[ccp4bb] Off-topic: X-ray equipment for grab. MAR345, Xenocs-mirror, Oxford cryo system and an RU-H3R etc.
Hi all, I have my home source X-ray equipment up for grab. I used all the equipment one month ago and collected a beautiful 1.9Å data on a nuclear receptor LBD so everything is in working order, but I give no garantees. It is yours if you come and pack and ship it yourselves. If anyone wants everything that is of course preferred but anything goes. Smaller things (e.g. the mirror) I can pack and ship if you cover the cost. - Detector: Imageplate MAR345 , 15 years old, but work well. Fully serviced 5 years ago. - X-ray-Mirror, Xenocs FOX 2D CU 25_25P - Oxford Cryo System 700, with dry air unit and LN2 tank - Auto-refill system for Oxford Cryosystem LN2 tank with two 180L tanks on weels. With this you never have icing problem with the cryo. - Rigaku RU-H3R rotating anode maybe difficult to move, but if you want it, it is yours! Please mail me your interest as soon as possible, preferable befor before May 8th . Next week I start hand out things, and then thing will go for recycling, sad but true. If you have trouble arrange transport at short notice, the equipment can potentially be here until mid-June. I reserve the right to choose among interested. If you have questions, please mail or call me. Björn Kauppi Structure Biology Karo Bio AB Novum SE-141 57 Huddinge SWEDEN Phone +46(0)86086083 __ This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only. Any unauthorized review, use, disclosure or distribution is prohibited. If you have received this message in error, please advise the sender and delete the e-mail and any attachments from your files. Thank you! __
Re: [ccp4bb] Alexander Rich
Dear Colleagues, I do not think it is highly inappropriate that a crucial episode in the history of crystallography is described/commmented on in this thread, and I am not sure by whom its removal will be highly appreciated, other than by Prof. Berger. I do not know any of the protagonists of this episode, except by reputation, and the only thing I would be ready to concede is that maybe the subject was brought up a bit too close to the sad death of Prof. Rich. But if someone is that distinguished, his/her life story will be discussed, for better (mostly) or worse (occasionally). Emmanuel Dr. Emmanuel Saridakis PhD Biophysics, MSc History and Philsophy of Science Institute of Nanscience and Nanotechnology N.C.S.R. Demokritos Athens 15310 Greece - Original Message - From: Edward A. Berry ber...@upstate.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 2 May, 2015 23:30:29 Subject: Re: [ccp4bb] Alexander Rich passed away Monday April 27, 2015 On 05/02/2015 12:23 PM, Imre Berger wrote: Dear Edward - Would you be so kind and explain why you went ahead to post that comment about Alex Rich on CCP4, in a thread which announced the sad news of his passing away? Yes- I realized after posting it that it was inappropriate. If there is any way to remove a post, I will be glad to do so. In any case an apology is due. As for the explanation, I did not intend it to be in any way derogatory. I have never met Alex Rich, but Prof Sung-Hou Kim was my mentor in crystallography, and I have no doubt that their actions were completely honorable. As explained on the page I linked, it was all a misunderstanding based on poor communications between Kim and Rich, and rapid progress on the part of Kim that Rich was not aware of at the previous meeting. There was no evidence of actual misconduct on the part of Rich or Kim, as grudgingly acknowledged in the final letter from Cambridge. If only I had pointed that out in the email, instead of linking to that first accusatory message, it wouldn't have looked so bad. I had forgotten how inflammatory that first letter was! I was thinking this followed in the lines of Bob Sweet's post, that Rich was a hard-driving man and maybe not afraid of stepping on some peoples toes in order to achieve his goals. I never meant to imply misconduct, although after reading back on my post I can see that interpretation. My sincere apologies to the community and to the memory of professor Rich, Ed Berry I have checked your home page and your CV and it is not obvious to me at all what motivation or stake you could possibly have. Besides, knowing both Alex Rich and Aaron Klug and having discussed with them years ago, I think it is fair to say that only those two are concerned with the issue, and one of them has - very sadly - just died. In any case - in my view it is highly inappropriate indeed that you placed those comments on CCP4. Maybe you could be so kind and remove your contribution from the thread - it would be greatly appreciated. De mortuis nihil nisi bonum Imre -- Imre Berger PhD HDR Professor of Biochemistry Wellcome Trust Senior Investigator Coordinator, EC FP7 ComplexINC project The School of Biochemistry, University of Bristol UK The European Molecular Biology Laboratory EMBL imre.ber...@bristol.ac.uk iber...@embl.fr
[ccp4bb] Scientific Computing in Structural Biology - Support Engineer - SCB Unit, EMBL Heidelberg
Dear Colleagues, The Structural and Computational Biology Unit at EMBL Heidelberg, Germany is looking to recruit an Engineer for Scientific Computing in Structural Biology to handle the following responsibilities: - Development and support of the scientific computing environment of the Unit. - Support scientists to leverage EMBL’s high-performance computing power in computational workflows and scientific data analysis, - Assist scientists in setting up customized solutions for data analysis and processing. - Linux server administration including system setup, OS deployment and software maintenance. - Support a network of about 100 Linux and Windows desktop and laptop workstations including OS and end user software deployment, network integration and troubleshooting of hardware and software issues. - Maintenance of a mainly Linux-based software repository for electron microscopy, X-ray crystallography, NMR and visualisation software including compilation and optimisation. IT support of the in-house crystallization and metabolomics research facilities. - Participation in EMBL-wide infrastructure and networking projects such as Bio-IT. Qualifications and Experience The ideal candidate will have a degree in computer science or related disciplines and at least 5 years work experience in an organization supporting large heterogeneous IT infrastructures. The position is particularly suitable for candidates with previous experience in scientific computing and who want to work in a cutting-edge research environment. The position requires technical expertise in managing current desktop operating systems including Linux and Windows. The successful candidate will have solid knowledge of current standard desktop and client application software packages. Experience in automation of systems and software installations and a broad overview of major aspects of networking and related technologies is required. Previous exposure to high-performance computing and different server technologies would be advantageous. Good communication and English skills are required and a basic knowledge of German would be advantageous. The ideal candidate will be able to work independently as well as working as a part of a team. A service-oriented attitude, excellent interpersonal skills and the ability to work well and professionally under high demand are essential. Please apply online through www.embl.org/jobs Closing Date: 31 May 2015 Reference Number: HD_00682 -- Dr. Christoph W. Müller Joint Head of Structural and Computational Biology Unit EMBL Meyerhofstrasse 1 69117 Heidelberg, Germany email: cmuel...@embl.de phone: 0049-6221-387-8320 fax: 0049-6221-387-519 http://www.embl.de http://www.embl.de/research/units/scb/mueller_christoph/index.html - HD_00682.pdf Description: Adobe PDF document
[ccp4bb] calculation of ASA between two helices
Hi all, I am trying to calculate accessible surface area between 2 helices from 2 different domains of protein. PISA gives me either total interface of the protein or per residue. Can anyone please suggest me what would be the best possible way to get it? Thanks and regards Atul
Re: [ccp4bb] calculation of ASA between two helices
How about cutting up the pdb file into the desired sections and using pisa on them? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Atul Kumar Sent: Monday, May 04, 2015 1:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] calculation of ASA between two helices Hi all, I am trying to calculate accessible surface area between 2 helices from 2 different domains of protein. PISA gives me either total interface of the protein or per residue. Can anyone please suggest me what would be the best possible way to get it? Thanks and regards Atul
[ccp4bb] cryo condition
Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] cryo condition
How long are you cryoprotecting for? You don't really need more than a few seconds. If I have sensitive crystals i tend to just swipe them slowly through the final CP solution and often that works. If I would leave them in the CP solution for more than say 30 seconds the crystals would behave like you describe. GL Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Monday, May 04, 2015 7:43 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cryo condition Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] cryo condition
High concentration of ammonium formate is a cryosolvent On Mon, May 4, 2015 at 5:20 PM, Tristan Croll tristan.cr...@qut.edu.au wrote: What about nature's favourite cryoprotectant, trehalose? From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of Roger Rowlett rrowl...@colgate.edu Sent: Tuesday, 5 May 2015 7:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] cryo condition We rarely use glycerol anymore, because it seems to fail so often for many of our current proteins. Try glucose, 25-30%. This is most conveniently done by weighing 125-150 mg of glucose in a microcentrifuge tube, then addding well solution to the 0.5 mL mark and mixing until completely dissolved. Then you can try dunking crystals in the cryo solution, or, you can try the no-fail method (which does fail on occasion) of cryoprotecting directly in the crystallization drop by slow addition of the cryoprotectant. See http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Mounting+Protein+Crystals . We have often found the slow addition of a glucose cryoprotectant works for fragile, high solvent content crystals that are prone to cracking under osmotic stress. Other alternatives include high concentrations of sodium malonate (1-2M), or high concentrations of sodium formate (I think around 4 M?). These could also be introduced gradually if required. Good luck! ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 5/4/2015 2:43 PM, Faisal Tarique wrote: Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance
Re: [ccp4bb] cryo condition
What about nature's favourite cryoprotectant, trehalose? From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of Roger Rowlett rrowl...@colgate.edu Sent: Tuesday, 5 May 2015 7:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] cryo condition We rarely use glycerol anymore, because it seems to fail so often for many of our current proteins. Try glucose, 25-30%. This is most conveniently done by weighing 125-150 mg of glucose in a microcentrifuge tube, then addding well solution to the 0.5 mL mark and mixing until completely dissolved. Then you can try dunking crystals in the cryo solution, or, you can try the no-fail method (which does fail on occasion) of cryoprotecting directly in the crystallization drop by slow addition of the cryoprotectant. See http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Mounting+Protein+Crystals. We have often found the slow addition of a glucose cryoprotectant works for fragile, high solvent content crystals that are prone to cracking under osmotic stress. Other alternatives include high concentrations of sodium malonate (1-2M), or high concentrations of sodium formate (I think around 4 M?). These could also be introduced gradually if required. Good luck! ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 5/4/2015 2:43 PM, Faisal Tarique wrote: Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance
[ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite
Dear All, when starting CCP4i via the icon, AutoSharp remains greyed out, suggesting it is not installed. However, when I start CCP4i in an XQuartz window (i.e. “ccp4i ”), AutoSharp can be run. I guess this may be because in first way my “.profile” file is not read, any ideas how to fix this? Greetings, Mark J van Raaij mjvanra...@cnb.csic.es mailto:mjvanra...@cnb.csic.es http://www.cnb.csic.es/~mjvanraaij http://www.cnb.csic.es/~mjvanraaij
Re: [ccp4bb] cryo condition
We rarely use glycerol anymore, because it seems to fail so often for many of our current proteins. Try glucose, 25-30%. This is most conveniently done by weighing 125-150 mg of glucose in a microcentrifuge tube, then addding well solution to the 0.5 mL mark and mixing until completely dissolved. Then you can try dunking crystals in the cryo solution, or, you can try the no-fail method (which does fail on occasion) of cryoprotecting directly in the crystallization drop by slow addition of the cryoprotectant. See http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Mounting+Protein+Crystals. We have often found the slow addition of a glucose cryoprotectant works for fragile, high solvent content crystals that are prone to cracking under osmotic stress. Other alternatives include high concentrations of sodium malonate (1-2M), or high concentrations of sodium formate (I think around 4 M?). These could also be introduced gradually if required. Good luck! ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 5/4/2015 2:43 PM, Faisal Tarique wrote: Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance
Re: [ccp4bb] cryo condition
If in doubt, try dragging the crystal through a 1:1 mix of Paratone-N and Mineral oil until most or all the mother liquor from surrounding the crystal has been removed. There are more tips here: http://hamptonresearch.com/tip_detail.aspx?id=99 Good luck! D On Mon, 4 May 2015 19:45 Faisal Tarique faisaltari...@gmail.com wrote: Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance -- Regards Faisal School of Life Sciences JNU
