[ccp4bb] Replacement for Paratone-N?

Hi there, I just noticed that Hampton Research discontinued Paratone-N and now recommends Santovac cryo oil. Has anyone tried Santovac and can comment on how it compares to Paratone? We had some previous success of using paratone for crystal annealing and felt it was a good cryoprotectant

[ccp4bb] Weird electron density on the two-fold axis

Dear all, I am now determining a structure at 2.2 A resolution. The space group is C2, and there is only one molecular in an ASU. During the refinement, some weird electron density appears right on the two-fold axis. Does anyone have any idea what could this be? Thanks a lot. Best regards Shutong

[ccp4bb]

Dear all, I am now determining a structure at 2.2 A resolution. The space group is C2, and there is only one molecular in an ASU. During the refinement, some weird electron density appears right on the two-fold axis. Does anyone have any idea what could this be? Thanks a lot. Best regards Shuton

Re: [ccp4bb] Nucleophilic attack by the side-chain carboxyl group of Asp?

atoms thus forming an octahedral geometry. Crystal 2012/7/23 Andrew Pannifer > Hi Crystal > > I reckon Roger Rowlett has the most likely explanation. The charge on the > Asp is delocalised over the carboxyl group and this tends to make it a > not-very-good nucleophile and co

[ccp4bb] Nucleophilic attack by the side-chain carboxyl group of Asp?

Hi everyone, I am studying the catalytic mechanism of an enzyme. My structural data indicates that an Asp is of most possibility to sever as a general base. The Asp residue is coordinated to a zinc ion. Would it be possible that the side-chain carboxyl group of Asp attacks a carbon atom of the sub

[ccp4bb] Postdoctoral Fellow Position in Ubiquitin Biology available at Toronto

Postdoctoral Fellow in Ubiquitin Biology Description: The Structural Genomics Consortium (SGC), Toronto, is seeking a talented and self-motivated PhD scientist to study the structure, function, and mechanism of HECT-type E3 ubiquitin ligases and ubiquitin-specific proteases. The successful ca

Re: [ccp4bb] peptide docking

> pius > > > On Mon, Jul 11, 2011 at 12:41 PM, crystal wrote: > > Hi all, > > Thanks for all the helpful suggestions. It seems like Phenix > LigandFit > > requires density for the ligand but unfortunately I only have the > > ligand-free model. I've

Re: [ccp4bb] peptide docking

PALMER wrote: > Hi > I'm sure I could help but need more details of the actual project you are > undertaking. > > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com > *From:* crystal > > *To:* C

Re: [ccp4bb] peptide docking

7034**** > > ** ** > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of * > crystal > *Sent:* Saturday, 9 July 2011 1:09 p.m. > > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] peptide docking > > ** ** > > Hi all, >As I'

[ccp4bb] peptide docking

Hi all, As I'm a newbie in peptide docking, I was wondering what programs/servers people would suggest for generating the peptide PDB (keeping all the proper stereochemistry)? Is it possible to extract a file from the PDB database? All comments will be much appreciated!

[ccp4bb] mail test

[ccp4bb] how generate maps only to cover atoms in pdb

Hi, I want to generate maps only covering atoms in the pdb file. I tried fft-creat map in ccp4i (output map to cover all atoms in pdb), but it actually also generated map in places other than pdb atoms. Are there any other ways to do this? Thank you. -- Best regards, Joe

Re: [ccp4bb] Interaction between the domains

Contact in CCP4i can calculate the distance between specified chains/residues. Pymol can display hydrogen bonds too. Joe peter hudson wrote: Hello all I have a very quick question. Is there any programme, which can calculate the H-bond pattern or residues involved in H-bonds formation betw

[ccp4bb] Refmac failed at the end of run

Hi all, I am using refmac in ccp4i 6.1.1 (installed in windows). It runs well when using automatic weight, but failed when using user-specified weight (0.12 in this case). I attach the error message as follow. Your help is very much appreciated. .. 18 0.2064 0.2348 0.8464076

[ccp4bb] Please recommend screen kits for membrane proteins

Sorry for the off-topic subject. I am new to membrane proteins. We already have Qiagen MB class I and II, Sigma Membrane, and Membrane Gold kits, but I want to know if there other kits out there you would recommend. Thanks a lot, Joe

[ccp4bb] Questions regarding Peptidoglycan-binding protein

Dear all, Thank you in advance for your expert opinions. I am working on a peptidoglycan (PG)-binding protein, which is composed of two functionally identical domains. Interestingly, when subjected to gel filtration chromatography (Superdex 200), both full-length protein and the single domains mi

[ccp4bb] X-Ray Crystallographer Position Available in New York (BNL)

X-Ray Crystallographer Position The New York Structural Biology Center (NYSBC), a consortium of ten leading biomedical research centers in New York, is seeking a beamline scientist to manage its two beamlines at NSLS at the Brookhaven National Laboratory and NYSBC's in-house crystallographic fa

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

Hi, Does anyone have information about how long it takes to set up a 96-well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time for setting up a 96-well tray. It is an important factor since we are talking

[ccp4bb] ---solved---Fwd: [ccp4bb] problem in running DM (NCS averaging)

7 8:13 AM Subject: RE: [ccp4bb] problem in running DM (NCS averaging) To: JOE CRYSTAL <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] Hi Your first error seems to have been caused by invalid input. The program seems to have read the lines AVERAGE REFI and LABOUT ... correctly, so the problem

[ccp4bb] problem in running DM (NCS averaging)

Dear all, I tried to run DM for NCS averaging (DM module in CCP4i 6.0.2 installed under Windows XP), but the running failed at different stages with various error message as listed below. I was told it could be an installation problem, but I don't know how to fix it. I am wondering if you have

[ccp4bb] need help--Rfree is not decreasing

Dear all, I am refining a structure at 2.0 A. The water molecules have been added using arp/warp resulting Rwork/Rfree=21/26% (about 370 HOH for 360 residues). After 10 cycles of refmac refinement (wt 0.3), Rwork/Rfree went up about 1.5% to 22.5/27.5%. I did some minor adjustments and add/del

Re: [ccp4bb] Protein-DNA complex for crystallization

Hi Kumar, I also have the same issue. If you get any helpful response, could you forward me a copy? Thank you. P.S. Could anyone who has any comments or suggestions on this issue also forward the response to ccp4bb? Thank you in advance. Best, Joe On 7/16/07, bputcha <[EMAIL PROTECTED]>

[ccp4bb] Fwd: extend resolution in refmac

Dear all, I am refining a structure in Refmac at 2.3 A and I set resolution range to 2.2 A to extend the resolution. However, Refmac seemed to ignore my setting and still refined structure at 2.3 A. Thank you in advance for your any helpful suggestions. Best, Joe

[ccp4bb] extend resolution in refmac

Dear all, I am refining a structure in Refmac at 2.3 A and I set resolution range to 2.2 A to extend the resolution. However, Refmac seemed to ignore my setting and still refined structure at 2.3 A. Thank you in advance for your any helpful suggestions. Best, Joe