[ccp4bb] Protein preps become a jelly
Dear Buddies, Sorry for bothering you with an off-ccp4 question. We recently are experiencing a very strange phenomena. A couple of protein preps with reasonably high concentration (10-20mg/ml) become a jelly after storages for overnight or a couple of days at 4C. All of them have been purified by gel filtration. Some of these proteins behave like this from very first preps but some of them had been very kind to us previously. We have googled extensively in CCP4BB and www but it appears this only happens to us. It would be highly appreciated that you could exchange their experiences or provide your suggestions. Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University Xiamen, Fujian 361005 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/
Re: [ccp4bb] Protein preps become a jelly
Dear Buddies, I truly appreciate many of you are so kind to spend your time in replying my email with a variety of suggestions regarding this strange problem. Most of you have pointed to oxidation damage. We tested quickly but high concentrations of DTT or TCEP including EDTA and/or glycerol seem to improve one of three proteins in our hands while other two are still the same. We are testing different factors, such as pH, salt concentration, detergents, additives and even temperature (Low temp is not good?). Whether it is intrinsic property of our proteins requires further experiments. I hope to write back as soon as we have clear conclusions. Many thanks again for sharing your priceless experiences. Cheers Aidong Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University Xiamen, Fujian 361005 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/
Re: [ccp4bb] [OFF-TOPIC] Site-Directed Mutagenesis
Hi Fred, While you are working on the optimization of your PCR, I strongly suggest you to read our paper on partial overlapping primer design from a link below, which will surely ease your mutagenesis: http://www.ncbi.nlm.nih.gov/pubmed/21530481 I would be happy to answer your questions should you have. Cheers Aidong On Feb 4, 2012, at 2:14 AM, Fred wrote: Hi CCP4 list, Thanks everyone who have answered my post concerning to mutagenesis. From quick reading most of the answers, the following seems to be a consensus: 1) Do not concentrate your PCR product; 2) Too much DNA and/or impurities like salts or whatever can inhibits transformation; 3) Purify your PCR product before transformation if possible or use 3 of 4 microL of it. This is more or less the amount of DNA showed in the uploaded image. Kind regards, Fred P.S.: I'll let you know the results. Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University Xiamen, Fujian 361005 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/
[ccp4bb] monomeric coiled coil
Sorry for this ccp4 unrelated question. We recently have a protein that a multicoil program (http://groups.csail.mit.edu/cb/multicoil/cgi-bin/multicoil.cgi/cgi-bin/multicoil ) predicts to have very high probability for dimer and trimer. Their scores are close to 0.4 and 0.6 for lengths of more than 60 amino acids. However, two constructs that cover this region have demonstrated monomers in solutions by Multiangle light scattering?! For the same question, we could not get any response from this program manager therefore we turn to ccp4 for help. We wonder whether some of you might have similar experience. Thank you in advance. Sincerely, Aidong
Re: [ccp4bb] monomeric coiled coil--updated
In light of several wonderful responses,I would like to provide an update for this question: 1. I would agree that SEC might not be able to identify monomer vs multimer forms for this likely rod-shaped protein. 2. It is extremely low kd for dimer. AUC and SAXS experiments have measured its kd at ~0.1 mM. 3. MALS might not be able to pick up dimer form since it might be only a few percent when the concentration is low. We might overcome concentration effect by direct injection to dawn heleos and refraction index. 4. Mass spec has found both monomer and dimer forms although the abundance of each one is not known. 5. Intramolecular coiled coil is quite possible since intermolecular dimer is unstable. We hope our structure might provide an answer. Many thanks for your time and ideas Cheers Aidong On Jul 4, 2010, at 1:09 AM, Anastassis Perrakis wrote: A few thoughts on these, since I do not fully agree. 1. Detection by light scattering is a method that can be used either without separation, or while separating. If you have a scattering detector, you can stick in a cuvette, or stick it to the end of a column, your choice. 2. Sec is not a good method to show if especially a coiled coil is monomer-multimer. A long coil, will have a hydrodynamic radius bigger than its MW, thus any prediction based on SEC will be misleading, especially for this class of proteins. 3. In AUC (although I am not an expert at it at all) I cant see the connection between the disassociation time and the run time. In sedimentation or equilibrium runs, depending on what you want to see, I think you can look at monomer-multimer equilibrium over a wide range of kD and combinations of k(on) and k(off). 4. The physiological concentration is a bit misleading. First, its clear now that cells have microenvironments, and 'physiological' concentrations are hard to define. Also, in a cell, I think (and I think others tend to agree) that kD plays little role at the end. kD is a combination of k(on) - which is concentration dependent but in a cell very likely diffusion limited - and of k(off) which I think is what matters most in the cell. Going to Aidong's question, I think that MALLS was a good experiment. The fact that these constructs do no associate, can mean that a. the prediction is wrong - likely with these scores, but not necessary b. the kD in solution is indeed higher that the concentration you used for MALLS c. The constructs are not well chosen for some reason You could use AUC to detect kD as high as ~100uM, depending on the concentration of the start sample of course. The next question will anyway be if that kD has any sort of physiological significance - which you cannot tell by magnitude - so you are back at the drawing board for mutants. Three years later the referees will still not believe it ... sorry, now it gets personal, so I stop here. My two cents. A. On 3 Jul 2010, at 18:10, chern wrote: The multimeric state depends on a protein concentration. You can get any multimer to dissociate if you dilute it to low enough concentration. If your complex is a homodimer, then Kdiss=[complex]/[monomer]^2. Let's say your Kdiss~10^(-3)M, and your protein concentration is ~10^(-4)M, then [complex]=Kdiss/[monomer]^2=10^(-3)/10^(-4)^2=10^(-5), that means, the dimer concentration is approximately ~10 times less then the monomer concentration at this particular protein concentration. Let's say, the mol weight is 50 kDa, then at 5mg/ml you will have only about ~10% of the dimer. Of course, if your Kdiss~10^(-4)M, then you will have approximately similar concentrations of monomers and dimers at 10^(-4). Because this is a dynamic equlibrium between multimers and monomers, some methods are not good for the determination of a multimeric state. Some reviewers demand to prove the multimeric state by size-exclusion chromatography (SEC) or analytical centrifugation. The analytical ultracentrifugation method will not work, as the characteristic time of the dissociation/association is much lower than the centrifugation time (`24 hours). The separated monomer will start association and the separated dimer will start dissociation according to Kdiss and the bands will be smeared. SEC is faster, like half an hour, it gives you a better chance. The methods without separation are the best Like light scattering), just make protein concentration high. Here comes the other question. What is the physiological concentration. You want to be close to it. I read some literature on this and it looks like it is between 10^-(4) to 10^-(6) for majority of proteins. - Original Message - From: "aidong" To: Sent: Saturday, July 03, 2010 6:26 AM Subject: [ccp4bb] monomeric coiled coil Sorry for this ccp4 unrelated question. We recently have a protein that a multicoil program (http://groups
[ccp4bb] laboratory phage infection
Hi All, Really sorry for my non-CCP4 related question. Our lab mainly uses bacterial cultures to produce targets proteins for crystallizations. However, we have been struggling with phage infections to our bacterial cultures for a quite long time. To control its devastating effects, we have regularly been using large-dose ozone treatments on the whole lab space. We have also tried anti-phage BL21/DE3 strains from Sigma USA but found it was still not avoidable. The lab has been maintained well hygienic and its outdoor environment is clean and neat. We keep good ventilations, including windows and central AC systems. However, phages are still eating up our cultures with very low percentage of survivals. Therefore, this has been our big headache. We wonder whether you have the same experience and how to keep a lab free of those bugs. Your suggestions are deeply appreciated. Thanks. Sincerely Aidong Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University 3 South Xiangan Road Xiangan, Xiamen 361102 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/
Re: [ccp4bb] laboratory phage infection [SEC=UNCLASSIFIED]
Many thanks for your rapid inputs. We used to make glyerol stocks but now we do not since the protein expression is not stable. Our lab is about 10 students, who have to make their own proteins so our three large-scale shakers are very crowded every day. We did try a formaldehyde gas treatment one time during our new year leave, however, the situation did not seem to improve. Since that gas is much harder to handle, we only stick to ozone treatment. Intriguingly, our neighbor lab, also a crystallography lab, which constantly uses bacterial cultures although not as much as we do, is just fine. Chloroform/phenol treatment might be a good one because some of our constructs are just very difficult to get any transformed colonies while some others are so easy. We have used gel extraction method to purify our plasmids because we thought some phage DNA is contaminated. This method slightly improved our situations but not complete. But I am thinking the entire phages are simply there in plasmid preps purified through miniprep columns. Cheers Aidong On Mar 2, 2013, at 7:30 PM, DUFF, Anthony wrote: Hi Aidong, some ideas... Do you use glycerol stocks of transformed expression cells (phage risk), or do you do fresh transformations each time? Do you have many people working together, or do you have periods of bacterial growth separated by periods of inactivity? Do you have neighboring labs who may be working with, or infected with phage? Do you have any old stocks, liquid media, antibiotics, etc, that could be contaminated? sincerely, Anthony From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of aidong [a...@xmu.edu.cn ] Sent: Saturday, 2 March 2013 7:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] laboratory phage infection Hi All, Really sorry for my non-CCP4 related question. Our lab mainly uses bacterial cultures to produce targets proteins for crystallizations. However, we have been struggling with phage infections to our bacterial cultures for a quite long time. To control its devastating effects, we have regularly been using large-dose ozone treatments on the whole lab space. We have also tried anti-phage BL21/DE3 strains from Sigma USA but found it was still not avoidable. The lab has been maintained well hygienic and its outdoor environment is clean and neat. We keep good ventilations, including windows and central AC systems. However, phages are still eating up our cultures with very low percentage of survivals. Therefore, this has been our big headache. We wonder whether you have the same experience and how to keep a lab free of those bugs. Your suggestions are deeply appreciated. Thanks. Sincerely Aidong Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University 3 South Xiangan Road Xiangan, Xiamen 361102 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/ Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University 3 South Xiangan Road Xiangan, Xiamen 361102 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/
Re: [ccp4bb] laboratory phage infection [SEC=UNCLASSIFIED]
Dear Opher, It was also our idea how to get over it since several years ago. We did it based on a philosophy that any bacteria infected with a phage will not be infected by the same phage again. Therefore, we let our BL21/DE3 strain infected in the lab and when most were died, some cells were survived. We picked these to make the competent cells for expression constructs. We believe these actually contained phages. In order to avoid this bomb to blow up, we managed to get a commercial strain (TonA and TonB deletion) purchased from Sigma USA but found it useless. I wonder how you screened your phage-resistant strains. In addition, it is our regular practice to use bleach to extensively disinfect all surfaces, including benches, used flasks, instruments and floors. Would virkon work more efficiently in our case? Sincerely, Aidong On Mar 3, 2013, at 3:36 AM, Opher Gileadi wrote: Hi, We had a massive phage infection at the SGC in 2004; all our washing and sterilization efforts could only solve the problem temporarily. I then recovered a phage-resistant subclone of BL21(DE3), and prepared derivative strains with pRARE2 (the tRNA plasmid in Rosetta2) or other plasmids. We have expressed thousands of protein since and never had a recurrence of phage problems. Although the resistance is to T1 phages, it seems these are the most common lab infections. Write me if you want the strains. Opher Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University 3 South Xiangan Road Xiangan, Xiamen 361102 China Phone: 0592-218-8172 (O) 0592-218-8173 (L) Web: http://life.xmu.edu.cn/adhanlab/
[ccp4bb] Postdoctoral positions available, Xiamen, China
A structural biology lab has now several openings. This lab conducts two aspects of research using X-ray crystallography and other biochemical approaches. One is to understand how a limited number of transcriptional factors regulate a large amount of genes. Our model is that two or more transcription factors work together and further recruit other protein modification factors to form high-order regulatory assemblies on gene promoters. Another is to study how the extracellular signals transfer to a specific set of transcription factors. This involves ligand-protein and protein-protein interaction and the proteins associated with cell membranes. For some details, please see http://life.xmu.edu.cn/teacher/HTML/1760.html. Those who have Ph.D in any biology or chemistry disciplines are welcome to apply. Experience in protein biochemistry and/or cell biology will be in higher priority. Training in crystallography will be big plus. Xiamen island is the most beautiful city, and Xiamen University has one of few best university campus over China. It is so comfortable to live that it grows a big foreigner community. Please see www.xmu.edu.cn/english for university and http://www.amoymagic.com for Xiamen. Successful candidates will be provided with a standard package from Xiamen University including convenient low-cost apartment, medical insurance and family assistance. If interested, please send your CV and contacts of 3 referees to Dr. Aidong Han through a...@xmu.edu.cn. Thank your attention.
[ccp4bb] weak magnet of goniometer of MAR345dtb
Hi, We have recently installed a new home source diffraction system using MAR 345 dtb. It works much better than the rigaku because this new device has automatic motor control system. However, we have a lot of trouble to mount crystals. The magnet of MAR goniometer is significantly weak so the pins do not stick on. The old pins we used nicely in old rigaku are not working most of time. The new pins from hampton research particularly designed for ALS high-through put data collection are not easily working either. I wonder whether anyone has similar experience and it could be fixed by replacing with a stronger magnet base. Thanks for your suggestions in advance. Sincerely, Aidong
[ccp4bb] Summary for weak magnet of goniometer of MAR345dtb
Dear everyone, I deeply appreciate many of you who took their time to write emails of your suggestions in response to my inquiry. I have realized that someone of you might also encounter it either now or in near future. I therefore summarize those good points here: 1. Inspired by Andrew, I talked to local sale rep and tech immediately. I indeed found the weak magnet is set by the manufacture. Because our MAR system has automatic motor control and automatic crystal mounting, the magnet can not set too strong. As a matter of fact, I believe that such a robot is really useless for home source X-ray. To solve this problem, as Manfred suggested, a sort of permanent magnet adapter can be used. However, our local sale requested a payment for such a fix although the system has only been installed for a little over 6 month. 2. As the problem might come from pins, many pointed to those HTP pins with matrix labels. I have indeed found there are clearly different for different types of pins, even though most types are from Hampton Research. Here I have to ask Hampton for an answer. However, when we removed those silly labels, as Bob suggested, it did not make any difference. Those pins from Mar research are significantly stronger and also much better manufactured, but I suspect its aperture design might cause moisture accumulation and ice build-up. Thank you again for your time and great suggestions. Cheers Aidong Aidong Han, Ph.D Department of Biomedical Sciences The School of Life Sciences Xiamen University Xiamen, Fujian 361005 Phone: 0592-218-8172(O) 0592-218-8173(L)
Re: [ccp4bb] Announcement regarding PyMOL
I fell deeply sorrow for what happened to young Dr. Warren L. DeLano. I will remember him for his great contribution to scientific community. Although he made pymol a commercial software against scientific spirit, pymol is still one of the best and most intuitive graphic tools. God bless him and his family forever. Aidong On Jan 9, 2010, at 8:06 AM, Thomas Stout wrote: Greetings everyone -- It has been brought to my attention that a deal has been struck to have Schrödinger assume responsibility for the continued development and maintenance of PyMOL. Also, Jason Vertrees has agreed to join Schrödinger to work in this capacity. Jason has been working closely with Warren for the past several years as a co-developer and is committed to carrying PyMOL forward in the same manner that Warren intended. Schrödinger has committed to keeping PyMOL open- source and operating in very much the same manner as under DeLano Scientific. Their announcement as posted on the PyMOL web site is included below. Best regards, Tom Stout -- ANNOUNCEMENT On January 8, 2010 Schrödinger reached an agreement with the estate of the late Dr. Warren L. DeLano to acquire PyMOL. Schrödinger will take over continued development and maintenance, as well as support and sales of PyMOL, including all current subscriptions. Schrödinger will also continue to actively support the open-source community of PyMOL. Prior to Warren's tragic and unexpected passing, he had been working closely with Schrödinger to progressively integrate PyMOL with Schrödinger's graphical interface, Maestro. With a great sense of humility, we will work hard to pick up as best we can where Warren left off and will strive to honor his memory by continuing in the spirit and tradition of PyMOL. This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems.
Re: [ccp4bb] Announcement regarding PyMOL
I am sorry for being so offensive. I did not realize such a consequence for my opinion or misunderstanding, which was not my intention. I just want to say I feel really bad for such a tragedy. Sorry again. Aidong On Jan 10, 2010, at 8:28 PM, Anastassis Perrakis wrote: Although he made pymol a commercial software against scientific spirit, PyMol was an open source, free software. It was never commercial, this is total nonsense to call Pymol commercial. You *could* buy a compiled version if you want to save you the trouble of compiling, but all the software was free, and very much into the scientific spirit of open collaboration. I would friendly suggest you to apologize to the ccp4bb community for your misunderstanding, or get prepared to get lots of emails like this. A.
Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays
I would like to draw your attention: Do not rush to set these up now. There are many problems with quadro card and 3D vision kit running on linux. We are wasting a lot of time to work out solutions. Cheers Aidong On Mar 3, 2010, at 11:50 PM, Christian Rausch wrote: Hello, is someone using Nvidia 3D vision + a compatible 1920x1080 23.5" Desktop Display e.g. ACER GD245HQ 120 Hz LCD display OR Alienware OptX AW2310 120 Hz LCD display? Is it running nicely with Linux + Nvidia's Linux driver? How is the stereo quality compared to Zalman's 3D-LCDs or the old CrystalEyes shutter glasses + CRT monitor? Thank you, Christian Rausch -- Dr. Christian Rausch rau...@wzw.tum.de Lehrstuhl f. Biologische Chemie Phone: +49 (0)8161 71-4050 Technische Universitaet MuenchenFax: -4352 85350 Freising-Weihenstephan Germany http://www.wzw.tum.de/bc
Re: [ccp4bb] nVidia quadro
Interestingly, we have both systems working in our lab. Our old station is 7 years old with FX3700, view sonic monitor and 3-pin stereo emitter. My new one has K5000 and VG278HR, which just requires a pair of nVidia shatter glasses. Hope this helps. Aidong On Apr 2, 2015, at 7:20 AM, Andreas Schenk wrote: > Thank you Kay for contacting the info site. The new categories are definitely > more helpful. > And thank you Lukasz, for the info about the FX3700. > > Best, > Andreas > > On 04/01/2015 03:57 PM, Lukasz Salwinski wrote: >> On 04/01/2015 12:31 PM, Kay Diederichs wrote: >>> On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk >>> wrote: >>> >>>> On 3/25/2015 18:10, Kay Diederichs wrote: >>>>> On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller >>>>> wrote: >>>>> >>>>>> You could check the nVidia page of officially supported displays. It >>>>>> includes a search tab so you can check for "Built-in Emitter." >>>>>> http://www.nvidia.com/object/3d-vision-displays.html >>>>>> >>>>>> Performing that search brings up 5 contenders. Good luck finding any of >>>>>> these products still for sale. >>>>> Unfortunately, this NVidia page has not been updated for years. >>>>> >>>>> The qualifier "3D-fähig (aktiv)" at >>>>> http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top >>>>> should indicate a built-in emitter, but I looked at some of the >>>>> descriptions of these 11 monitors and was unable to confirm that they >>>>> indeed have a built-in emitter. So one has to research every specific >>>>> case. >>>>> >>>>> I changed the wording on the wiki page. >>>>> >>>>> Kay >>>>> >>>> I went through the specs for the monitors on the Heise list, and none of >>>> them seems to have a built in emitter compatible with Nvidia 3D Vision >>>> 2. It looks like it is a bad time to buy a 3D monitor. At this point it >>>> might be easier to just go for a Quadro with 3-pin connector. >>>> >>>> Best, >>>> Andreas >>>> >>> I asked the company who runs the price info site to check their >>> assignments, and they fixed the categories: >>> http://geizhals.eu/?cat=monlcd19wide now has a "inkl. 3D-emitter" >>> attribute. This currently only returns the Asus 278HR which can only be >>> bought in Poland, or through EBay. >>> >>> The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo >>> connector (needed for Linux) is the K4200 >>> (http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts >>> at ~ €700. >>> >>> best, >>> >>> Kay >> FX3700 is the oldest Quadro model with 3-pin DIN Stereo connector that is >> supported by the current nvidia drivers. it can be bought on ebay >> for about $30-$40. works fine with coot/pymol. >> >> lukasz >> >>
[ccp4bb] postdoctoral positions in Xiamen
Postdoctoral positions available This lab conducts two aspects of research using X-ray crystallography and other biochemical approaches. One is to understand how a limited number of transcriptional factors regulate larger amount of genes. Our model is that two or more transcription factors work together and further recruit other protein modification factors to form high-order regulatory assemblies on gene promoters. Another is to study how the extracellular signals are transferred to a specific set of transcription factors. These projects include structural characterization of ligand-protein and protein-protein interaction and proteins associated with cell membranes. Please refer http://life.xmu.edu.cn/teacher/teachersy/2008-02-18/1760.html for more information. Those who have Ph.D in any biological or medical disciplines are strongly encouraged to apply. Any experience in protein biochemistry is a plus. Training in crystallography is welcome but not required. You will be provided with a standard package from Xiamen University including low-cost oncampus apartment, medical insurance and family assistance. Additional salary will be offered to compensate your credentials. Initial contract is 1-2 years and expected to start within 6 months. Please send your CV including personal statement and contact information of three referees to Dr. Aidong Han at [EMAIL PROTECTED] Xiamen is one of the most beautiful cities and the best place to live in China. Xiamen University, in particular, the School of Life Sciences, has been quickly arising with strong financial support from the government. The lab is fully equipped and among the excellent academic environment.
[ccp4bb] Eiger 16M detector in HKL2000
Hi All, We have recently collected several data sets in the Shanghai synchrotron facility with a newly installed Eiger 16M. However, we are not able to process these data using our home HKL2000 package. Even though we can easily add this detector in, we can not display images. I believe ours has not been properly set up. While we are still waiting for a response from HKL2000 administration managers (it has been a few days), I wonder whether someone can provide me your solution since this detector has been in market for more than a year. Thank you for your help. Sincerely, Aidong
Re: [ccp4bb] Eiger 16M detector in HKL2000
Probably it is the reason. We are working on upgrading our HKL and getting a new license. I will let you know when our problem is solved. Thank you so much. Aidong On Dec 19, 2017, at 2:49 PM, Raghurama P Hegde wrote: > Dear Aidong, > > As Dr. Förster has rightly pointed out you need to have the latest version of > HKL2000 to work with the HDF5 files from the Eiger detectors and as you must > be aware the HKL2000 license should include use of Eiger detectors. We have > recently used HKL2000 to process data from MASSIF-3 beamline at ESRF which > uses a EIGER X 4M detector but we had to upgrade to the latest version of > HKL2000. > > With regards, > Raghu > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of Andreas > Förster > Sent: Tuesday, December 19, 2017 11:47 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Eiger 16M detector in HKL2000 > > Dear Aidong, > > as I don't have access to HKL2000 myself, I can't tell you what might need to > be done to have the software display EIGER X 16M images. Wladek showed me > that it was possible. It might just be a question of getting the latest > version. > > There are alternatives to HKL-2000. > > DIALS can process EIGER data with no questions asked > (https://dials.github.io/). It is free, open-source software. DIALS exists > as a powerful command line tool but can also be run through the xia2 pipeline > (https://xia2.github.io/). Both are part of CCP4, but I'd recommend > installing the latest DIALS nightly because development is rapid. The > developers respond quickly to questions. > > XDS can process EIGER data > (http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html). It is free to > academic users. To process data in HDF5 format (*.h5), make sure to download > the neggia plugin (https://www.dectris.com/support/downloads/software/neggia, > free, but registration required) and adjust the LIB= parameter to point to > where the plugin is saved. XDS is a command line tool, but several GUIs > exist. > > Please give DIALS or XDS a try and tell me how you get along. If you > continue to encounter problems, let me and the beamline staff at SSRF know. > > All best. > > > > Andreas > > > > On Tue, Dec 19, 2017 at 6:48 AM, Aidong Han wrote: > Hi All, > > We have recently collected several data sets in the Shanghai synchrotron > facility with a newly installed Eiger 16M. However, we are not able to > process these data using our home HKL2000 package. Even though we can easily > add this detector in, we can not display images. I believe ours has not been > properly set up. While we are still waiting for a response from HKL2000 > administration managers (it has been a few days), I wonder whether someone > can provide me your solution since this detector has been in market for more > than a year. Thank you for your help. > > Sincerely, > > Aidong
[ccp4bb] Postdoc in Xiamen, China
Dear Buddies Those who have a Ph.D in biology or chemistry are welcome to join a lab of structural biology in Xiamen University. Experience in protein biochemistry and/or cell biology is in higher priority. Training in crystallography is a big plus, but not required. Xiamen island is one of the most beautiful cities in China. It is so comfortable to live that it grows a big foreigner community. Please see http://en.xmu.edu.cn/ <http://www.xmu.edu.cn/en/> for our university and http://www.amoymagic.com <http://www.amoymagic.com/> for Xiamen. Successful candidates will be provided with a standard package from Xiamen University including convenient low-cost apartment, medical insurance and family assistance. In particular, those graduated from the world-top 100 universities will have an opportunity to get an award of 300,000 RMB. If interested, please send your CV and contacts of 3 referees to Dr. Aidong Han through a...@xmu.edu.cn <mailto:a...@xmu.edu.cn> before May 30. Thanks you for your attention. Aidong Aidong Han, Ph.D Department of Biomedical Sciences School of Life Sciences Xiamen University 3 South Xiang’an Road Xiang’an, Xiamen 361102 China Homepage: http://ahan.xmu.edu.cn/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
