[ccp4bb] MrBUMP

Hi everyone, I am trying to run MrBUMP through the CCP4 6.1.1 but the program is complaining that no multiple alignment programs like mafft, clustalw, clustalw2, probcons, or t_coffee were found on the system. Will I need to install all these programs and will they need to be in the CCP4 director

[ccp4bb] selenomethionine labeled protein expression in insect cells

Hi everyone, I am looking for a method for expressing selenomethionine labeled protein in insect cells. Can anyone point me to a suitable protocol ? Additionally, is anyone aware of companies that may provide this service for a fee ? Thanks

Re: [ccp4bb] Phasing at Low Resolution

I have two questions regarding derivatization: (i) Is there a pH dependence to making derivatives ? i.e. effectiveness of getting derivatives at low vs high pH ? (ii) Any thoughts on the effectiveness of Barium for phasing low resolution structures (especially for magnesium binding proteins ) ???

[ccp4bb] predicted secondary structure based alignment

hello everyone, Is there a good program to align two sequences based on their predicted secondary structure...something that could be useful to align low homology sequences ? Thanks

[ccp4bb] ANISOU

Hello Everyone, I am trying to refine a structure with CNS. The initial model consists of protein with ANISOU B factors. However, when I run generate, the program crashes with the message %COOR-ERR: unrecognized command: ANISOU ^^ I want to keep the aniso B factors since the resolution of my

[ccp4bb] restraints in refmac

Hello everyone, I have two ligands in my structure that I need to keep at a specific distance from each other. How can I specify this restraint in refmac ? Thanks

[ccp4bb] Transfer Rfree flag

Hello: Can someone tell me if there is a relatively straightforward way of transferring Free R flags between two CNS format reflection files ? Thanks

[ccp4bb] Ab initio structure prediction

Dear All, I will be very grateful if someone can point me to a program for ab initio structure prediction of small peptide fragments (50-100 amino acids). Thanks Riya

[ccp4bb] summary: crystals from skin

are grown at 18 or RT (vi) Lower protein concentration and (vii) Fiddling around with the drop which may break the skin and free the crystals On Sun, Dec 28, 2008 at 8:24 PM, riya doreen wrote: > *Hello All, > > I am trying to optimize protein crystals that grow from skin. All eff

[ccp4bb] crystals from skin

*Hello All, I am trying to optimize protein crystals that grow from skin. All efforts to separate crystals from skin have failed since it is fairly thick. Crystallization under oil eliminates skin but the resultant crystals are very thin and small needles. I would appreciate any suggestions on ho

[ccp4bb] 3D modeling program

Hello everyone, I am looking for a modeling program that will allow me to input a sequence alignment and coordinates of a template for 3D structure prediction of a target molecule. I know Modeller can do the job. Are there other web based programs that can do the same ? Thanks