[ccp4bb] Problem in molecular replacement

2014-07-24 Thread dusky dew
DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in

Re: [ccp4bb] Problem in molecular replacement

2014-07-24 Thread Antony Oliver
Try using DNA as a search model - this has worked very successfully in our hands before. Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton,

Re: [ccp4bb] Problem in molecular replacement

2014-07-24 Thread Randy Read
In addition to that good suggestion, with a model at such high sequence identity and with reasonable resolution data, it would be a good idea to search for smaller models, like a single dimer or even a monomer, because the assembly may have changed conformation. Another possibility you should

Re: [ccp4bb] Problem in molecular replacement

2014-07-24 Thread dusky dew
] Envoyé : jeudi 24 juillet 2014 13:50 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Problem in molecular replacement DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has

Re: [ccp4bb] Problem in molecular replacement

2014-07-24 Thread FOOS Nicolas
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Problem in molecular replacement DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity

Re: [ccp4bb] Problem about Molecular Replacement with identity 30% model

2009-06-23 Thread Martyn Winn
30% is getting difficult - it may or may not work. But it is worth trying. Search model preparation programs such as Chainsaw rely on an accurate sequence alignment (between model and target), and this also gets difficult at 30%. You should try something more sophisticated than simple pairwise

Re: [ccp4bb] Problem about Molecular Replacement with identity 30% model

2009-06-23 Thread Frank Murphy
Hey! I have found the FFAS server ( http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl ) to build the best models for low homology MR searches. A relevant paper: 2004 Acta Cryst D60 1229-1236. Best of luck, Frank 2009/6/21 孙建 sunjian00...@gmail.com Dear all: Recently,I have a problem

Re: [ccp4bb] Problem about Molecular Replacement with identity 30% model

2009-06-22 Thread junfeng liu
孙建 wrote: Dear all: Recently,I have a problem about molecular replacement with identity 30% model. There are two moleculars in AU.Through self-rotation analyze,there are a two-fold axis in AU along X axis or Z axis.Then I rotate and translate the model with CNS MR module. several

Re: [ccp4bb] Problem about Molecular Replacement with identity 30% model

2009-06-22 Thread Mark J. van Raaij
Dear Sunjian, what is important is the structural similarity of your model to the unsolved structure, for instance in r.m.s.d - of course, this cannot be determined until you have solved the structure! The % identity is only an indication of how similar the structures may be, sometimes

[ccp4bb] Problem about Molecular Replacement with identity 30% model

2009-06-21 Thread 孙建
Dear all: Recently,I have a problem about molecular replacement with identity 30% model. There are two moleculars in AU.Through self-rotation analyze,there are a two-fold axis in AU along X axis or Z axis.Then I rotate and translate the model with CNS MR module. several models have been