[ccp4bb] BSR-2013 News and A call for BSR-2016 bids
Dear All, with this mail we would like to draw your attention to the upcoming 11th Biology and Synchrotron Radiation Conference in Hamburg ( Sunday 8th September until Wednesday 11th September 2013). We were able to compile an exciting Conference Programme which is now available at http://www.bsr2013.org/BSR13-01/programme/index.html. Please note that the registration without abstract is open until August, 15th, so there is still an opportunity for participation! We are also pleased to announce a bid for hosting the next Biology and Synchrotron Radiation Conference in 2016. The decision about the venue for BSR-2016 will be taken during BSR-2013. Further information regarding the bid can be found under the following link: http://www.bsr2013.org/BSR13-01/info/Bid2016/index.html We look forward to welcoming you all here in downtown Hamburg! With best regards Matthias Wilmanns, Dmitri Svergun, BSR-2013 Co-Chairs
[ccp4bb] [ot] looking for Crystal Farm 400 service maintenance
Dear all, sorry to bother you with an off-topic request. Does anybody have a contact for a person or a firm that provides maintenance and service for Crystal Farm plate imagers? They used to be serviced by Bruker, but they don't support them anymore, as far as I know. Any help highly appreciated, best regards, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990
Re: [ccp4bb] frosted crystals during storage in pucks
At Elspeth's request, here's a link to a picture of the rack we use for drying out shipping dewars. https://www.dropbox.com/s/8ber2iikra9x73y/2013-02-21%2013.39.38.JPG Very simple and both we and the Lea group here have found it to make a huge difference the the effectiveness and longevity of our dewars. Ed. -- Dr. E.D. Lowe Department of Biochemistry University of Oxford South Parks Road Oxford, UK OX1 3QU e:edward.l...@bioch.ox.ac.uk t: +44 (0) 1865 613288 f: +44 (0) 1865 613201 On 12/07/2013 14:27, Edward Snell esn...@hwi.buffalo.edu wrote: Ditto - I was always impressed with the contraption in the Garman lab which, if I remember correctly, is made of a thick block of wood and some plumbing pipes. It is designed to hold empty open Dewars inverted so they could dry. Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Senior Scientist, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here! -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ginell, Stephan L. Sent: Friday, July 12, 2013 12:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] frosted crystals during storage in pucks My experience with xtals frosting in LN2 either in a dewar, while freezing, or in pucks, has been because the LN2 was contaminated with ice crystals The fog you see above your dewar when freezing xtals is frozen water vapor...it will fall and collect in the LN2 and also deposit on the xtals. Dewars filled with recycled LN2 get contaminated with ice. Dewars dried upside down allow the cold gas to flow out and warm moist air to flow in and the water to condense inside the dewar (basic physics). To dry shipping dewars keep up right while warming. Steve Sent from my iPad On Jul 11, 2013, at 5:25 PM, Nathaniel Clark nathanielcl...@gmail.commailto:nathanielcl...@gmail.com wrote: At our last synchrotron trip, the beamline staff suggested that the problem was due to moisture accumulation in the dry shipper. They recommended storing them inverted (for a few weeks, if I recall), and/or putting a supply of dry air in the dewer. Haven't tried it yet! Nat On Thu, Jul 11, 2013 at 5:08 PM, Rain Field rainfiel...@163.commailto:rainfiel...@163.com wrote: Hi All, We found if the crystals are storaged in pucks for 3-4 days in shipping dewar (with liquid nitrogen), they are almost frosted. Although I can wash them with liquid nitrogen, but it's not convenient to do that for each crystals. I doubt it's because the humid air in North West America. Does anyone has an idea how to avoid this? Thank you!
Re: [ccp4bb] Dose anyone see this ligand before?
Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Dose anyone see this ligand before?
It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Tuesday, July 16, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] Dose anyone see this ligand before?
Dear wei, i think you have to keep in mind what do you have in your cristal growing condition, and in you protein buffer. Because maybe you can find which molecules this ligand could be. It's difficult to help more, because we don't know you level of sigma for the map and the resolution of your dataset. But in all case, if you have an idea of what it could be, and you don't find restraint and molecules in existing library, you can use monomer library sketcher in ccp4 to sketch manually your molecule, and generate library of restraints. Hope to help you. Nicolas Le 16/07/13 17:56, Oganesyan, Vaheh a écrit : It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. /*/Vaheh/*/ *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Bosch, Juergen *Sent:* Tuesday, July 16, 2013 11:53 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei ** picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] Dose anyone see this ligand before?
Yes that was what I was thinking as well, that's why the size-comparisson. Jürgen On Jul 16, 2013, at 11:56 AM, Oganesyan, Vaheh wrote: It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Tuesday, July 16, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Dose anyone see this ligand before?
Its look like pyrophosphate to me . wts you protein's nature is this phosphatase or ATPase ?? vandna On Tue, Jul 16, 2013 at 11:19 AM, Bosch, Juergen jubo...@jhsph.edu wrote: Yes that was what I was thinking as well, that's why the size-comparisson. Jürgen On Jul 16, 2013, at 11:56 AM, Oganesyan, Vaheh wrote: It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. * Vaheh* -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Bosch, Juergen *Sent:* Tuesday, July 16, 2013 11:53 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei * * picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
Re: [ccp4bb] Dose anyone see this ligand before?
hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” From: sonali dhindwal sonali11dhind...@yahoo.co.in To: ccp4...@hotmail.com ccp4...@hotmail.com Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” From: Wei Feng ccp4...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 16 July 2013 9:05 PM Subject: [ccp4bb] Dose anyone see this ligand before? Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei
