Re: [ccp4bb] problem with pdb its symmetry molecule

Dear Ramanuj Banerjee, from the attached picture it is difficult to make out N- and C-terminus of your protein and it looks like two closed molecules intertwined- which would indeed be very surprising. However, if you think there is space for the molecules to form such a homodimer (either in

Re: [ccp4bb] problem with pdb its symmetry molecule

Yes, its surely possible. If there are no clashes start thinking if this dimer is the physiological molecule in solution. Check probability that this dimer is stable in solution in Pisa - ebiFold If so, check first with size exclusion columns if it behaves like dimer in solution, preferably

Re: [ccp4bb] Using chaperones to boost expression in E. coli

Michael, We have put together a review about use of folding modulators to improve expression in E. coli some time ago which might be useful to you (Kolaj et al Microb Cell Fact. 2009 Jan 27;8:9). Here is the link: http://www.ncbi.nlm.nih.gov/pubmed/19173718

Re: [ccp4bb] problem with pdb its symmetry molecule

Ramanuj, This is definitely possible. Cases of intertwined homodimers are rare, but there are several known structures that demonstrate this phenomenon, and they are very interesting (especially with respect to studying knotted proteins - see reference below). Examples are pdb IDs: 2ouf, 1myk,

Re: [ccp4bb] problem with pdb its symmetry molecule

Ramanuj, This is definitely possible. Cases of intertwined homodimers are rare, but there are several known structures that demonstrate this phenomenon, and they are very interesting (especially with respect to studying knotted proteins - see reference below). Examples are pdb IDs: 2ouf, 1myk,

Re: [ccp4bb] problem with pdb its symmetry molecule

This intertwined conformation is very possible and is reminiscent of Trp repressor (at least in the view you provided). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype:

Re: [ccp4bb] problem with pdb its symmetry molecule

Dear All, Thank you for your kind reply. After reading the suggestions, I too think that this is the solution. Thank you once again.

[ccp4bb] Mock Dataset

My PI has mentioned a Mock Dataset made available by the ACA for various programs (HKL etc) to practice with, but I haven't been able to find it and was wondering if anyone knew of any, Thanks, Peter Randolph

Re: [ccp4bb] Mock Dataset

On Tue, 2011-04-26 at 08:48 -0400, Peter Randolph wrote: My PI has mentioned a Mock Dataset made available by the ACA for various programs (HKL etc) to practice with, but I haven't been able to find it and was wondering if anyone knew of any, Thanks, Peter Randolph If you are looking for

Re: [ccp4bb] Mock Dataset

Dear Peter, Perhaps your PI is referring to the collection of datasets and tutorials being compiled at the following link. Raw data (diffraction images) are available for various datasets exhibiting different challenges and tutorials, put together by the authors of various

[ccp4bb] Workshop Diffraction Data Collection Using Synchrotron Radiation - Deadline approaching

Please note that there is only a few more days left to register for the workshop announced below. Manfred After the successful first two workshops on Diffraction Data Collection Using Synchrotron Radiation, which took place in 2007 and

[ccp4bb] In XDS, anomalous correction column has negative values

Dear All: What does it mean when I get negative values under Anomalous Corr column after running XDS? I set the Friedel Law=False even though I suspect that my signal is very very weak. Thanks Subbu

[ccp4bb] Phenix refine has a problem with the added H, plz help

Dear All, I normally refine my structure without the hydrogens until the final stages. But today I'm facing a real trouble with phenix.refine!! It seems phenix.refine does not recognize the hydrogen atoms and writes out this message: Fatal problems interpreting PDB file: number of atoms with

Re: [ccp4bb] Phenix refine has a problem with the added H, plz help

Dear Mohd, FYI: there is specific mailing list for PHENIX specific questions ( http://phenix-online.org/). Pavel. On Tue, Apr 26, 2011 at 10:56 AM, Salameh, Mohd A., Ph.D. salameh.m...@mayo.edu wrote: Dear All, I normally refine my structure without the hydrogens until the final stages .