Re: [ccp4bb] Bad density for chains

2017-01-27 Thread Pooja Kesari
the assigned space group and assess whether another choice > might also be possible. > > > > Good luck! > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Pooja Kesari > *Gesendet:* Donnerstag, 26. Januar 2017 15:1

Re: [ccp4bb] Bad density for chains

2017-01-26 Thread benjamin bax
You could try the diffraction anisotropy server: http://services.mbi.ucla.edu/anisoscale/. Sometimes it helps maps become more interpretable. Ben On 26 Jan 2017, at 14:11, Pooja Kesari wrote: We have a 2.6 A structure showing four chains in an asymmetric unit. Our protein is 360 res

[ccp4bb] AW: [ccp4bb] Bad density for chains

2017-01-26 Thread Herman . Schreuder
Kesari Gesendet: Donnerstag, 26. Januar 2017 15:12 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Bad density for chains We have a 2.6 A structure showing four chains in an asymmetric unit. Our protein is 360 residues around 40 kDa . Mattews shows four chain in an assymetric unit (solvent 49

Re: [ccp4bb] Bad density for chains

2017-01-26 Thread Eleanor Dodson
Well - first Solvent content.. 1) there could be 4 molecules, or 3, or 2.. Solvent content varies a lot as you know. Is there reasonable density for parts of all the chains? 2) Does the MR search clearly show 4 molecules? ie improvement in scores with extra molecules? 3) Have you checked for sen

Re: [ccp4bb] Bad density for chains

2017-01-26 Thread Pavel Afonine
Hi, assuming you've exhausted modeling choices and applied proper refinement strategies, after all Rree=32% is not unheard of at 2.6A resolution (which actually may be even worse than 2.6A if data set is not 100% complete). Have a look at R-factors of models in PDB with data resolution around 2.6A

Re: [ccp4bb] Bad density for chains

2017-01-26 Thread Pooja Kesari
We have a 2.6 A structure showing four chains in an asymmetric unit. Our protein is 360 residues around 40 kDa . Mattews shows four chain in an assymetric unit (solvent 49% mattews coeff 2.44). The template has about 60% homologous with our protein. The molecular replacement against this template g

Re: [ccp4bb] Bad density for chains

2017-01-26 Thread Eleanor Dodson
This is a bit too vague to help much. How did you solve the structure? Eleanor On 26 January 2017 at 03:50, Pooja Kesari wrote: > Dear All, > Thank you all for reply. > > We have checked the data for twinning. > Our protein is 360 residues around 40 kDa protein. > We have tried TLS refinement. >

Re: [ccp4bb] Bad density for chains

2017-01-25 Thread Pooja Kesari
Dear All, Thank you all for reply. We have checked the data for twinning. Our protein is 360 residues around 40 kDa protein. We have tried TLS refinement. chain A and B don't superimpose well with chain C and D. (A and B chains also share slight difference ) Since we don't have proper density for

Re: [ccp4bb] Bad density for chains

2017-01-25 Thread Phoebe A. Rice
CP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bad density for chains Dear All, I have a 2.6 A resolution structure having four chains in an asymmetric unit. The chain A and B have density for almost all residues however we don't have proper residue density in chain C and D.What can be tried to bui

Re: [ccp4bb] Bad density for chains

2017-01-24 Thread Debanu
Hi Pooja, Are you positive you have the correct space group and there are no other issues like twinning, etc? If sure, did you define NCS groups in refinement? TLS refinement? Try different refinement programs? How big is the molecule? Was it solved by MR or experimental phasing? You can try

[ccp4bb] Bad density for chains

2017-01-24 Thread Pooja Kesari
Dear All, I have a 2.6 A resolution structure having four chains in an asymmetric unit. The chain A and B have density for almost all residues however we don't have proper residue density in chain C and D.What can be tried to build chain C and D ? Many Thanks Pooja