Re: [ccp4bb] how to remove part of data with bad signal to noise ratio

Dear Dale, For me, a high quality map is a map which clearly shows where the model is correct and where adjustments are needed, e.g. in places where the search model is different from the structure to be solved and in places where the model is missing. This is not the same as a difference in

Re: [ccp4bb] Peptide Crystallization

NMR ... synthesize with a few labeled aa according to taste of local NMR guru. If they cant do a15-aa peptide in a day, let the bb know, it will be entertaining ;-) A. On May 25, 2011, at 14:04, Buz Barstow wrote: Dear all, I am considering trying to crystallize a small peptide (around

Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?

Thank you for replies. I understand that real space refinement using maps generated by REFMAC doesn't affect cross validation. I found the documentation of REFMAC about this topic. http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#mapcalc Oops, I should have found this earlier.

Re: [ccp4bb] Peptide Crystallization

I would discourage using pre-made screens on a project outside the norm. The main problems are: Zinc: At mM concentrations will easily crystallize and give false positives in many screens. It will also act as a precipitant for the peptide. The best approach would be to separate the zinc adduct

Re: [ccp4bb] Peptide Crystallization

You could also consider organic solvents (or a mix) for crystallisation trials too. If you scan through the literature you will find that small peptides have in the past been treated as small molecules in terms of crystallization. Once the peptide gets over say 20 amino acids (not the exact

[ccp4bb] Position available at Syngenta

Protein Crystallographer Jealott's Hill, Bracknell, Berkshire, UK We are looking for a postdoctoral fellow with a PhD in biochemistry or equivalent who is enthusiastic about working across the range of protein crystallography activities, from protein production to structure refinement of

[ccp4bb] Software for Conserved Solvent

Dear Crystallographers, does anyone know of a program to compare multiple structures and identify which solvent molecules (water, ions, etc.) are conserved between the structures? I guess it would be nice also if it could identify when, for example, a Cl- in structure A was re-occupied by an HOH

Re: [ccp4bb] Software for Conserved Solvent

Hi Jacob, On Wed, 2011-05-25 11:58 EDT, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, does anyone know of a program to compare multiple structures and identify which solvent molecules (water, ions, etc.) are conserved between the structures? I guess it would

[ccp4bb] Problem running WinCoot

Hey Everyone, I am having some problems running Probe Clashes on WinCoot. I am running phenix.refine to obtain the pdb file and then WinCoot for manual building. I have the following installed: WinCoot (6.0.1), probe (2.12.110413) and reduce (3.14.080821) REDUCE_HET_DICT points to

[ccp4bb] PreScission Protease protein sequence

Dear All, I apologize for a non-crystallography question, but does anyone know the sequence of the PreScission Protease? I would like to make it for use in my own lab. It is just too expensive to purchase from GE! Thanks ray

[ccp4bb] off topic question

Hi, A nuclear receptor is purified only in the presence of strong affinity bound ligand. Is there some method to study and quantitate binding affinities of this protein with other ligands (it is bound to the high affinity ligand after purification)? Attempts to purify in presence of low affinity

[ccp4bb] Pymol question

Hi everyone, I have two questions: 1- Does anybody know what are the units on the display ruler after you calculate the vaccum electrostatics using pymol? 2- What are the default kT/e values used by pymol? Thank you, Maher

Re: [ccp4bb] PreScission Protease protein sequence

Dear All, Thanks to all who replied me so quickly. In case you do not know, like myself until a few hours ago, that this protease is also known as the 3C protease from human rhinovirus. Thanks to Dima, the sequence is here if anyone is interested: gpeheflnal irrnchiitt dkgefnllgi ysncavvpth

Re: [ccp4bb] PreScission Protease protein sequence

Dear BBlers, Would the kind donor of the prescission protease plasmid be willing to share another round? I would love to make this stuff in the lab... Best wishes Marc On 26/05/11 12:04 PM, Lieh Yoon Low liehy...@gmail.com wrote: Dear All, Thanks to all who replied me so quickly. In case

[ccp4bb] Histogram/Plot of Buried Surface Areas

Dear Crystallographers, is anyone aware of a reference or plot addressing buried surface area (or PISA output values) versus veracity of a complex? I am trying to determine the physiological relevance of a crystallographically-observed assembly, and would love to put my PISA output in the context

Re: [ccp4bb] PreScission Protease protein sequence

You all might want to be careful about patent infringements, if such exist for prescission. At least don't flaunt it on a BB... JPK On Wed, May 25, 2011 at 9:29 PM, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Dear BBlers, Would the kind donor of the prescission protease plasmid be