[ccp4bb] Water chains and ligand accessibility

Hello everyone I just solved a structure of a catalytic protein with very long water chains (35 to 40 continuous water molecules) recently and found that the catalytic bed is with less polarity (compared to other orthologues) using computaional methods. I believe that these can help in ligand acce

Re: [ccp4bb] Water at AU boundary

Thanks to Eugene, Mark, and Rajiv. All suggested a change in occupancy. Best wishes, Chris Virus-free. www.avg.com

Re: [ccp4bb] Water at AU boundary

Chris, you can reduce occupancy of the water molecule, like: 0.5 if water lies on 2-fold axis, or 1/3 if it is on 3-fold axis and so on ср, 6 нояб. 2019 г. в 11:18, Chris Fage : > Dear BB Users, > > Within my unit cell, I see overlapping spherical blobs of Fo-Fc and 2Fo-Fc > density in Coot. Thes

[ccp4bb] Water at AU boundary

Dear BB Users, Within my unit cell, I see overlapping spherical blobs of Fo-Fc and 2Fo-Fc density in Coot. These blobs appear directly at the symmetry boundary, such that building a water molecule at the position results in overlaid symmetry-related molecules (see water 420, between three copies o

Re: [ccp4bb] Water molecules after refinement

Dear Jeorge, as you add water molecules to a model, the R _and_ Rfree are bound to drop. It is important to do it the other way round: let coot add waters, then check the added waters in coot if they make chemically sense, then run refmac5. Don't trust automatic procedures more than your chemical

Re: [ccp4bb] Water molecules after refinement

bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jeorgemarley thomas [kirtswab...@gmail.com] Sent: Wednesday, November 19, 2014 6:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Water molecules after refinement Dear All, I am sorry to ask this s

Re: [ccp4bb] Water molecules after refinement

Dear Jeorge are the water molecules without electron density properly coordinated? These could be ghosts... Additionally, did you solve the structure by molecular replacement? If so, in your search model, do you see these water molecules at the same / nearby location? Again, those could be mode

[ccp4bb] Water molecules after refinement

Dear All, I am sorry to ask this simple question, but I really need suggestions for this. As the refinement has been done at 3.0 Angstrom after refinement the water molecules were added by using "find waters" in coot. After adding water refinement was done using Refmac 05. Now when I look on the a

Re: [ccp4bb] AW: [ccp4bb] water at the same exactly position

removes them. //www-bmb.ijs.si/ best regards, dusan On Nov 1, 2014, at 1:00 AM, CCP4BB automatic digest system wrote: > Date:Fri, 31 Oct 2014 08:32:56 +0800 > From:luzuok > Subject: Re: AW: [ccp4bb] water at the same exactly position > > Dear Herman, > &g

[ccp4bb] AW: Re:[ccp4bb] AW: [ccp4bb] water at the same exactly position

ould just crash and do not have options to clean-up the waters before starting refinement. Best regards, Herman Von: luzuok [mailto:luzuo...@126.com] Gesendet: Freitag, 31. Oktober 2014 01:33 An: Schreuder, Herman R&D/DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re:[ccp4bb] AW: [ccp4bb] water at

Re: [ccp4bb] AW: [ccp4bb] water at the same exactly position

n Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von luzuok Gesendet: Donnerstag, 30. Oktober 2014 04:54 An:CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] water at the same exactly position Dear Nicolas, It is really time-consuming! Philip told me to run the s

Re: [ccp4bb] water at the same exactly position

Hi Luzuok, Any validation program that detects clashes should hind these. Cheers, Robbie Sent from my Windows Phone Van: luzuok Verzonden: 30-10-2014 10:58 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] water at the same exactly position Dear Nat, But if

[ccp4bb] AW: [ccp4bb] water at the same exactly position

or not to fit a water in some blob of density. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von luzuok Gesendet: Donnerstag, 30. Oktober 2014 04:54 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] water at the same exactly position Dear Nicolas, It is

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] water at the same exactly position

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Lu Zuokun, it may appear tedious, but for a good quality model you should check every position and decide yourself what to place there. Automation will not replace your chemical understanding. Regards, Tim On 10/30/2014 10:56 AM, luzuok wrote:

Re: [ccp4bb] water at the same exactly position

Dear Nat, But if there are other solvent molecules, such as Mg2+, SO4-,, in the same position. How can this problem be solved? Lu Zuokun -- 卢作焜 南开大学新生物站A202 在 2014-10-30 12:57:31，"Nat Echols" 写道： On Wed, Oct 29, 2014 at 8:53 PM, luzuok wrote: I think it is better for COOT t

Re: [ccp4bb] water at the same exactly position

On Wed, Oct 29, 2014 at 8:53 PM, luzuok wrote: > I think it is better for COOT to solve this issue. > Coot already can be used to solve this issue - I think the automation is somewhat lacking, but it's vastly preferable to anything involving a text editor or shell commands. 1. Load molecule

Re: [ccp4bb] water at the same exactly position

From: Pavel Afonine Date:10/30/2014 12:27 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] water at the same exactly position This conversation makes me more and more certain that water update (add/remove/refine water) done as part of (a default) refinement run is a good idea

Re: [ccp4bb] water at the same exactly position

ge not automatically, and it maybe time consuming. Hope to help Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok [luzuo...@126.com] Envoyé : mercredi 29 octobre 2014 13:08 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] water at the

Re: [ccp4bb] water at the same exactly position

This conversation makes me more and more certain that water update (add/remove/refine water) done as part of (a default) refinement run is a good idea -:) Pavel On Wed, Oct 29, 2014 at 5:08 AM, luzuok wrote: > Dear all, > I found that there are some water molecules in my pdb that share the

Re: [ccp4bb] water at the same exactly position

luzuo...@126.com] >Envoyé : mercredi 29 octobre 2014 13:08 >À : CCP4BB@JISCMAIL.AC.UK >Objet : [ccp4bb] water at the same exactly position > >Dear all, >I found that there are some water molecules in my pdb that share the same > position. This maybe cause by merging molecules

Re: [ccp4bb] water at the same exactly position

automatically, and it maybe time consuming. Hope to help Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok [luzuo...@126.com] Envoyé : mercredi 29 octobre 2014 13:08 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] water at the same exactly

[ccp4bb] water at the same exactly position

Dear all, I found that there are some water molecules in my pdb that share the same position. This maybe cause by merging molecules in coot. It seems that I have mereged water molecules into my protein for more than one time. Does anyone tell me how to fix this problem? Best regards! Lu Zu

Re: [ccp4bb] Water or ion

Dear All: Many thanks for your comments and inputs! Uma On Sat, Nov 23, 2013 at 7:14 PM, Uma Ratu wrote: > Dear All: > > > I use Coot to check water molecules in my model. > Most of them are in good coordinates for water. > > Some of these waters have unusual coordinates. > > For example, one

Re: [ccp4bb] Water or ion

. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Water or ion Dear All: I use Coot to check water molecules in my model. Most of them are in good coordinates for water. Some of these waters have unusual coordinates. For example, one is in the H-bond distance with 2 nitrogen and 2 oxygen of protein

Re: [ccp4bb] Water or ion

: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Water or ion Dear All: I use Coot to check water molecules in my model. Most of them are in good coordinates for water. Some of these waters have unusual coordinates. For example, one is in the H-bond distance with 2 nitrogen and 2 oxygen of protein

Re: [ccp4bb] water picking

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear , according to my 'man watpeak' and 'man peakmax' in ccp4-6.2.993 there is no restrictionof these programs to Patterson peaks (which would anyhow require a total rewrite, considering that peakmax acts on maps rather than Pattersion maps). May

[ccp4bb] water picking

All, For those who still don't use Coot is there an automatic water picking procedure in CCP4? Many years ago there was a peakmax which is now for Patterson peaks only. Then there was routine through Arp/wArp. Now is Coot only. Is this right? Thanks. Vaheh Oganesyan, PhD Antibody Discovery a

Re: [ccp4bb] Water

Dear All: I appreciate for your comments and inputs. Thank you Uma On Thu, Mar 8, 2012 at 12:16 AM, Shekhar Mande wrote: > Welljust to add, it has been our contention that many of the metal > ions have been modelled as waters in several structures- due perhaps to the > lack of sufficiently

Re: [ccp4bb] Water

Welljust to add, it has been our contention that many of the metal ions have been modelled as waters in several structures- due perhaps to the lack of sufficiently high resolution data. We published some of the potential metal binding sites in many structures a few years ago: Proteins. 2008 M

Re: [ccp4bb] Water

Dear Uma, The water pictured in W12-1.jpg: could this be a potential metal ion? If you flip the side chain on Asn at 3.08Angstrom, then this has 3 or 4 coordination with oxygen atoms. So, provided your crystallization condition or buffer contains metal ion(s), you could attempt to see if it fits b

Re: [ccp4bb] Water

I guess we would all like to be able to do that! High resolution structures show that a) there are well defined H2Os with tidy H bonds. b) there are multiple networks where the waters (and many side chains) have partial occupancy c) there is a soup of other "stuff" which was in the crystallisa

Re: [ccp4bb] Water

Ø Some of these 'water' have more than 4 contacts, I would consider them as 'false'. How about bifurcated hydrogen bonds? BR

Re: [ccp4bb] Water

ra Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 56 Otepoti 9054 > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > ** ** > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of

Re: [ccp4bb] Water

: [ccp4bb] Water Dear Roger: Thank you very much for your comments. I use them as guideline and remove many 'false waters". Still, I am not clear of some of these 'waters' are real or not. I have the pic attached. In Pic-W11-1, the 'water' is connected to the adjust re

Re: [ccp4bb] Water

Uma, Remember that your structure, ultimately, is a model. A model is your best judgment of the true representation of the protein structure in your crystal. Your model should make chemical sense. Coot is pretty good at placing waters, but it cannot substit

[ccp4bb] Water

Dear All: I try to add water to my model. Here is how I did: Coot: Find Wates Map: FWT PHWT; 1.8 rmsd; Distances to protein atoms: 2.4 min/3.2 max Coot found 270 water molecules. I then examed these waters. Most of them had ball shape. Some had two or more balls together. Some

[ccp4bb] water picking

Hi all, I know there are a lot of criteria for water picking. It depends on the resolution, data quality, etc... Can somebody point me a good literature on this topic? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of

Re: [ccp4bb] water soluble protein that needs detergent to be stable

I have not dealt myself with this type of protein, but Alex McPherson tested the detergent beta-octylglucoside (at a concentration of 1.5 %, i.e. above the cmc) for the crystallisation of soluble protein and tRNA (1986, J.Biol.Chem 261:1969-75), the detergent did not hampered the crystallisation, a

Re: [ccp4bb] water soluble protein that needs detergent to be stable

otein to be more soluble, etc. etc. Artem _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Daniel Jin Sent: Tuesday, August 28, 2007 1:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] water soluble protein that needs detergent to be stable Hi, I am working on a 60 k

[ccp4bb] water soluble protein that needs detergent to be stable

Hi, I am working on a 60 kDa C. elegans protein that is predicted to be mostly alpha-helix. It is over-expressed in E.coli and the yield is about 1 mg/L of cell culture. The CD spec at 4 degree showed the presence of dominant alpha-helix. However, we don’t have any functional assay to conf

Re: [ccp4bb] Water is about 60% everywhere

> > Are there any methods that allow one to input such ions as possible > candidates? What would be ideal is to have a program that says something > like "The density peak at x,y,z, has a .0973 chance of being real. It is > only 2.2 Å from N7 of G12, precluding water. Based on the mother liquor

Re: [ccp4bb] Water is about 60% everywhere

> One can only assume that there is 2 schools of thought - > 1) water is part of the problem of model building > 2) water is the solution to residual reduction. I'm a bit of an atheist when it comes to all supernatural phenomenon, whether deities, water molecules floating 4.5 Å in outer space, too

[ccp4bb] Water is about 60% everywhere

With respect to water structure in Xtal structures. I have studied water "order" (or should that be sensibility) within xtal structures by studying water shell statistics. It is possible to divide xtal structures into 2 camps. The first show some sensible water shell structure that correlates t

Re: [ccp4bb] water water everywhere

I've often wondered whether it would be more fair to report R-factors with and without waters, since waters can be used to beautify statistics. I also think providing pdb coordinates and Fobs with experimental phases as supplementary information in a standard format to be supplied automatically to

[ccp4bb] water water everywhere

While we're still on the subject of good model-building habits and reviewing pitfalls, I've been shocked to download a couple of structures recently that seem to have solvent channels chock full of allegedly ordered water (many "layers" deep, and not exactly at 0.5A resolution). To any new stu