[ccp4bb] Density is not clear

Hi all !! I am working with two data sets of same protein (130a/a) with resolutions 2.8 and 3.2 A. In both the cases the density for 100-130 aa is not very clear.. it forms couple of helices.. i can see a long tube going but it is feature less.. It is a MR solution.. i have tried TLS refinement

Re: [ccp4bb] CCP4 & Coot on Ubuntu

synaptic for lib32 package lib32stdc++6 helped me over a > similar problem. You may need others. > > m > > > On Tue, 2008-06-10 at 20:16 +0530, john kryst wrote: > > Thanks Tim that worked fine.. my ccp4i interface is starting but the > > programs are not running... i have

Re: [ccp4bb] CCP4 & Coot on Ubuntu

Thanks Tim that worked fine.. my ccp4i interface is starting but the programs are not running... i have RH 8 binaries... even when i tried to run in the command line for example go to $CCP4/bin and try ./pdbset or whatever it may be it is telling command not found.. i am sure that i have sourced th

[ccp4bb] CCP4 & Coot on Ubuntu

Hi all !! Sorry for the off topic question. Has anyone tried installing CCP4 and coot in Ubuntu Heran Hardy 64 bit... I have been googling and tried the suggestions of Bill & Martyn's page... but no success with the amd 64 bit machine.. all the instructions i get are for 32bit machines.. P

[ccp4bb] Off Topic:Docking

Dear ccp4 Community, I am sorry for the off topic question. As you all aware there are many docking programs available from commercial vendors/. And everyone claims that their product is the best in the business. Here i would like to ask for some experiences from this wonderful commun

Re: [ccp4bb] Twinning

Hi CCP4bb , Thanks for your suggestions... here is the summary of the structure... I am working in deletion and point mutants. I have a mutant (P61 resoln 3.1A) with partial twinning with twinning fraction 0.28. Wilson b-factor is 50. The data collected in the home source with norma

[ccp4bb] Twinning

Hi ccp4bb !! I am refining a 3.1 A resolution structure which has partial twinning with twinning fraction 0.27 (space group P61). When i refined in CNS with twin_lsq target i got 0.1529 and 0.2384 as R and Rfree. There is almost 8-9% gap in R and Rfree. Map quality is good enough to trace al

[ccp4bb] bfactor, freeR problems!!

Hi all !! I am working on some deletion mutants. Mutants crystallized in the same space group with similar cell dimensions. My questions are the following?? 1. Is the free R flag has to be maintained across all the mutants with respect to the native. 2. Does B-factor has to be flatte

[ccp4bb] Phaser question !!!

Hi all !!! Is it possible to fix one domain and search for the second one in phaser !!! What are the keywords to use. I have a protein with two domains. It i give both the domains together or as two ensembles it is not finding the solution. If i give only one domain it is giving the soluti

[ccp4bb] RMSD

Hi ccp4bb !!! Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program we use ?? Example : shifting from Refmac to CNS. There appears to be an increase in rmsd of bonds even without refining the structure in CNS. Is the estimation methods are different or am i doing something wrong