Re: [ccp4bb] pdb file deposition

2010-03-12 Thread Vellieux Frederic
Hi, What happens usually is that some solvent atoms are in fact closer to a symmetry-related molecule than the one you are working on. The PDB has programs to reposition these water molecules closer to the "correct" macromolecule or subunit, and they will provide you with the modified waters

[ccp4bb] Any simple way to scale 2 MTZ?

2010-03-12 Thread Francois Berenger
Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallograph

Re: [ccp4bb] Any simple way to scale 2 MTZ?

2010-03-12 Thread Graeme Winter
Hi Francois, SCALEIT in CCP4 sounds like the tool you want - this is for scaling e.g. native and derivitive data sets together. You will need to cad together the two files first though. This is illustrated in the tutorials here: http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-ma

[ccp4bb] protein crystallization problem

2010-03-12 Thread Xingding Zhou
Dear All, I have several proteins that share a common problem. When crystallization, once the precipitant is PEG, the protein will be precipitated in seconds. Even the protein concentration is just 2 mg/ml. But if the precipitant is salt such as NH2SO4. The drop is clear for months, even high

Re: [ccp4bb] Any simple way to scale 2 MTZ?

2010-03-12 Thread Francois Berenger
Graeme Winter wrote: Hi Francois, SCALEIT in CCP4 sounds like the tool you want - this is for scaling e.g. native and derivitive data sets together. You will need to cad together the two files first though. My crystallographer colleague tells me that if we use scaleit there is a risk if there

Re: [ccp4bb] Any simple way to scale 2 MTZ?

2010-03-12 Thread Graeme Winter
Hi Francois, As I understand this, they (the F's) should be already on an "absolute" scale as determined by the Wilson stats as TRUNCATE does this scaling. What SCALEIT does is to scale the data sets together in terms of an overall (or anisotropic) temperature factor and overall scale, so that the

Re: [ccp4bb] protein crystallization problem

2010-03-12 Thread junfeng liu
Have you ever tried the condition of AS as precipitant and PEG as the additive? They have opposite functions on your protein's solubility:one increases and decrease it. Maybe you can vary the ratio of them to control your protein's solubility. And the xtals may be seen in some conditions. Go

[ccp4bb] Soaking at pH 4.0 ?

2010-03-12 Thread Paul Lindblom
Hi, I am trying to soak some sugars in my crystals, but the cystallization condition has a pH of 4.0. Does anybody has any experience with acidic oxidation in such a case. I think I can´t avoid oxidation at this pH? Any suggestions, or do I have to screen for other conditions? Thanks, P.

Re: [ccp4bb] Soaking at pH 4.0 ?

2010-03-12 Thread Nathaniel Clark
Hi, I have soaked various crystals at that pH with various sugars and never had a problem with oxidation of the sugar. I wouldn't worry about it. What group do you think will be oxidized? Nat On Fri, Mar 12, 2010 at 5:35 AM, Paul Lindblom wrote: > Hi, > > I am trying to soak some sugars in my

[ccp4bb] pdb dep

2010-03-12 Thread Azadeh Shahsavar
Dear all, in the process of pdb file deposition, after some error removal, suddenly pdbdep made errors on the "covalent bond angles" of all PRO residues. Does any one has any suggestion? :( Regards, Azadeh

[ccp4bb] Postdoctoral position at NIH: Membrane-associated protein complexes

2010-03-12 Thread Jim Hurley
A postdoctoral position is available for a skilled protein crystallographer interested in challenging projects in the Hurley lab, NIDDK, NIH. We are seeking to understand the structure and function of membrane-associated multiprotein complexes involved in protein and lipid trafficking. Some of the

[ccp4bb] phenix target weight refinement

2010-03-12 Thread Salameh, Mohd A., Ph.D.
Dear All, In every refinement round the wxc and wcu are out of control, although I modify the def file and change the values of wxc=1 and wxu=1 so they are tightly restrained, but it failed to fix the problem, wxc and wxu values keep fluctuating, in my latest refinement round wxc=256!! wxu=3. T

Re: [ccp4bb] Soaking at pH 4.0 ?

2010-03-12 Thread Maia Cherney
Could you transfer your crystals in a higher pH buffer? Maia Paul Lindblom wrote: Hi, I am trying to soak some sugars in my crystals, but the cystallization condition has a pH of 4.0. Does anybody has any experience with acidic oxidation in such a case. I think I can´t avoid oxidation at this

Re: [ccp4bb] phenix target weight refinement

2010-03-12 Thread Salameh, Mohd A., Ph.D.
Yes Im using wxc_scale and wxu_scale but I also use tls refinement,so in this case if the weights need to be tightly restrained, I should not use tls refinement! ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San

[ccp4bb] inexpensive source of DDM

2010-03-12 Thread Tony Wu
Hello, I am looking for an inexpensive US source for large quantities of dodecylmaltoside. Can anyone help me? Thank you!

[ccp4bb] Computational Systems Biology Postdoctoral Positions

2010-03-12 Thread Jessica Gilmore
Computational Systems Biology Postdoctoral Positions Center for the Study of Systems Biology at the Georgia Institute of Technology Outstanding Postdoctoral applicants are sought in Computational Systems Biology to work with Professor Jeffrey Skolnick at the Georgia Tech Center for the

Re: [ccp4bb] inexpensive source of DDM

2010-03-12 Thread Edward A. Berry
You get what you pay for, and this is not a cheap detergent! If your application is not sensitive to a little bit of the alpha- anomer, try Anatrace sol-grade, 25 g for $803.01: http://www.affymetrix.com/estore/browse/brand/anatrace/product.jsp?productId=131630&categoryId=35662#1_1 If you find som

Re: [ccp4bb] phenix target weight refinement

2010-03-12 Thread Nian Huang
Which version did you use? I remember the old version of phenix (1.3) will automatically change your setting (wxc and wxu) each round. And v1.5 will automatically choose wxu if you use tls. I haven't tried 1.6 yet. Maybe there are some bugs associated with it? The default wxc is 0.5 and wxu is 1. S