Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

A way to achieve a feeling for the significance of the different map features that you are looking at in your current project, is the old control technique to omit both a well ordered part of the model (residue, alpha-helical turn, part of a beta-strand, ...) and a less well ordered part

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hi Dale, You're absolutely right - the multiple hypothesis testing problem is one that is often not considered, let alone properly accounted for. Whilst this can be accounted for by appropriate adjustment of significance levels when a known number of explicit hypotheses are tested (and when

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hi, Dr Nicholls brings up many interesting points, but doesn't touch on the major point I had hoped to make in my letter. Whenever you start making multiple tests of your hypothesis you have to evaluate each of those tests with a higher standard than you would if you only applied one.

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear all, I feel the need to respond following last week’s critique of the use of Coot’s map blurring tool for providing diagnostic insight and aiding ligand identification… > On 24 Nov 2020, at 16:02, Dale Tronrud > wrote: > > To me, this sounds like a very

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear all, coming back to those map questions again: On Wed, Nov 25, 2020 at 12:56:16PM +, Mooers, Blaine H.M. (HSC) wrote: > The question is about a Fo-Fc map and the replies have been focused on such > maps. > However, I question why you are bothering with Fo-Fc maps. > The ligand was

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear all, Coming back to map blurring... > On 24 Nov 2020, at 16:41, John R Helliwell > wrote: > > [...] Coot’s blurring and sharpening tool is tethered directly to one’s > measured diffraction data. > [...] But, I have just rechecked the Coot manual and see no

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear Nika, as a possible alternative or second opinion, you could have a look at the ligand-detection modes [1] in BUSTER too - see e.g. https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes It's very similar to the Phenix Polder maps - so might not tell you anything

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hi Nika, - As Herman wrote, you should use common sense to interpret a polder map: if the ligand is not there, this kind of map may show only bulk solvent. So the appearance of some density in the area of the ligand does not "prove" that the ligand is there. Also, map interpretation should be

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

/10./febs.14320 Good luck, BR From: CCP4 bulletin board On Behalf Of Nika Žibrat Sent: Tuesday, November 24, 2020 03:29 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] phenix.refine with ligand with ambiguous electron density Hello, I have a question about protein-ligand, of which

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear Jon, I don't think we have any disagreement. I just wanted to emphasize that you should have your plan thought out at the start. You may have decided that you will compare your ligands shape with your map using a Real Space R Factor. If you don't like that number the fault isn't in

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

etin board On Behalf Of Jon Cooper Sent: Wednesday, November 25, 2020 05:20 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density Hello Dale, the statistical rigour you describe is, of course, excellent, but in a learning environment, if so

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

t bloody obvious, your ligand is not > there. At least not all the time. > > Cheers, > Robbie > > > From: CCP4 bulletin board On Behalf Of Jon Cooper > Sent: Wednesday, November 25, 2020 05:20 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] phenix.refine with ligand

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

@JISCMAIL.AC.UK Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density Hello Dale, the statistical rigour you describe is, of course, excellent, but in a learning environment, if someone gets a negative result, you have to go into overdrive to check that everything has been

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello Dale, the statistical rigour you describe is, of course, excellent, but in a learning environment, if someone gets a negative result, you have to go into overdrive to check that everything has been done correctly, since there is a fair chance that human error is the cause. It may be a

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello Dale, Well, warming to your theme, I start with a trust in Coot before a new project. Secondly, Coot’s blurring and sharpening tool is tethered directly to one’s measured diffraction data. Thirdly, scrutinising it at a sigma level above 5, Coot’s default, is certainly not the same as

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hi, To me, this sounds like a very dangerous way to use this tool decide if a ligand has bound. I would be very reluctant to modify my map with a range of arbitrary parameters until it looked like what I wanted to see. The sharpening and blurring of this tool is not guided or limited by

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello, I was wondering if you are refining the ligand occupancy. Eleanor mentioned resolution which is important here. If it's good enough, occupancy refinement of the ligand or the fragment will clean the map up, assuming the occupancy is much less than one. Sorry, if I'm just saying the

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hi Nika, A couple of other things you could try to improve maps to add to what the others have suggested. One, I am assuming that you are refining the occupancy of the ligand, but if not, that should reduce the negative density? 2. Since you mention soaking the ligand, do you have a good X-ray

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear Nika, A tool I am gaining experience with, but for a challenge like you describe, may help:- In Coot>Calculate you see “Blurring/Sharpening tool”. You are presented with a choice of electron density map (here you would select your Fo-Fc). There is then a slider tool, to the left and to

[ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello, I have a question about protein-ligand, of which ligand displays an ambiguous electron density. I am solving a structure of protein with ligand which was obtained via soaking. Structural characteristics indicate the ligand is present however the electron density is quite vague and too