Re: [ccp4bb] Picking water molecules at 4A structure.

shell)? Tx Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of John R Helliwell [jrhelliw...@gmail.com] Sent: Friday, April 17, 2015 5:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Picking water molecules at 4A structure. Hi, This paper:- doi:10.1107

Re: [ccp4bb] Picking water molecules at 4A structure.

Good morning Pavel, That's interesting. In our study 'ghosts' of waters in our truncated maps did not occur. Waters and hydrogens behave differently as ghost objects presumably? Greetings, John On 17 Apr 2015, at 20:10, Pavel Afonine pafon...@gmail.com wrote: Hello, John, the

Re: [ccp4bb] Picking water molecules at 4A structure.

[CCP4BB@JISCMAIL.AC.UK] on behalf of Sudipta Bhattacharyya [sudiptabhattacharyya.iit...@gmail.com] *Sent:* Monday, April 13, 2015 1:14 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Picking water molecules at 4A structure. Dear community, Recently we have been able to solve a crystal structure

Re: [ccp4bb] Picking water molecules at 4A structure.

: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of John R Helliwell [jrhelliw...@gmail.com] Sent: Friday, April 17, 2015 5:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Picking water molecules at 4A structure. Hi, This paper:- doi:10.1107/S0907444903004219http://dx.doi.org/10.1107

Re: [ccp4bb] Picking water molecules at 4A structure.

Hi, This paper:- doi:10.1107/S0907444903004219 http://dx.doi.org/10.1107/S0907444903004219 I think will be of interest. Whilst 4 Angstrom resolution is not covered the article will indicate the tests you could make to evaluate your 'possible water like densities'. Best wishes, John On Mon, Apr

Re: [ccp4bb] Picking water molecules at 4A structure.

Hello, John, the lower-resolution datasets in your paper were generated by truncating a high-res dataset, i.e. the lo-res datasets are of great quality. Would the conclusions still be valid if the data are true low-res? (i.e. I/sigI 1.5-2 in last shell)? genuinely low-res data set is

Re: [ccp4bb] Picking water molecules at 4A structure.

Dear all, I thank you all for your kind suggestions and remarks. So the bottom line appeared to me is - one should not pick water molecules at low resolution (grater than 3.0/3.5A) data (not a truncated data I guess) unless there is sufficient reasons/evidences (like presence of water molecules

[ccp4bb] Picking water molecules at 4A structure.

Dear community, Recently we have been able to solve a crystal structure of a DNA/protein complex at 4A resolution. After almost the final cycles of model building and refinement (with R/Rfree of ~ 22/27) we could see some small water like densities...all throughout the complex. Now my query is,

Re: [ccp4bb] Picking water molecules at 4A structure.

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sudipta Bhattacharyya [sudiptabhattacharyya.iit...@gmail.com] Sent: Monday, April 13, 2015 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Picking water molecules at 4A structure. Dear community, Recently we have been

Re: [ccp4bb] Picking water molecules at 4A structure.

Now my query is, whether one should pick water molecules at this low resolutions or it is totally unscientific to do so? Your question is justified in intent, but ill phrased. The question you are faced with is “How plausible would the assignment of a given electron density