[ccp4bb] Issues with Phenix refinement

Dear all, I am trying to fit Cd in a protein structure using Phenix. However, the refinement returns me a result with DC (2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also,

Re: [ccp4bb] Off topic: denaturing urea gels

Dear all, Thanks for all the replies. I adjusted my volumes and stopped reactions with 8 M urea and 25 mM EDTA. The gels now run fine :) -Mohammad On 05-Oct-2017 7:29 PM, "Phoebe A. Rice" wrote: > Even though the protein should be denatured by all that urea, we find such >

[ccp4bb] Off topic: denaturing urea gels

Dear all, I am working with an exonuclease and I run the digested DNA on a 8Murea-20%acrylamide gel in TBE buffer. I use the Mini-Protean BioRad system and cast gels of about 8.6x6.5 cm dimensions with 1.5 mm thickness. I use a 15 well comb. I run my gels at 70 V for as long as 4 hours till my

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=TE > > Invention, my dear friends, is 93% perspiration, 6% electricity, 4% > evaporation, and 2% butterscotch ripple. ~Willy Wonka > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Mohammad &g

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

t; What is your difference between the maximum and minimum value ? Have you > try to change the probe concentration? > > Best, > > Didier > > Le 21 juil. 2017 15:34, "Mohammad Khan" <mohdkhan0...@gmail.com> a écrit : > > Dear all, > > I am trying to meas

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

clude a good control, e.g. DNA with Cy3, but sequence that does not bind > to test for nonspecific, concentration dependent effects. > I hope this helps, if you have any questions, feel free to email me! > Best, > Julius > > > > On 21 Jul 2017, at 15:32, Mohammad Khan <mo

[ccp4bb] Off topic: Flourescence anisotropy measurement

Dear all, I am trying to measure the difference in polarization upon the binding of the DNA to my protein. I take 1-5 nM of Cy3-labelled DNA and add varying dilutions of my protein to it (100 microM to 1 nM). I do get a decrease in difference of polarization with decrease in protein

Re: [ccp4bb] Problems with an exonuclease

, 2017 at 3:36 PM, Mohammad Khan <mohdkhan0...@gmail.com> wrote: > Dear all, > > I am working with an exonuclease by refolding it from inclusion bodies > (IBs). I tried various constructs and hosts, but couldn't get it in soluble > form. > > I lyse my cells using a cell disru

[ccp4bb] Problems with an exonuclease

Dear all, I am working with an exonuclease by refolding it from inclusion bodies (IBs). I tried various constructs and hosts, but couldn't get it in soluble form. I lyse my cells using a cell disruptor and after solubilizing IBs with urea, I refold the protein by rapid dilution and get an

[ccp4bb] Auto-proteolysis

Dear all, I am working on a His-tag recombinant protein with two domains, which I purify using affinity chromatography. When I set up crystallization of the same, it gave me crystals in two different conditions- one was the complete protein. The other just had the Domain2. Even on SDS-PAGE, I

[ccp4bb] Online server for generation of topology cartoons

Dear all, Is there any good online server for the generation of topology cartoons of proteins, where one can have a clear layout of the various secondary structures? I have tried Pro-Origami, but however I am not veru happy with the output. I have used the default options. Maybe if someone can

Re: [ccp4bb] Online server for generation of topology cartoons

Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 20 May 2015, at 11:50, Mohammad Khan wrote: Dear all, Is there any good online server for the generation of topology cartoons

[ccp4bb] Deletion of hydrogens

Dear all, I have added hydrogens on my molecule using the Refmac option in Coot. I now want to remove them. I tried various syntax but they didn't work. Is there a simple way to remove them from the pdb? Moreover, if I do my refinemnets with hydrogens in it, will it affect my results, other than