[ccp4bb] XDS
Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave out wedges like this? I have tried like so, but I have the Impression it only takes then the last number of Frames, in this example it would only take 1001 to 1200. Thanks a lot. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] XDS
Hi Almudena, if you run XDS through xia2, you can define multiple wedges in your info: BEGIN SWEEP SWEEP1 IMAGE image_0001.cbf DIRECTORY /path/to/files/ START_END 1 900 END SWEEP BEGIN SWEEP SWEEP2 IMAGE image_0001.cbf DIRECTORY /path/to/files/ START_END 1001 1200 END SWEEP Andreas On 29/09/2014 10:56, Almudena Ponce Salvatierra wrote: Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave out wedges like this? I have tried like so, but I have the Impression it only takes then the last number of Frames, in this example it would only take 1001 to 1200. Thanks a lot. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] XDS
Hi Almudena, Greeting from Oulu.Other possibility would be, process the group of Frames separately in XDS and merge them in the end. Thank you Rajesh On Mon, Sep 29, 2014 at 12:56 PM, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave out wedges like this? I have tried like so, but I have the Impression it only takes then the last number of Frames, in this example it would only take 1001 to 1200. Thanks a lot. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- ---x With regards Rajesh K. Harijan Phd Researcher Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 417064469 http://www.biocenter.oulu.fi/projects/wierenga.html
Re: [ccp4bb] XDS
Hi, Another option to do it in xds (following advice of a Kay) is to rename the frames you don't like differently than the template. Boaz Original message From: Almudena Ponce Salvatierra maps.fa...@gmail.com Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] XDS Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave out wedges like this? I have tried like so, but I have the Impression it only takes then the last number of Frames, in this example it would only take 1001 to 1200. Thanks a lot. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] AW: [ccp4bb] XDS
Dear Almudena, Doing two different runs (1-900 and 1001-1200) will do what you want. You will have to do it from 2 different directories (called e.g. wedge1 and wedge2, or whatever). With XSCALE you can merge the runs. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Almudena Ponce Salvatierra Gesendet: Montag, 29. September 2014 11:57 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] XDS Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave out wedges like this? I have tried like so, but I have the Impression it only takes then the last number of Frames, in this example it would only take 1001 to 1200. Thanks a lot. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] XDS
Hi, Also, if you go from XDS to aimless with the INTEGRATE_ASCII.HKL or XDS_ASCII.HKL file, aimless has an option to omit batches (frames) as you wish from scaling or merging. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena Ponce Salvatierra [maps.fa...@gmail.com] Sent: Monday, September 29, 2014 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] XDS Dear all, I would like to ask something regarding XDS. Is it possible, without changing the Name of the Frames, to leave some out while processing? i.e. something like defining twice the data range DATA_RANGE= 1 900 !DATA_RANGE= 901 1000 DATA_RANGE= 1001 1200 Is there a way to do so? to leave out wedges like this? I have tried like so, but I have the Impression it only takes then the last number of Frames, in this example it would only take 1001 to 1200. Thanks a lot. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] Pipettes
Hi, This is way off topic but relevant. Does anyone routinely use the Rainin Classic Pipet series? If so, what are your thoughts and how often do they need to be calibrated? Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org
[ccp4bb] frozen pellet insoluble protein
Dear all, I've encountered people who refuse to freeze cells and always lyse fresh pellets. Better protein, they say. I've never had reason to do so myself, or even to believe in their voodoo. Up until now, maybe. My protein expresses well and is almost all in the soluble fraction in an expression test from a fresh pellet. The large-scale expression from the same pellet, now frozen and thawed, yielded 90% insoluble protein. If it's the freezing that dooms the protein, I'm happy to redo the fermentor run. Are there other examples out there of this? Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] frozen pellet insoluble protein
I have experience with some proteins that don't tolerate freeze-thawing very well. It's hard to say exactly what the physical chemistry of this is, but it probably relates to (1) aggregation due to high concentration or protein or salts during the freezing process as water is removed, and/or (2) pH shifts due to changes in pKa of buffers/proteins as the temperature is lowered. Usually freezing in whole cells is less problematic than freezing purified protein solutions, but there are no absolutes. One protein we worked on could only be stabilized from cradle to grave in 20% glycerol, 100 mM DTT, and 4 deg C. Would not tolerate freezing, ever. Not even in cell pellets. Died at 25 deg C in a couple of hours--had to work quickly to do kinetics. Worst...protein...to work on...ever. Cheers, ___ 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 9/29/2014 11:02 AM, Andreas Förster wrote: Dear all, I've encountered people who refuse to freeze cells and always lyse fresh pellets. Better protein, they say. I've never had reason to do so myself, or even to believe in their voodoo. Up until now, maybe. My protein expresses well and is almost all in the soluble fraction in an expression test from a fresh pellet. The large-scale expression from the same pellet, now frozen and thawed, yielded 90% insoluble protein. If it's the freezing that dooms the protein, I'm happy to redo the fermentor run. Are there other examples out there of this? Thanks. Andreas
[ccp4bb] Fedora Core 20 issues
Hi all, So, I know this probably isn’t the right place, but I’m certain most of you here have battled/fixed this issue. I just did a clean install of FC20 on an AMD dual core system. I opted for the 32 bit version, as these workstations are used for multiple things (and I find that it’s just easier most of the time, though 64 bit may be where I need to go eventually). Anyway - when running chimera - my computer constantly freezes. Obviously I’m missing something. I’m not doing anything fancy - I use Zalman monitors connected to generic video cards. I can run coot fine - I don’t know about ccp4i (it seems to run, but I haven’t challenged it in any way). Any thoughts on where I should start here? Thanks Dave
[ccp4bb] Postdoctoral position availiable at the University of Massachusetts
Hi all, An NIH-funded postdoctoral position is available in the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School in Worcester, MA. Our multidisciplinary lab focuses on using biochemical, structural, cell biological, microscopy and genetic studies to elucidate the structure and function of the exocyst complex, SNARE proteins and other key regulators of membrane trafficking in yeast and mammalian cells. Applicants must have (or expect to obtain shortly) a Ph.D. in Biochemistry, Molecular or Cell Biology, or a related field. Previous hands-on experience with protein biochemistry, purification, and analysis of protein-protein interactions is necessary. In addition, experience with protein crystallography, mass spectrometry, tissue culture, electron microscopy and/or fluorescence microscopy is desired, but not required. Preference will be given to candidates who recently received their Ph.D. degree and who are available for an in-person interview. Lab website: http://www.umassmed.edu/bmp/faculty/munson/ To be considered, please send CV, brief description of research interests and contact information of references to Dr. Mary Munson at mary.mun...@umassmed.edumailto:mary.mun...@umassmed.edu. Cheers, -Mary
