[ccp4bb] Research Scientist at Accelagen, San Diego CA, USA

Accelagen (http://www.accelagen.com/) a fast growing gene-to-protein company providing protein expression and purification services. We are seeking a highly motivated Ph.D scientist to fill a full-time Research Scientist position for recombinant protein expression and purification. Extensive experi

[ccp4bb] Post-doctoral Fellowships at the University of Texas

*Macromolecular Crystallography, Biophysics and Biochemistry* Two post-doctoral fellowship positions are available at the University of Texas Medical Branch (UTMB) located in the greater Houston area in the research team of Dr. Gabrielle Rudenko. We study molecules that mediate the formation, mai

[ccp4bb] Postdoc position available at the Clare Hall Laboratories, Cancer Research UK

Dear all, a postdoc position is available now at the Clare Hall laboratories, London Research Institute, Cancer Research UK. Best Alessandro About the job A postdoctoral position is available at the Clare Hall Laboratories, Cancer Research UK, in the research team of Dr. Alessandro Costa.

Re: [ccp4bb] SA-omit map

Maybe try CNS or SFCheck: http://groups.yahoo.com/neo/groups/cnsbb/conversations/messages/1720 To improve Phenix maps, maybe try increasing the number of boxes (the parameter IIRC "n_box_target=" ) http://www.phenix-online.org/documentation/autobuild.htm In CNS, you can decrease the starting temp

Re: [ccp4bb] SA-omit map

I have two bits of advice. 1. If the SA omit map for the ssDNA is "really bad", perhaps you should reconsider whether your model is a faithful representation of the experimental data. 2. You could use anomalous difference Fourier analysis to locate the P atoms of the DNA backbone. We did thi

Re: [ccp4bb] SA-omit map

Hi Deng - Can you tell why the reviewer was asking for the SA-omit map? Is there some doubt about the conformation of your ssDNA, or even whether it is present in the first place? Is there a question about the sequence, or the sequence register (which nucleotides go in which positions)? Ev

Re: [ccp4bb] SA-omit map

Hi Deng, > Recently, I received the comments from referees, they asked for the > SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated > annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven > thymidine nucleotide. Our data diffracted to 2.65A，but th

Re: [ccp4bb] Comparison of Water Positions across PDBs

Thanks Bernhard    you have helpfully distinguished between the two processes - there is certainly a movement of waters to symmetry replacements closer to a chain - and that gets documented in Remark 525 of the PDB file returned to authors - although then it is stripped out, I think, before the

Re: [ccp4bb] Comparison of Water Positions across PDBs

As far as confusion as a result of PDB renumbering is concerned: It was useful to run the old REM525 standalone program (I think I got it from PDBe/Kim Hendrick) at the end of solvent building. It does what the PDB did with water renumbering when creating the REMARK 525 (probably based on ccp4 cont

[ccp4bb] International Conference Membranes and Modules 2014

Dear all, Some of you might be interested in our international conference "Membranes and Modules" which takes place in Berlin from March 26-29, 2014. We have a fantastic list of speakers with many structural biology talks around the topics of protein quality control, plasma membrane scaffold

Re: [ccp4bb] Comparison of Water Positions across PDBs

Thank you for that, Rachel Even though the tone of your comment does not suggest that you want to carry on a dialogue about this, I thought I would reply in any case - since dialogue is what this forum is supposed to be about. Thing is,  I was sort of looking for an explanation of why the rule

[ccp4bb] Available Faculty Position at Purdue University

Dear Colleagues, I want to bring this position to your attention: Faculty Position in Structural Biology Purdue University The Department of Biological Sciences and the Markey Center for Structural Biology at Purdue University invite applications for a tenure-track faculty position in Structura

Re: [ccp4bb] SA-omit map

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear zq Deng, you may actually have some anomalous signal from the P-atoms in your structure, even if you collected at short wavelength - if you have a data set collected at, say, 1.5A, it would be even stronger. In that case you could create an anom

Re: [ccp4bb] SA-omit map

What does a straight difference map look like? i.e. omit one nucleotide at a time, do a few cycles of refinement and then inspect the weighted difference map - SA may be too violent for your structure. Eleanor On 4 Nov 2013, at 06:36, dengzq1987 wrote: > Dear all, > > Recently, I received th