Re: [ccp4bb] DNA version converter
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, # pdbvconv -p udo.pdb -o udov.pdb # pdbvconv -p udov.pdb -o udovv.pdb # diff -q udo.pdb udov.pdb Files udo.pdb and udov.pdb differ # diff -q udov.pdb udovv.pdb Files udov.pdb and udovv.pdb differ # diff -q udo.pdb udovv.pdb # it works for me, Version: 1.0 (11 June 2008) from buster 2.10. Which version of pdbvconv are you using? Best, Tim On 05/21/2013 10:40 PM, Ed Pozharski wrote: On 05/21/2013 04:35 PM, Francis Reyes wrote: Since you're using buster, have you tried global phasing's own pdbvconv tool? Naturally, but it leaves file unchanged. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRnGG4UxlJ7aRr7hoRAsnXAKC+r79WizxvilEzrSch9t2/TgQwFwCeOpwy 5sRFm0fJArN+1WWYiTQcYgA= =KM83 -END PGP SIGNATURE-
[ccp4bb] Workshop - The Future of Microfocus Protein Crystallography - 24-25 September, 2013, Lund, Sweden
Dear all, I would like to announce a workshop on The Future of Microfocus Protein Crystallography which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting. Registration will be through the user meeting website which will open for registration soon. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.sehttp://www.mps.lu.se/ PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX
[ccp4bb] cryocrystals
Hi Does anybody know how long one could store a crystal in liquid nitrogen for before it will no longer diffract well? I'm talking in the order of weeks to months... careina
Re: [ccp4bb] cryocrystals
I dare say indefinitely. Your crystal life expectancy drops rapidly though with somebody not remembering to fill up the dewar. Transferring crystals to pucks etc. is another problem. I had some crystals which I could not remember what they were (label broke off the cane) and we simply reshoot them after 1 year and figured out it was the usual suspect from the cell dimensions. Jürgen On May 22, 2013, at 8:38 AM, Careina Edgooms wrote: Hi Does anybody know how long one could store a crystal in liquid nitrogen for before it will no longer diffract well? I'm talking in the order of weeks to months... careina .. 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] cryocrystals
careina Cryocrystals will last several months and more. Make sure that your LN2 is dry. On Wed, 22 May 2013 14:38:51 +0200, Careina Edgooms careinaedgo...@yahoo.com wrote: Hi Does anybody know how long one could store a crystal in liquid nitrogen for before it will no longer diffract well? I'm talking in the order of weeks to months... careina -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab http://www-dsv.cea.fr/ibitecs/simopro/ltmb/cristallogenese LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://scholar.google.com/citations?hl=enuser=Kvm06WIoPAsCpagesize=100sortby=pubdate http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] cryocrystals
in theory I would say decades/eons. in practice it probably depends on how much water/ice your liquid nitrogen contains, multiple refillings of the liquid nitrogen might slowly deposit tiny ice crystals on the crystals and slowly make diffraction worse... Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 22 May 2013, at 14:38, Careina Edgooms wrote: Hi Does anybody know how long one could store a crystal in liquid nitrogen for before it will no longer diffract well? I'm talking in the order of weeks to months... careina
Re: [ccp4bb] cryocrystals
Theoretically? Millions to billions of years. Practically? They will last until the first time you forget to fill the dewar. Or until the Sun explodes and in the rush to leave Earth your descendants forget to pack it. Whichever comes first. Seriously, as long as the crystals have actually stayed below ~130 K they are as stable as glass beads. This is because they actually ARE glass beads at this temperature. The diffusion rate, however, goes up by a factor of a million at ~140K and that seems to be why there are so many rumors floating around out there that crystals change under lN2. Perhaps perpetuated by people who want space in the storage dewar. For example, there is a rumor that gasses like xenon will slowly leach out of cryo-cooled samples. I heard that one about 10 years ago, and since then I have been periodically checking the occupancy of the Xe sites in a particular cryo-cooled lysozyme crystal. So far, I can see no change. But if I ever make a mistake opening the tongs and warm it to 140K, even for a millisecond, I'm sure it will be ruined. As for ice that accumulates at 100K, this is always easy to remove with a jet of liquid nitrogen. We use this commercial product: http://brymill.com/brymill-cryosurgical-devices/brymill-cry-ac-cry-ac-3.html and there is a new one from MiTeGen http://www.mitegen.com/mic_catalog.php?c=iceoff which is cheaper as it is not a medical device. You just have to be careful not to knock the crystal off with it, and not to blow the cryo stream out of the way. Can't just point and shoot. You need to sweep the liquid stream over the crystal. It is surprisingly effective. You can also check out these studies on dewar life: http://dx.doi.org/10.1107/S0021889804025403 and on the thermal spike you can encounter while mounting/unmounting with cryovials: http://dx.doi.org/10.1007/s10969-007-9029-0 -James Holton MAD Scientist On 5/22/2013 5:38 AM, Careina Edgooms wrote: Hi Does anybody know how long one could store a crystal in liquid nitrogen for before it will no longer diffract well? I'm talking in the order of weeks to months... careina
[ccp4bb] 43rd Mid-Atlantic Macromolecular Crystallography Meeting -- reminder
*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held next week, May 30-June 01 at Duke University in Durham, North Carolina. Registration and details can be found at http://www.mid-atlantic.org. We encourage you to submit your abstracts for a poster presentation as the deadline is fast approaching! *DEADLINES (updated):* Abstract submission for poster - Next Monday, May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pem...@duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.
Re: [ccp4bb] DNA version converter
Tim, naturally, the issue is specific to a particular pdb file (it would be indeed strange if the conversion tool from a major software package would fail in general sense). Ed. On Wed, 2013-05-22 at 08:12 +0200, Tim Gruene wrote: Hi Ed, # pdbvconv -p udo.pdb -o udov.pdb # pdbvconv -p udov.pdb -o udovv.pdb # diff -q udo.pdb udov.pdb Files udo.pdb and udov.pdb differ # diff -q udov.pdb udovv.pdb Files udov.pdb and udovv.pdb differ # diff -q udo.pdb udovv.pdb # it works for me, Version: 1.0 (11 June 2008) from buster 2.10. Which version of pdbvconv are you using? Best, Tim On 05/21/2013 10:40 PM, Ed Pozharski wrote: On 05/21/2013 04:35 PM, Francis Reyes wrote: Since you're using buster, have you tried global phasing's own pdbvconv tool? Naturally, but it leaves file unchanged. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] DNA version converter
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ed, the answers you received were correct with respect to the question you asked. If they are not satisfactory, you have not given sufficient information. Regards, Tim On 05/22/2013 05:54 PM, Ed Pozharski wrote: Tim, naturally, the issue is specific to a particular pdb file (it would be indeed strange if the conversion tool from a major software package would fail in general sense). Ed. On Wed, 2013-05-22 at 08:12 +0200, Tim Gruene wrote: Hi Ed, # pdbvconv -p udo.pdb -o udov.pdb # pdbvconv -p udov.pdb -o udovv.pdb # diff -q udo.pdb udov.pdb Files udo.pdb and udov.pdb differ # diff -q udov.pdb udovv.pdb Files udov.pdb and udovv.pdb differ # diff -q udo.pdb udovv.pdb # it works for me, Version: 1.0 (11 June 2008) from buster 2.10. Which version of pdbvconv are you using? Best, Tim On 05/21/2013 10:40 PM, Ed Pozharski wrote: On 05/21/2013 04:35 PM, Francis Reyes wrote: Since you're using buster, have you tried global phasing's own pdbvconv tool? Naturally, but it leaves file unchanged. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRnO2kUxlJ7aRr7hoRAvDBAKDBPEpwMp0Q/jwxn2XxrgUR+d/uzgCgsxjw OAc8Y6g2PdhIeQc3t6m6WFE= =Ht30 -END PGP SIGNATURE-
Re: [ccp4bb] DNA version converter
On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote: the answers you received were correct with respect to the question you asked. If they are not satisfactory, you have not given sufficient information. Tim, Not sure when I expressed any dissatisfaction with replies I received. I asked whether someone had a simple tool to turn v3 DNA records back to v2. I got an excellent off-list suggestion to use Remediator tool from kinemage/molprobity (writen by Jeff Headd and Robert Immormino). It was probably easy to guess that I tried pdbvconv and ran into problems (in fact, buster takes care of conversion internally unless it fails). I appreciate your initial comment that pdbvconv works for you and was simply pointing out that my observations are not of general nature and obviously specific to a particular file I was trying to convert. It appears that you were offended by that and if so, it was not my intent. In my defense, I only asked for available conversion tools and did not ask specifically for help with pdbvconv. With this in mind, I hope I can be forgiven for not posting unpublished structural model on a bulletin board in order to provide sufficient information for answering a question I did not ask. If you are interested in specifics, the problem was that some other program made residue names left-justified. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
[ccp4bb] Off-topic looking for unusual expression promoter
Does anyone know of an expression vector (or really what I am interested in is the existence of and/or sequence of a promoter/operator) for E. coli protein expression that is NOT cAMP dependent and that is NOT a derivative of the lac operon? Something like a pBAD or pPRO promoter mutant that did NOT require cAMP/CRP/CAP binding in the bug for expression? I can't find anything yet by lit. searches. Thanks Laurie Betts
Re: [ccp4bb] DNA version converter
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ed, I do feel offended because I follow the ccp4bb with the intention of helping people with my answers, which does take time. If it turns out the I wasted my time because of the lack of information I consider the question asked not follow what I consider netiquette. I doubt that one line from a PDB file or the point that you have used pbdvconv before (especially in case you were aware of the problem being due to a simple shift - of course I do not know whether you were aware of it when opening the thread) and it failed would have revealed any information that would give your competitors any advantage, but it would have narrowed down the problem and probably the number of people spending time trying to find and give a helpful answer. Regards, Tim On 05/22/2013 07:55 PM, Ed Pozharski wrote: On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote: the answers you received were correct with respect to the question you asked. If they are not satisfactory, you have not given sufficient information. Tim, Not sure when I expressed any dissatisfaction with replies I received. I asked whether someone had a simple tool to turn v3 DNA records back to v2. I got an excellent off-list suggestion to use Remediator tool from kinemage/molprobity (writen by Jeff Headd and Robert Immormino). It was probably easy to guess that I tried pdbvconv and ran into problems (in fact, buster takes care of conversion internally unless it fails). I appreciate your initial comment that pdbvconv works for you and was simply pointing out that my observations are not of general nature and obviously specific to a particular file I was trying to convert. It appears that you were offended by that and if so, it was not my intent. In my defense, I only asked for available conversion tools and did not ask specifically for help with pdbvconv. With this in mind, I hope I can be forgiven for not posting unpublished structural model on a bulletin board in order to provide sufficient information for answering a question I did not ask. If you are interested in specifics, the problem was that some other program made residue names left-justified. Cheers, Ed. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRnSKmUxlJ7aRr7hoRAvjDAJwKvSZSrSsqajOGLBcnpPFdglPaiQCdFs74 5A4aVA4K8aRdg0EkFA/IZqU= =4FWF -END PGP SIGNATURE-
Re: [ccp4bb] DNA version converter
Dear Tim, I am sorry that you feel offended. It is rather unfortunate that you got an impression from my secondary comment that I am asking for help with pdbvconv when I wasn't. It is also rather unfortunate that I have figured out what the problem was myself and therefore did not have an opportunity to ask for and fully utilize your help and that of other ccp4bb members. In general, it is rather unfortunate that helping others often feels and occasionally is a waste of time. Hopefully this unfortunate experience will not dissuade you from positively contributing to the ccp4bb to the same extent to which it dissuades me from ever again soliciting any advice through this venue. Cheers, Ed. PS. Naturally, at the time of the original post and the subsequent one you responded to I did not yet know what was wrong with the specific pdb file. To have such knowledge and yet ask why pdbvconv fails (which I did not ask) would be both stupid and evil. Then again, I may be both of these things. On Wed, 2013-05-22 at 21:55 +0200, Tim Gruene wrote: Dear Ed, I do feel offended because I follow the ccp4bb with the intention of helping people with my answers, which does take time. If it turns out the I wasted my time because of the lack of information I consider the question asked not follow what I consider netiquette. I doubt that one line from a PDB file or the point that you have used pbdvconv before (especially in case you were aware of the problem being due to a simple shift - of course I do not know whether you were aware of it when opening the thread) and it failed would have revealed any information that would give your competitors any advantage, but it would have narrowed down the problem and probably the number of people spending time trying to find and give a helpful answer. Regards, Tim On 05/22/2013 07:55 PM, Ed Pozharski wrote: On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote: the answers you received were correct with respect to the question you asked. If they are not satisfactory, you have not given sufficient information. Tim, Not sure when I expressed any dissatisfaction with replies I received. I asked whether someone had a simple tool to turn v3 DNA records back to v2. I got an excellent off-list suggestion to use Remediator tool from kinemage/molprobity (writen by Jeff Headd and Robert Immormino). It was probably easy to guess that I tried pdbvconv and ran into problems (in fact, buster takes care of conversion internally unless it fails). I appreciate your initial comment that pdbvconv works for you and was simply pointing out that my observations are not of general nature and obviously specific to a particular file I was trying to convert. It appears that you were offended by that and if so, it was not my intent. In my defense, I only asked for available conversion tools and did not ask specifically for help with pdbvconv. With this in mind, I hope I can be forgiven for not posting unpublished structural model on a bulletin board in order to provide sufficient information for answering a question I did not ask. If you are interested in specifics, the problem was that some other program made residue names left-justified. Cheers, Ed. -- Bullseye! Excellent shot, Maurice. Julian, King of Lemurs.
