[ccp4bb] Query - inhibitor screening by fluorescence based assay.

2010-05-19 Thread suresh mattegunta
Dear All, Sorry for the non crystallography related question We are performing a fluorescence based assay to screen for inhibitor compounds of our enzyme and ultimately crystallize the enzyme along with inhibitor. We see that some of our compounds are autofluorescent and thus are effecting

Re: [ccp4bb] different compilers for ccp4 code

2010-05-19 Thread Kay Diederichs
Charles Ballard schrieb: Hi Francois configure linux_intel_compilers should do the trick. We distribute ccp4 built with the intel compilers for OS X. Part of this is that the macs cover a much smaller range of cpus than linux boxes, so optimisation is less of a problem. If you want

Re: [ccp4bb] different compilers for ccp4 code

2010-05-19 Thread Justin Lecher
On 19/05/10 09:40, Kay Diederichs wrote: Charles Ballard schrieb: Hi Francois configure linux_intel_compilers should do the trick. We distribute ccp4 built with the intel compilers for OS X. Part of this is that the macs cover a much smaller range of cpus than linux boxes, so

[ccp4bb] About seeding in microbatch under oil crystallization

2010-05-19 Thread wu donghui
Hi ccp4bbers, I want to know if anyone has any experience about seeding (streak seeding or microseeding) in microbatch under oil crystallization. I wonder if the oil might block or wipe away the seeds if cat whisker is used for streak seeding. Thank you for your input ahead. Best regards,

Re: [ccp4bb] Should I be worried about negative electron density?

2010-05-19 Thread Clemens Vonrhein
Hi Jay, there have been a few discussions about sigma/rms levels, absolute values (e/A*3), significance levels etc on ccp4bb. See e.g. http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg06969.html http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg15273.html which are the ones I could

Re: [ccp4bb] About seeding in microbatch under oil crystallization

2010-05-19 Thread Harm Otten
Hello Donghui we used a robot to setup the batch crystallization screens with some microseed stock solution and the relevant protein and reservoir stocks. That worked fine. I only mention a collegues work here, so if there are more detailed questions, I will approach him. Good luck, Harm On Wed,

Re: [ccp4bb] Should I be worried about negative electron density?

2010-05-19 Thread Thomas Womack
On 19 May 2010, at 00:36, Paul Emsley wrote: Jay Pan wrote: Hello Everyone, I have a reasonably well fitted electron density map through molecular replacement. However, there is always some red region left no matter how hard I tried when the mtz file is loaded into Coot. Is this because

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Jürgen Bosch
Not quite correct, look into Blue Native PAGE. There you can seperate natively by mass. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street,

Re: [ccp4bb] About seeding in microbatch under oil crystallization

2010-05-19 Thread wu donghui
Dear Patrick, I have Oryx robot in our lab. I got my initial crystallization hit from sitting drop vapor diffusion method. This hit can be reproduced by sitting drop through spontaneous nucleation with many tiny crystals after around 1 week but seeding into sitting drop failed and I found once

Re: [ccp4bb] About seeding in microbatch under oil crystallization

2010-05-19 Thread Ravindra Makde
Hi Donghui, I tried the microseeding using Hampton seeding tool (http://hamptonresearch.com/product_detail.aspx?cid=18sid=157pid=448)  for under oil microbatch (without caring about wiping out seed by oil). It is possible to seed the microbatch drop this way. cheers, ravi Ravindra D. Makde

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

2010-05-19 Thread Marius Schmidt
Interestingly, Maxwell's demon pops up here, wh... , don't do it. If you change the reaction rate in one direction 1000 times slower than in the other direction, then the reaction becomes practically irreversible. And the system might not be at equilibrium. Maia R. M. Garavito

Re: [ccp4bb] Query - inhibitor screening by fluorescence based assay.

2010-05-19 Thread Nadir T. Mrabet
You are measuring fluorescence changes which are likely to be due to compound binding by your enzyme. In this case your blank must be your compound blank and no other. Then you measure changes in fluorescence intensity and lambda max of emission as you add your enzyme. I do not know you

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Nadir T. Mrabet
Maia speaks about native PAGE for which protein mobility (migration) depends on 3 different parameters as she states: charge, mass and shape. Blue native PAGE, which might be the answer to Jacob's question, is a 2D gel: Native in the first direction, then SDS-PAGE in the second one. You

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread David Briggs
Dear Jacob, I know that this is not the answer you were seeking, but for a modest increase in the amount of protein required, a couple of analytical ultracentrifugation experiments would be able to determine stoichiometry and binding affinity for such a system. AUC has the added benefit of being

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Jürgen Bosch
You don't necessarily need the second dimension. BN-PAGE gel: protein A alone| some proteins you know the size as reference|protein B alone| your mixture You will be able to see in the mixture a) one or b) multiple bands, since the Coomassie is equally distributed and attached to your protein

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Nadir T. Mrabet
Thanks Jürgen. Yes, you may show dissociation. However, especially if you deal with assembly, then it might be difficult, if not impossible, to tell your exact subunit composition if you runBNP only in the first direction. Jacob mentions the possible occurrence of complex assemblies (AB, BB,

[ccp4bb] Postdoctoral opportunity in Structural Biology at Genzyme Corporation (apply online at www.genzyme.com/careers) (requisition ID 21308).

2010-05-19 Thread Liu, Jinyu
We have a postdoctoral position open in the Fragment-Based Drug Discovery (FBDD) group in Drug and Biomaterial RD at Genzyme Corporation in Waltham, MA. We are seeking a highly motivated recent PhD graduate in Structural Biology for a two-year position with a possible one-year extension. This

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Hannes Uchtenhagen
Dear Jacob, somewhat adding to list of 'not really answering your question', here is the reference for native page that still uses a dye thereby trying to limit the influence of the charge on the speed. Might be helpful as they discuss some applications. Otherwise AUC really sounds like the

Re: [ccp4bb] different compilers for ccp4 code

2010-05-19 Thread Adam Ralph
I believe that Francois is correct in saying that a feature of intel compilers is that they do not work well on non-intel CPUs. Can't imagine why that would be. If you have a an intel CPU then using an intel compiler would be an advantage. Code optimization is usually architecture specific, so

[ccp4bb] Job Opening for Industrial Post Doc (or other early career) in Xray Crystallography Software Development

2010-05-19 Thread Lance Westerhoff
Hello All- We have an opening at QuantumBio Inc. for an Industrial Post Doc (or other early career) in Xray Crystallography Software Development. Below is the short job description. Please feel free to contact me if you have any questions or comments about the position. === Contact: Dr.

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

2010-05-19 Thread Maia Cherney
You absolutely right, I thought about it. Maia Marius Schmidt wrote: Interestingly, Maxwell's demon pops up here, wh... , don't do it. If you change the reaction rate in one direction 1000 times slower than in the other direction, then the reaction becomes practically

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Maia Cherney
That's interesting. Thanks. Maia Nadir T. Mrabet wrote: Maia speaks about native PAGE for which protein mobility (migration) depends on 3 different parameters as she states: charge, mass and shape. Blue native PAGE, which might be the answer to Jacob's question, is a 2D gel: Native in the

[ccp4bb] Help needed in solving a MAD dataset

2010-05-19 Thread Qing Lu
Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as

[ccp4bb] Help needed in solving a MAD dataset

2010-05-19 Thread Qing Lu
Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as

Re: [ccp4bb] Help needed in solving a MAD dataset

2010-05-19 Thread Jürgen Bosch
CCP4 way: locate the Se sites with SHELX (if you use the CCP4I gui it's technically a ccp4 program :-) ) Try using only your peak data set first. If you can't locate your sites with the single wavelength then add remote (DAD) and if that doesn't work go MAD. non-ccp4 way run hkl2map as frontend

Re: [ccp4bb] Help needed in solving a MAD dataset

2010-05-19 Thread James Holton
First, you will need CCP4 installed and set up properly. You will also need to know your protein sequence. Put the latter into a text file (FASTA format will do). Next, download the file Elves from: http://ucxray.berkeley.edu/~jamesh/elves/download.html then type: chmod a+x Elves Elves

[ccp4bb] translational NCS

2010-05-19 Thread Nicolas Soler
Dear CCP4bbs, I am dealing with a case involving pseudo-translational symmetry. I wanted to know what was the simplest way to draw NCS copies of a molecule deduced from the positions I observed in native Patterson. Is there a translate option where on can give fractional coordinates in Coot

[ccp4bb] Question: Refmac5 stats reported in pdb REMARK 3

2010-05-19 Thread Phil Jeffrey
Compare these two lines from phenix.refine: REMARK 3 NUMBER OF REFLECTIONS : 46001 REMARK 3 FREE R VALUE TEST SET COUNT : 2339 with those from refmac, ostensibly using the same data and start pdb: REMARK 3 NUMBER OF REFLECTIONS : 43672 REMARK 3 FREE

Re: [ccp4bb] Question: Refmac5 stats reported in pdb REMARK 3

2010-05-19 Thread Ian Tickle
Phil, I think the PDB documentation in this area (such as it is) is unclear, and it's not easy to fathom what was the original intent. The first line you refer to: REMARK 3 NUMBER OF REFLECTIONS : appears in the section with the sub-heading: REMARK 3 DATA USED IN

[ccp4bb] Postdoctoral Position Available in Structural Biophysics and Protein Engineering in Rockville, Maryland, USA

2010-05-19 Thread Scott Walsh
Postdoctoral Position Available in Structural Biophysics and Protein Engineering in Rockville, Maryland, USA A NIH funded postdoctoral position is available for a highly motivated individual at the Center for the Advanced Research in Biotechnology (CARB) at the University of Maryland

Re: [ccp4bb] Native Gel Theory and Practice

2010-05-19 Thread Sheemei Lok
How about using static light scattering to determine the actual molecular weight or dynamic light scattering to measure the diameter of the complex. Sheemei From: Jürgen Bosch jubo...@jhsph.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 19 May 2010 11:00:24