Re: [ccp4bb] Average B-factor

Dear Dhana, Calculate average B for each chain? You could try baverage (in CCP4). Best, Xun Sent from my iPhone On Aug 30, 2013, at 5:45 PM, Dhanasekaran Varudharasu wrote: > > Dear crystallographers, > > I need to complete my crystal-data table. S

Re: [ccp4bb] Pisa application

Hi Careina, I asked the exactly same question in this year's CCP4 summer school @APS, and the answer I got was "no ... PISA is not for predicting...". Cheers, Xun Sent from my iPad On Aug 8, 2012, at 2:33 AM, Careina Edgooms wrote: > Dear ccp4ers > > I just wonder whether anybody

[ccp4bb] Do my SAXS data agree with the crystal structure?

Dear all, I have solved a protein-DNA structure, and I also did SAXS to get some ideas of the solution structure. The SAXS data were good, no aggregation at all three tested concentrations. I tried to use Crysol to see if my crystal structure fits the SAXS. The fitting to the scat

Re: [ccp4bb] Off-topic: Site-directed mutagenesis

Hi, Theresa, Our lab uses Phusion high-fidelity DNA polymerase. It might not be better though. Regards, Xun Sent from my iPad On Apr 17, 2012, at 5:53 PM, Theresa Hsu wrote: > Dear all > > I would like to get some opinions on site-directed mutagenesis. What are the > current methods

[ccp4bb] pdbcur wont remove hydrogens on the residues that have alternative conformations

Just want to point this out although it's pretty easy to remove these hydrogens manually... Or, maybe this only happened to me. Xun -- Department of Molecular and Structural Biochemistry North Carolina State University

Re: [ccp4bb] DNA length for crystallization

Hi Lisa, I will second James' suggestion. DNA packing seems really important, and making the DNA length as X half turns is usually good for packing (X=2, 3, 4 ...). Another thing you might want to try is Hoogstein base pairing. Cheers, Xun On Wednesday, February 15, 2012, James Stroud wrote: >

Re: [ccp4bb] DNA in coot

Hi Lisa, Please go check your PDB file. Are those bases written out like "DT" or "THY" or "Td". Coot recognizes certain format for DNA bases but I forgot which one coot likes. I don't have my laptop with me right now. My guess would be "Td". :) Best, Xun On Wednesday, February 15, 2012, LIS

[ccp4bb] Faculty position in X-ray crystallography at NC State University

Dear all, The link is: http://biochem.ncsu.edu/ad.php "The Department of Molecular and Structural Biochemistryat North Carolina State University invites applications for a tenure-track faculty position in X-ray crystallography, with preference given to candidates at the

[ccp4bb] EMSA: non-specific binding is quite strong ??

Dear all, I have a protein-DNA crystal structure, and am doing EMSA to confirm the protein-DNA interactions that I am seeing in the structure. I am using IRD dyes, which can be analyzed by Odyssey system (LiCor). The Kd is estimated to be around 2nM (assayed with 0.3nM probe and 1-1

Re: [ccp4bb] Help! low resolution protein-DNA complex

Thank you!! It's really encouraging & refreshing to begin a day with so many advices! ccp4bb is always helpful~ Thanks to one of my committee member who suggested me to get out a paper from the structure, and thanks to all the people at the mid-Atlantic crystallography meeting who told me my struct

[ccp4bb] Help! low resolution protein-DNA complex

Hi, I have a 3.2A dataset for a protein-DNA complex. The protein is a homodimer, and the DNA is almost palindromic (except one base pair in the middle and two or three base pairs at both two ends). It is my first time solving structures, and unfortunately the resolution is low. No body in ou

[ccp4bb] Perfect crystals but Low resolution

Dear All, I took over this project last September. Since the information in the lab are not well managed, it's kind of starting over (WRONG plasmids sequences; even WRONG oligo length/sequence in the complex which has been successfully crystallized. Those crystals only gave low resolution da

[ccp4bb] how to deal with the DNA in Refmac?

Dear all, I am dealing with a protein/DNA complex. After restrained refinement in Refmac, the bases have been brought closer to each other (about 2A instead of 3A for H-bonding). But in our model, the geometry of the DNA is fine (I even replaced my DNA with theirs by superimposing and edi

[ccp4bb] cannot find the other molecule in the asymmetric unit

roblem of missing density for DNA still exists... Maybe I haven't described my problem clearly... sorry for bottering... Any suggestion and comment are welcome. Thanks! Xun Lu Department of Molecular and Structral Biochemistry North Carolina State University

[ccp4bb] How to install Mapslicer into CCP4?

r. I couldn't find the installation files for MapSlicer. So how to install it into CCP4? Or, How do you view patterson maps? Thanks, Xun Lu Department of Molecular and Structural Biochemistry North Carolina State University