Re: [ccp4bb] Glycoprotein expression question

We had experience with a relatively small glycoprotein - when glycosylation sites were deleted, solubility went drastically down - we could not express soluble any more. Back to eukaryotic expression system which worked. So may be you were really lucky. Jan On Tue, Apr 11, 2017 at 10:34 PM, Ber

Re: [ccp4bb] electronic lab notebook suggestions

Dear Markus, For the last years I have been using LabArchives, since I got an account for "free" with my Graphpad Prism license. I've been mostly happy with it. It can automatically upload attachments from a watched folder, and integrates with some useful software such as Prism and chemdoodle.

[ccp4bb] Coot Find Ligand Places Ligand In Density Outside Where Model Is Built

I am new to this, so forgive the perhaps naive question. Does anyone know why Coot is placing ligand outside the electron density where my model is built. I have put the cursor to where I want it to search, but when it fits, it places the ligand in the equivalent spot, but outside the model and not

Re: [ccp4bb] CCP4BB Digest - 10 Apr 2017 to 11 Apr 2017 (#2017-100)

Let's step back a little bit first: Do these 3 to 4 diffraction data sets (when kept separate) process nicely individually and have good Rmeas and other results when scaled separately from each other? If so, then do they also have the same unit cell dimensions? Jim Date:Tue, 11 Apr 2017 1

[ccp4bb] Glycoprotein expression question

Hi Fellows, a humble question for our glyco-expressionists: I have mutated out the Asns of the N-glycoslation consensus sites for Asp (Asp simply because the PNGaseF treated protein stays stable so I thought that might be a good guess) and indeed the unglycosilated mutant expresses wel

[ccp4bb] High Rfree: Phasing issue or partial crystal disorder

Dear All, I am stuck with this problem for 2 months and hope you could help. We have a 2.1 A dataset for a 380 amino acid long protein. The space group is I4 (single molecule in asymmetric unit, 48% solvent content) and the dataset is quite perfect (no obvious pathologies). The protein itself is o

[ccp4bb] Pymol point mutagenesis turns out to be deletion of a residue

Dear All, I am using MacPymol 1.8.6, I did Pymol point mutagenesis using Wizard, everytime after I choose a residue for mutation, choosing a mutated target residue and a rotamer and click apply, the text of the sequence on top of the main window shows my selected residue is mutated but the graphic

Re: [ccp4bb] Some problems in data processing

Could you please provide more information: a) what is crystal symmetry, i.e. are you sure that you indexed consistently in the case of polar symmetries? b) what is the completeness of each data set separately? c) what is the multiplicity of observations, i.e. do you have enough data to get R-m

[ccp4bb] electronic lab notebook suggestions

Dear all, This may be off-topic but this year our university has asked for suggestions to move to a electronic lab notebook system. Are there any good ones? Due to data protection regulations they prefer hosted solutions. Many of the hosted solutions I found by google are proprietary. I am wonderin

Re: [ccp4bb] Some problems in data processing

You don't say what you mean by "too high", but if you are in a space group with multiple possible indexing conventions (eg different choices for the direction of b in a polar spacegroup) you can get very high Rmerge values. In the scalepack section of the old HKL manual ( http://hkl-xray.com/hkl-ma

Re: [ccp4bb] Some problems in data processing

Hi First thing I would do is throw xia2 at it (from ccp4i2, of course ;-)) and go and have a cup of coffee, and see if the statistics were similar after a Danish pastry. If the stats are better from xia2 than from HKL, go with the xia2 processing, if they are the same (or worse) I'd look more

[ccp4bb] Beamtime @ SLS

=== SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS === Proposal application deadline: Thursday, April 20, 2017 Periods: July 1, 2017 - December

Re: [ccp4bb] Some problems in data processing

Quite a few papers on this in recent years, including from the Sasha Popov (ESRF) and Wayne Hendrickson - don't have references to hand, the Google should sort you out. And then of course the CCP4 program BLEND - that's both published and runnable. But overall: this is the top problem in da

Re: [ccp4bb] off topic: MacPymol and macOS Sierra

Hi, I had this problem with Yosemite. Clicking on the icon still doesn’t open the program, but I can start it using the sh command in XQuartz.. I’m not sure if there was something else I had to do in order for this to work (it’s been a while since I started using it like this), but perhaps just

[ccp4bb] off topic: Change of bottom filter

Dear All I am wondering if its possible to change the bottom filter of the sepharose 12 gel filteration column. best Adriana

Re: [ccp4bb] Some problems in data processing

Hi Gaoyina, I guess your crystals ended up in slightly different lattices or with slightly different ordering during flash-cooling. I this case can see two possible solutions: - collect more complete data from a single crystal, you may have to "sacrifice" some resolution by collecting shorter i