Re: [ccp4bb] Invisible atoms in ligands

protein) atom has been modeled into a region with no density. Best, Isaac Westwood > > >> On 13 June 2014 11:35, Robbie Joosten wrote: >> >>> Hi Tim, >>> >>> The problem with missing atoms in ligands is that you cannot use the >>> coordina

Re: [ccp4bb] Inverse 3D profile/threading

Hi Jason, While it's not quite what you described, I'd recommend you check out the Secondary Structure Matching server at the EBI: http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html That will (hopefully!) give you previously deposited structures which share a similar fold to your query pdb file.

Re: [ccp4bb] Calculating volume of Ligands

ods already mentioned! Isaac -- Dr Isaac Westwood Department of Pharmacology University of Oxford Mansfield Road Oxford OX1 3QT tel: 01865 271595 email: [EMAIL PROTECTED] _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Rajan Pillai Sent: 15 Janu

Re: [ccp4bb] Measuring the volume and surface area of an active site

Also VOIDOO is an excellent program for this. HYPERLINK "http://xray.bmc.uu.se/~gerard/manuals/voidoo.html"http://xray.bmc.uu.se/~ge rard/manuals/voidoo.html Isaac _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Rajan Pillai Sent: 13 December 2007 22:45 To:

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

I'm a fairly inexperienced crystallographer, but I have worked on a few cases very recently (from separate protein systems) in which the ligand was not "clear" in the electron density until quite a long way through refinement: in the latest case, it wasn't possible to be too confident of the ligand