Re: [ccp4bb] electron density close Histidine side chain

From: samer halabi Sent: 21 July 2020 11:08 To: ccp4bb@jiscmail.ac.uk ; David Briggs Subject: Re: [ccp4bb] electron density close Histidine side chain Hello, Thank you for your kind reply. If the distances are still less than 2.2Å, would coot and Refmac still consider

Re: [ccp4bb] electron density close Histidine side chain

Hello,Thank you for your kind reply.In this case that could be either Zinc or Nickel. Sorry, I should've mentioned how I purified the protein complex. The protein is secreted in HighFive cells, to purify it  by its 6xHis tag, I used Ni sepharose excel beads, eluted with Imidazole and then furthe

Re: [ccp4bb] electron density close Histidine side chain

Sent: Monday, July 20, 2020 5:27:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] electron density close Histidine side chain ‌Dear Samer, What king of cryo-protectant did you use ? Such a bent density, with that size, looks like an ethylene-diol. Best regards, Nils Marech

Re: [ccp4bb] electron density close Histidine side chain

"samer halabi" <30c2162795b2-dmarc-requ...@jiscmail.ac.uk> A : CCP4BB@JISCMAIL.AC.UK Envoyé: lundi 20 Juillet 2020 18:17 Objet : [ccp4bb] electron density close Histidine side chain  Hello all, I have few blobs in an MHC II structure I am working on, especially opposite t

Re: [ccp4bb] electron density close Histidine side chain

Hello,Thank you for your kind reply.Do I need to link them together in the structure? Is there a method for that? >From the other replies I thought I should mention how I purified the protein >complex.The protein is secreted in HighFive cells, to purify it  by its 6xHis >tag, I used Ni sepharos

Re: [ccp4bb] electron density close Histidine side chain

Hello, do you have any negative difference density for the current position of the His side chain? If so, it may be in two confirmations. Just a thought. Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com Original Message On 20 Jul 2020, 17:16, samer halabi wrote: >

Re: [ccp4bb] electron density close Histidine side chain

Almost certainly a metal ion, possibly Ni(2+) if a Ni-NTA column was used for purification. Ni-N bond lengths are typically around 2.0 A. Additional density is probably coordinated water molecules, which should have similar Ni-O bond distances around 1.9 A. It is fairly common to find adventitious

Re: [ccp4bb] electron density close Histidine side chain

on behalf of Nils Marechal <4954a024d277-dmarc-requ...@jiscmail.ac.uk> Sent: Monday, July 20, 2020 5:27:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] electron density close Histidine side chain ‌Dear Samer, What king of cryo-protectant did you use ? Such a bent density, with

Re: [ccp4bb] electron density close Histidine side chain

2020 18:17 Objet : [ccp4bb] electron density close Histidine side chain   Hello all, I have few blobs in an MHC II structure I am working on, especially opposite to Histidine as in the accompanying screenshot, that I am confused about. In the crystal conditions, I have Tris, Imidazole, Acetate,

Re: [ccp4bb] electron density close Histidine side chain

If there is a covalent link, maybe sending a sample off to mass spec would be a good idea. That would remove some of the guesswork. Dale Tronrud On 7/20/2020 9:16 AM, samer halabi wrote: > Hello all, > I have few blobs in an MHC II structure I am working on, especially > opposite to Histidine

Re: [ccp4bb] electron density close Histidine side chain

Hello, what immediately comes into mind is phosphohistidine, especially since the density looks rather large, but the geometry seems a bit off for that but I cannot judge only from one angle. You could of course try to fit it in and see how it looks. Cheers, Arne On Mon, Jul 20, 2020 at 6:17 PM

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

mobile phone… John From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li Sent: 10 September 2018 20:42 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures. Hi Kevin, a) If your goal is merely to

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

o:CCP4BB@JISCMAIL.AC.UK> *Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures. Hi Marin I was about to comment on that too but then I realised that Pavel is referring to the map _contours_  (which is what most people using a map visualisation

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

ontour level as you like. >> >> >> >> Of course, if the authors did not deposit their EM-map, you cannot >> download it, but the same is true for X-ray structure factors. >> >> >> >> Happy viewing! >> >> >> >> Herman &g

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

the authors did not deposit their EM-map, you cannot download > it, but the same is true for X-ray structure factors. > > > > Happy viewing! > > > > Herman > > > > > > > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > <mailto:

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

structure factors. > > > > Happy viewing! > > > > Herman > > > > > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Ian Tickle > *Gesendet:* Montag, 10. September 2018 12:58 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Dear Kevin, Are you referring to "generating a map" from the model (PDB coordinates) generated from tracing the chain in the ab-initio EM map? Best wishes, Natesh On Mon, 10 Sep 2018 at 09:58, Kevin Jin wrote: > Dear All, > > Is there any sever available to create electron density

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

download it, but the same is true for X-ray structure factors. Happy viewing! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian Tickle Gesendet: Montag, 10. September 2018 12:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps for

[ccp4bb] AW: [ccp4bb] Electron density maps for Cryo-EM structures.

] Electron density maps for Cryo-EM structures. Hi Marin I was about to comment on that too but then I realised that Pavel is referring to the map _contours_ (which is what most people using a map visualisation program like Coot actually see). So the contoured map does represent an iso

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Great, thanks! On Sun, Sep 9, 2018 at 9:49 PM Pavel Afonine wrote: > P.S.: all questions are welcome of course, no labeling. It's just some of > them are so orthogonal to common sense that answers my be such as well. > Best, > Pavel > > On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine wrote: > >>

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

P.S.: all questions are welcome of course, no labeling. It's just some of them are so orthogonal to common sense that answers my be such as well. Best, Pavel On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine wrote: > Hi, > > Is there any sever available to create electron density maps for cryo-em >>

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Hi, Is there any sever available to create electron density maps for cryo-em > structures? > The questions are nonsensical. Here is why: 1) In cryo-EM maps are not electron density maps but surfaces representing electric potential. 2) Creating such a map is essentially carrying on from cryo-EM

[ccp4bb] Electron density maps for Cryo-EM structures.

Dear All, Is there any sever available to create electron density maps for cryo-em structures? Or, we should create the maps from mmCIF. I am particularly interested in those cryo-em structures with high resolution, like 2.6~2.8A. Please give me an education. Thanks, Kevin ###

Re: [ccp4bb] Electron density

: Sunday, May 13, 2018 8:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density Dear all, I am currently refining a structure and found a intriguing electron density at the protein surface (pictures attached, the Fo-Fc map is contoured at >3.5 sigma). My first candidates were molecu

Re: [ccp4bb] Electron density

Thanks for your quick responses. I used ethylene glycol as cryoprotectant. Indeed I had 1% DMSO as part of the crystallisation condition (I forgot to include that), but DMSO is too small to fit this density and DMSO has a trigonal pyramidal structure, which differs a bit to what I have in my struct

Re: [ccp4bb] Electron density

On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote: > Dear all, > > I am currently refining a structure and found a intriguing electron density > at the protein surface (pictures attached, the Fo-Fc map is contoured at > >3.5 sigma). My first candidates were molecules from my protein prep or > cr

Re: [ccp4bb] Electron density

Did you happen to use glycerol as a cryoprotectant? From: CCP4 bulletin board On Behalf Of Daniel Garcia Sent: Monday, 14 May 2018 12:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density Dear all, I am currently refining a structure and found a intriguing electron density at the

Re: [ccp4bb] Electron density map for publications

gt; Usually, fo-fc is the best way to show. > > > best, > > > -- > chenzhonghao...@163.com > > > *From:* raj kumar > *Date:* 2017-12-19 13:07 > *To:* CCP4BB > *Subject:* [ccp4bb] Electron density map for publications > Hi > W

Re: [ccp4bb] Electron density map for publications

2-19 13:07 *To:* CCP4BB *Subject:* [ccp4bb] Electron density map for publications Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the bound ligand? Thanks Raj

Re: [ccp4bb] Electron density map for publications

Dear Raj, Usually, fo-fc is the best way to show. best, chenzhonghao...@163.com From: raj kumar Date: 2017-12-19 13:07 To: CCP4BB Subject: [ccp4bb] Electron density map for publications Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the

Re: [ccp4bb] Electron density map for publications

http://journals.iucr.org/d/issues/2013/02/00/index.html Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of raj kumar Sent: Monday, December 18, 2017 8:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density map for publications Hi Which electron

[ccp4bb] Electron density map for publications

Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the bound ligand? Thanks Raj

Re: [ccp4bb] Electron density in PDBe

o.edu/phoebericelab/ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Anastassis Perrakis [a.perra...@nki.nl] Sent: Thursday, November 30, 2017 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Electron density in PDBe Interesting structure: a=b=c=α=β=γ=

[ccp4bb] Electron density of penicillin (Re: [ccp4bb] Google Gets it Right)

Dear Gregg et al., On Mon, May 12, 2014 at 4:28 PM, Gregg Crichlow wrote: > Actually, it was noticing penG that made me mouse over it myself. After > spending many years completing a thesis on beta-lactamases, I was very > surprised - and excited - to see that on something as main-stream as > Goo

Re: [ccp4bb] Electron density server

The server has been rebooted and appears to be working again. --Gerard On Fri, 25 Oct 2013, Rojan Shrestha wrote: Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan Best wishes, --Gerard **

Re: [ccp4bb] Electron density server

Dear Rojan, Get the mmCIF, then use CIF2MTZ from CCP4. Cheers, Clement On 10/25/13 3:07 PM, Rojan Shrestha wrote: Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan

[ccp4bb] Electron density server

Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan

Re: [ccp4bb] electron density assignment

Subject: [ccp4bb] electron density assignment > *** > This message has been scanned by the InterScan for CSC SSM at IICT and found > to be free of known security risks. > *** > > Dear all, > > Here are some "hexmeric"

Re: [ccp4bb] electron density assignment

Hi, I observed a very similar hexagonal arrangement of electron density blobs in one of my structures recentely and asked the CCP4bb community to help me explain it. Unfortunately, noone could come up with some satisfactory explanation, so I gave up on interpreting this rogue density. What was ce

Re: [ccp4bb] electron density assignment

Generate an anomalous map and look for peaks. Many metals would generate anomalous. On 02/04/13 07:39, Gang Dong wrote: Dear all, Here are some "hexmeric" densities we observed in our 1.6-A resolution 2Fo-Fc map. They are located in between two dimers. Although 7 waters would fit nicely in

Re: [ccp4bb] electron density peak volume

On 07/06/2012 09:40 AM, Andrew Pannifer wrote: Hi, Is there a way to ask peakmax to output the volume of each electron density peak that it detects (or is there a reasonably straightforward way to do this via an alternative command line runnable approach?) Cheers, Alan There might be a

Re: [ccp4bb] electron density peak volume

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Pavel, that's probably how I'd program it, too. Still I am not aware of an existing (command line) program which does that, and I am not sure of its benefit from a users point of view. I can imagine that many programs internally make use of the 'bl

Re: [ccp4bb] electron density peak volume

Hi Tim, a possible way of thinking about this is: say you have N (=nx*ny*nz) nodes of the grid on which you sampled the map, and the unit cell volume is Vcell, and you are looking at a blob identified at some level. Then the volume of this blob can be defined as Vblob = np*Vcell/N, where np is th

Re: [ccp4bb] electron density peak volume

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Alan, do you think the notion of 'volume of a peak' makes sense? You are probably asking for the number of connected pixels around a local maximum above a certain threshold - again, not sure whether this is a useful concept and I am not aware of

[ccp4bb] electron density peak volume

Hi, Is there a way to ask peakmax to output the volume of each electron density peak that it detects (or is there a reasonably straightforward way to do this via an alternative command line runnable approach?) Cheers, Alan

Re: [ccp4bb] Electron density improvement with resolution graphic

You may also have a look at James Holton's page http://ucxray.berkeley.edu/~jamesh/movies/ and take a screenshot of one of his movies. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 4 Dec 2009, Brad Bennett wrote: Hi all-

Re: [ccp4bb] Electron density improvement with resolution graphic

This could be useful: http://www.ruppweb.org/Xray/resolution.html BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Brad Bennett Sent: Friday, December 04, 2009 5:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density improvement with resolution

Re: [ccp4bb] Electron density improvement with resolution graphic

James Holton has a great little movie showing how electron density changes with decreasing resolution: http://ucxray.berkeley.edu/~jamesh/movies/resolution.mpeg Jon On Dec 4, 2009, at 5:37 PM, Jim Fairman wrote: You can find one here on the Cambridge X-ray crystallography course website:

Re: [ccp4bb] Electron density improvement with resolution graphic

You can find one here on the Cambridge X-ray crystallography course website: http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett wrote: > Hi all- > I recall seeing a long time ago a figure which showed the progressive > improvement of

[ccp4bb] Electron density improvement with resolution graphic

Hi all- I recall seeing a long time ago a figure which showed the progressive improvement of electron density as one increases resolution, say from 6 to 3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing the ability to model side chains of alpha helices at higher resolution

Re: [ccp4bb] electron density slabs

Slabs are almost always due to rogue huge reflection(s). If you run mtzdump on the refmac_output.mtz you will find the maximum value and average value of each column. If you run fft hklin refmac_output.mtz LABI F1=FWT PHI=PHWT then the log file gives you the indices of the largest reflection

[ccp4bb] Fwd: [ccp4bb] electron density slabs

umo...@gmail.com>Date: 8. sep 2009 11.37.07 GMT+02:00To: CCP4BB@JISCMAIL.AC.UKSubject: [ccp4bb] electron density slabsReply-To: hayato Jumonji <hay.jumo...@gmail.com> Dear all, I've phased 3 wavelength SeMet dataset with SHELX and the resulting mtz on Coot  shows ~5.4 A apart slabs in wa

[ccp4bb] electron density slabs

Dear all, I've phased 3 wavelength SeMet dataset with SHELX and the resulting mtz on Coot shows ~5.4 A apart slabs in water channel. I've captured part of the electron density at 0.4sigma. The slabs appear through out the electron density and parallel to AB plane (space group P21212). Most of the

Re: [ccp4bb] electron density map

Tassos is absolutely right. While it's unlikely that many subscribers of the ccp4bb today suffer the indecency of checking their mailbox over 4kbps flaky modem connection (also known as wishful staring at the progress bar), it still seems pointless to distribute hundreds of megabytes into mailboxe

Re: [ccp4bb] electron density map

hi - my two cents: 1. I am puzzled to see only positive and no negative density in the picture 2. I would contour difference maps at 3.5 in general for significant features 3. why is the 2fofc 'heavily biased' ? Its a 2mFo-DFc map presumably, and lots have been said about these maps not bei

Re: [ccp4bb] electron density map

I agree with Artem. I also don't think you have a register problem. All of the residues show typical 2fofc density for their types, especially considering the 3A data. The disappearing act of the asp carboxyl is typical of solvent exposed aspartates. Assuming the register is correct, you ha

Re: [ccp4bb] electron density map

uild as if the sand were stone" Jorge Luis Borges _ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Mike England Sent: Thursday, August 20, 2009 7:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] electron density map Hi all, I will appreciate the comments

Re: [ccp4bb] Electron Density Maps

If you want to display CNS maps in Coot and have them on the right scale, then you need to do one of two things. Either: 1. Don't use the map file, use the reflection file containing the map coefficients, or 2. Change the setting in CNS which controls the extent of the output map. Instead of

Re: [ccp4bb] Electron Density Maps

Dear Pascal, 2009/8/10 Pascal Egea : > Dear All, > I am currently carrying the refinement of a structure and comparing the > results obtained in Refmac, Phenix and CNS. > While Phenix and Refmac write maps and their corresponding coefficients in > mtz format allowing display of 2Fo-Fc and Fo-Fc ma

[ccp4bb] Electron Density Maps

Dear All, I am currently carrying the refinement of a structure and comparing the results obtained in Refmac, Phenix and CNS. While Phenix and Refmac write maps and their corresponding coefficients in mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the corresponding Fo-Fc map as writ

Re: [ccp4bb] Electron density function for ligands in real space?

If you put the coordinates into COOT it will give you a validation score. If you use the CCP$i map correlation procedures it will also give you a CC for the density match. The input in each case is the reflection file with appropriate amplitude and phase terms. What you use depends on what p

[ccp4bb] Electron density function for ligands in real space?

Hello, I'm new in x-ray crystallography and trying to compute real-space electron density for ligands. The goal is to evaluate match of ligands with density peaks (like computing local R values in real space). What would be the best electron density function that considers ligand atomic numbe

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

In addition to contouring differences, your mapmask script asks for a border of only 2 A around the pdb file. If you're looking for waters, unbuilt loops, or things on the edge of your pdb file, this will need to be larger. When I used O and created the maps over the pdb file of interest

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

I am guessing it is a difference in normalization, but I would love to hear a definitive answer from someone. Steve -Original Message- From: CCP4 bulletin board on behalf of mac minista Sent: Wed 2/14/2007 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] electron density maps in

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

Hi Mac, > I have noticed that going from refmac 5 (script) to generate fo-fc and > 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. > I have used the following columns in Coot (latest version): FOFCW

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

Hi, thank you for your suggestions, the difference I am seeing in the maps is mainly with the Fo-Fc maps i.e. what appears in coot does not always appear in O/Pymol. Here are the scripts for FFT and MAPMASK: FFT #!/bin/sh set -e fft hklin model.mtz mapout fofc_f.map

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

On Wed, 2007-02-14 at 07:59 -0800, mac minista wrote: > Dear all, > > I have noticed that going from refmac 5 (script) to generate fo-fc and > 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is > not exactly the same electron density maps-I mean some differences are > seen. I ha

Re: [ccp4bb] electron density maps in Coot vs O / Pymol

I use this to get the same maps: http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcover http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcoverdiff I used zsh but I think it should work with current versions of bash. mac minista wrote: > Dear all, > > I have notice

[ccp4bb] electron density maps in Coot vs O / Pymol

Dear all, I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. I have used the following columns in Coot (latest version): FOF