[ccp4bb] XDS vs SADABS absorption correction factors

All, Sorry, this is a little bit off topic. I could not find a thorough definition of the "Correction Factors" for absorption correction in XDS nor of the "Transmittance factors" in SADABS. We collected small molecule samples on a synchrotron beamline, processed the data with XDS and the user

Re: [ccp4bb] Recovering crystals from dry drops

I recently had a similar situation for a protein crystal that was sitting in very thick, sticky goop. I put three drops of Paratone N on a coverslip and harvested the crystal by using a Mitegen yoke tool to "dig" around the crystal, then a regular nylon loop to move the crystal into a drop of Pa

Re: [ccp4bb] Recovering crystals from dry drops

Hi Debasish, I had a go at fishing crystals out of dried-out sitting drops some time ago: " The crystals were retrieved from the surrounding viscous liquid by dropping 1 µl cryoprotectant over the drop. This immediately started to thin the liquid, freeing the crystals within, so that one could

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Please join us for the SBGrid/NE-CAT Computing School: Quo Vadis Structural Biology 2014? Data Processing in Crystallography SBGrid/NE-CAT Computing School June 5-7th, 2014 Harvard Medical School, Boston, MA Registration Fee: $200 Register here

Re: [ccp4bb] Trouble cleaving SUMO tag off of membrane protein

Thanks to everyone who responded to my post (especially, John Lee and Brad Bennett) with helpful comments and suggestions. The good news is that I was able to get the Ulp1 protease cleavage step to 100% completion at 4C by using between 1:3-to-1:2 enzyme:substrate ratios and incubating the reaction

[ccp4bb] identifying protein crystals via visible light only?

Well, Ellen, the opinion of us in Agilent is that if you're wanting to make a judgement of the diffraction qualities (resolution limit, mosaicity and unit cell, etc.) of (putative) protein crystals, in situ, then don't bother with visible light at all: instead use X-rays !! For this reaso

Re: [ccp4bb] identifying protein crystals via visible light only?

Hi Richard and All, At Formulatrix we haven't yet seen an algorithm that can come even close to what the human brain can do for drop scoring. Crystals come in too many shapes, sizes, plates, and confusing backgrounds making automated detection extraordinarily difficult. Because of this, we have

Re: [ccp4bb] Recovering crystals from dry drops

Debasish Assuming you do not need seeds, just lift the coverslip, add a small amount of water to the reservoir, close and allow the drop to equilibrate for 20min, or untill you are sure that you have enough liquid to avoid that the drops becomes solid while you pick up the crystals with a

Re: [ccp4bb] Recovering crystals from dry drops

Hi Debasish, I would first use some of those crystals to make seeds and grow some new crystals so that I would not lose the crystal. Dehydration, even done systematically (eg, http://www.mitegen.com/mic_catalog.php?c=jenCrystaloptdehydrate), may or may not improve the diffraction. Like most ot

[ccp4bb] Recovering crystals from dry drops

Would you please share your experience and comments on recovering protein crystals from dry (or almost dry hanging drops) for data collection. I found some beautiful crystals in hanging drops that were set up three years ago; from the color of the crystals ( the protein binds a colored substrate

Re: [ccp4bb] Symmetry problem

I thought I saw this problem before. Though I wouldn't try it if you had solutions from different space groups. http://www.phenix-online.org/documentation/find_alt_orig_sym_mate.htm F On Feb 20, 2014, at 6:09 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear

Re: [ccp4bb] Symmetry problem

Dear Tim, I have used coot. "merge molecules" (calculate -> merge molecules). Using coot I have moved the molecules to the same asymmetric unit. I have the same problem with two different proteins in one case it works. However, for the other I am still working :-( Greetings, Mônika 2014-

[ccp4bb] Beamline Scientist position in XALOC beamline at the ALBA Synchrotron

Dear all, The BL13-XALOC Macromolecular Crystallography beamline at the Alba synchrotron (Barcelona) has currently an open Beamline Scientist position. We are seeking a positive, motivated scientist, with a PhD on a related topic, keen to join our beamline team in an exciting environment. Besides

Re: [ccp4bb] Symmetry problem

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Monika, would you mind summarising how you solved your problem? It might help people with similar problems! Regards, Tim On 02/20/2014 02:45 PM, Monika Coronado wrote: > Dear users, > > thanks alot for the tips. The problem was solved! > > Wa

Re: [ccp4bb] Symmetry problem

Dear users, thanks alot for the tips. The problem was solved! Warmest regard, Monika Coronado 2014-02-20 0:57 GMT-03:00 Jens Kaiser : > Monika, > There are several possible causes for the problem you are > encountering, but your description is a little too vague to discern > them. > Sce

Re: [ccp4bb] Calcium soaking

Masaki, If your crystals crack when you add calcium it implies that calcium binding induces a conformational change. You should try co-crystallization with an "epitaxial jump" approach: Stura, E. A., Charbonnier, J.-B. & Taussig, M. J.(1999) Epitaxial jumps. J. Cryst. Growth 196: 250-260.

Re: [ccp4bb] keep ligand conformation

Dear Koji, In addition to all the things Tim said, you may also have a conflict between the ligand conformation you modelled and the conformation described in your restraint file. The Refmac logfile will mark any really severe outliers, but smaller problems can still exist. Try regularising you

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The IUCr has launched a photo competition "Crystallography in everyday life" to celebrate the International Year of Crystallography. Photographs "that capture the spirit of crystallography in the places, objects and experiences of everyday life" can be submitted at http://www.iycr2014.org/parti

[ccp4bb] Calcium soaking

Dear all Apologies for the off-topic question: We are studying an enzyme that is activated by Ca2+. We obtained the crystals of the substrate and Ca2+-free form and solved the structure at 2.7 A resolution. However, the active site electron density map was not clear, although other regions are cl

Re: [ccp4bb] keep ligand conformation

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Koji, some ligands tend to be where the users wishes them to be. If your ligands moves away, maybe it is not really there? Maybe there is a stereochemical clash which acts more strongly than the restraints you are applying? And maybe harmonic res

Re: [ccp4bb] CCP4 BB email change

Hi Arnau, You can find all the information you need here: http://www.ccp4.ac.uk/ccp4bb.php Just subscribe with your new adress, and unsubscribe your old one. Best regards, Folmer ps: actually the following information is available in the header of the emails sent to the CCP4bb: List-Help:

[ccp4bb] CCP4 BB email change

Hi, is it possible to change the email to which my ccp4i bulletin board emails get sent? The new email address is arnau.casa...@psi.ch Thank you very much, Arnau Casañas, PhD Institute of Molecular Biology and Biophysics ETH Zurich Schafmattstr. 20 HPK H10 8093 Zurich Switzerland +41.44.633845