[ccp4bb] normal protein in detergent?
Dear all, sorry for the off-topic and possibly very naive question- but does anyone know what happens if normal protein is put in detergent-containing aqueous solution? how much detergent can a regular protein tolerate? I was trying to search literature but couldn't find any... Thank you greatly for your attention and inputs. Best, Melody
Re: [ccp4bb] normal protein in detergent?
Helps sometimes, Start with: A. McPherson, S. Koszelak, H. Axelrod, J. Day, R. Williams, L. Robinson, M. McGrath and D. Cascio (1986) An experiment regarding crystallization of soluble proteins in the presence of beta-octyl glucoside. J Biol Chem 261:1969-1975. Twenty-one soluble proteins, five tRNAs, and three protein-nucleic acid complexes were studied in a systematic manner with regard to their crystallization behavior from polyethylene glycol and ammonium sulfate solutions in the presence of 0 to 1.5% beta-octyl glucoside. Our observations suggest that this neutral detergent does influence in a very positive way the growth characteristics of the macromolecules included in this experiment. In general, more reproducible and rapid growth was noted with an increased number of large individual crystals at the expense of microcrystals. In several cases, new crystal forms were discovered. Selected x-ray diffraction analyses imply that crystals grown in the presence of beta-octyl glucoside diffract as well or better than those grown in its absence. In addition, a screen of two proteins grown in the presence of 14 different common detergents suggested that a general detergent effect may be beneficial for the growth of crystals of biological macromolecules. Then check out the detergent screens from Hampton and others Joe Becker - Merck Research Labs From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Melody Lin Sent: Friday, March 14, 2008 9:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] normal protein in detergent? Dear all, sorry for the off-topic and possibly very naive question- but does anyone know what happens if normal protein is put in detergent-containing aqueous solution? how much detergent can a regular protein tolerate? I was trying to search literature but couldn't find any... Thank you greatly for your attention and inputs. Best, Melody -- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] normal protein in detergent?
Melody, While Joe addressed the possible effects of detergents on the crystallization of proteins, the possible effects (both negative and positive) of detergents on proteins are quite variable. Often there are no general rules except to avoid ionic detergents (from anionic detergents like SDS or sarcoyl or cationic detergents like cetylamine- Br). Also some zwitterionic detergents can become ionic at pH extremes (<5 and >9). As the effects are protein dependent, few general rules have emerged. Sometimes nonionic detergents reduce aggregation or the proteins are stable at high detergent concentrations (>1% w/w). For others, they interfere with activity in the presence of small amounts of detergents. For example, maltose binding protein, which is often used as a fusion protein to aid in purification and to enhance solubility, loses its capacity to bind to amylose columns in the presence of many nonionic detergents. While one might suspect that only glycoside detergents (like octyl glucoside or dodecyl maltoside) might do this, the effect is more general. Hence, when we purify a MBP fusion protein in the presence of nonionic detergents, we often add a His-tag to circumvent this problem, if it arises. The bottom line is that the solution effects of detergents are protein dependent, and few general rules have emerged Cheers, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: [EMAIL PROTECTED] On Mar 14, 2008, at 9:59 AM, Becker, Joseph W wrote: Helps sometimes, Start with: A. McPherson, S. Koszelak, H. Axelrod, J. Day, R. Williams, L. Robinson, M. McGrath and D. Cascio (1986) An experiment regarding crystallization of soluble proteins in the presence of beta-octyl glucoside. J Biol Chem 261:1969-1975. Twenty-one soluble proteins, five tRNAs, and three protein-nucleic acid complexes were studied in a systematic manner with regard to their crystallization behavior from polyethylene glycol and ammonium sulfate solutions in the presence of 0 to 1.5% beta-octyl glucoside. Our observations suggest that this neutral detergent does influence in a very positive way the growth characteristics of the macromolecules included in this experiment. In general, more reproducible and rapid growth was noted with an increased number of large individual crystals at the expense of microcrystals. In several cases, new crystal forms were discovered. Selected x-ray diffraction analyses imply that crystals grown in the presence of beta-octyl glucoside diffract as well or better than those grown in its absence. In addition, a screen of two proteins grown in the presence of 14 different common detergents suggested that a general detergent effect may be beneficial for the growth of crystals of biological macromolecules. Then check out the detergent screens from Hampton and others Joe Becker - Merck Research Labs From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Melody Lin Sent: Friday, March 14, 2008 9:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] normal protein in detergent? Dear all, sorry for the off-topic and possibly very naive question- but does anyone know what happens if normal protein is put in detergent- containing aqueous solution? how much detergent can a regular protein tolerate? I was trying to search literature but couldn't find any... Thank you greatly for your attention and inputs. Best, Melody -- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
[ccp4bb] Announcement: EMBO Practical course on X-ray crystal structure determination
Dear community,Dear community, This is an announcement for a EMBO/MAX-INF2 practical course X-ray crystal structure determination of macromolecules to be held at the Soleil Synchrotron near Paris (France), from the 14th-21st of September 2008. This course is meant as an introduction to the determination of protein/DNA X-ray structures, and covers the process from construct design till validation & deposition of the structure in the PDB. Lectures will be combined with practicals on crystallization, SAD/MAD structure determination, structure refinement, model building and validation. Tutors include: Kevin Cowtan, Anastassis Perrakis, Jim Pflugrath, Randy Read, Jane Richardson, Thomas Schneider, Bill Shepard, Enrico Stura, Piotr Sliz, Andy Thompson, Herman van Tilbeurgh, Clemens Vonrhein and Peter Zwart. Course registration and accommodation/meals are free for academic participants. There are four travel grants available for students from Croatia, Czech Republic, Estonia, Greece, Hungary, Israel, Poland, Portugal, Slovakia, Slovenia and Turkey. For more information and participant registration, please visit the course website at: http://cwp.embo.org/pc08-26 Best regards, Rob Meijers Beamline Scientist PROXIMA II Synchrotron Soleil - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
[ccp4bb] trim back to Cbeta in coot : summary
Hi ccp4'ers: Thanks for the quick response on the coot side chain trimming issue. --- I received an email from Patricia Legler to try Chainsaw (a ccp4 program I'm not familiar with) and clustal to trim sidechains. Paul Emsley tweaked my scheme script which I retweak and present here . Paul's script didn't work with my version of coot ((I'm using coot prerelease 0.4), the one I present below takes advantage of the delete-sidechain-range function to trim back either a single (give start and finish residue as the same) or range of residues to Cbeta. Best - Byron Coot "trim back sidechain" scheme code: - ;; Delete (back to the CB stub) the side change in the range ;; resno-start to resno-end ;; (define trim-sidechain-range (lambda (imol chain-id resno-start resno-end) (delete-sidechain-range imol chain-id resno-start resno-end))) (let ((menu (coot-menubar-menu "Extensions"))) (add-simple-coot-menu-menuitem menu "Trim back sidechains" (lambda () (generic-chooser-and-entry "Choose a molecule to have its sidechains chopped" "Chain ID: ""A" (lambda (imol chain-id) (generic-double-entry "Starting Resno" "End Resno" "" "" #f #f " Chop Sidechains " (lambda (text-1 text-2 dummy) (let ((resno-1 (string->number text-1)) (resno-2 (string->number text-2))) (if (and (number? resno-1) (number? resno-2)) (trim-sidechain-range imol chain-id resno-1 resno-2)) - -- Byron DeLaBarre, Ph.D. Structural Biology Group Millennium Pharmaceuticals Cambridge, MA "In Reciprocal Space, I'm a Somebody"
Re: [ccp4bb] Color of heme containing Xtals
Hello, A more precise view on the spectroscopic signature of your crystalline heme protein can be obtained by microspectrophotometry (UV-vis absorption, Raman or fluorescence). For such studies, people are welcome to apply for using the Cryobench lab at ESRF (http://www.esrf.eu/UsersAndScience/Experiments/MX/Cryobench/). A number of microspec are also lying around or can be purchased (for example: http://www.4dx.se/spectrop.htm). Dominique. Jan Schoepe a écrit : Hello everybody, I wonder if anybody has experience with heme (or to be more precise: heme b) containing proteins which Xtals do not look red under the microscope. How might the technique for crystallization (e.g. sitting drop, hanging drop) influence the intensity of the color? Many thanks! Jan Lesen Sie Ihre E-Mails jetzt einfach von unterwegs.. -- Dominique BOURGEOIS /\ Dominique Bourgeois/\/\ / \ LCCP IBS/\/ /\ /\/\ UMR 5075 / \/ \ / \ \ 41 Rue Jules Horowitz \ \ \ \ 38027 GRENOBLE Cedex 1\ \ \ \ FRANCE \ \ ** phone: (+33) (0)4 38 78 96 44 ** ** fax: (+33) (0)4 38 78 51 22 ** ** e-mail: [EMAIL PROTECTED] ***
[ccp4bb] energy minimise ligand model
Dear BB, I have a structure of a protein domain that binds to a peptide ligand containing either a lysine or an arginine. There are homologs in the PDB with the peptide in complex both with lysine and arginine. I would like to model both alternative ligands bound to the new domain. It looks like there is a slightly narrowed binding site in my new struture for the end of a lysine side chain, so I'm speculating that the preference will be for lysine over arginine, but I'd like to do something like an energy minimisation and see whether either there is a lower energy complex for the ligand with lysine, or if the arginine moves to an alternate binding site - there is a possible alternate site. Can anybody suggest a quick and easy (idiots) way of doing this? Many thanks. Again, Ed
[ccp4bb] exclude range within data in scala , discontinuous run in scala problem
Hi I am trying to exclude a bad wedge of data during scaling in scala in the newest ccp4 ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so they should be version 6) The batches I need are 1 to 200 and 400-720 I have clicked the "Override automatic definition of runs to mark discontinuities in data" button as well as created two runs to contain the required data But I get a "Run 2 has not been assigned to a dataset" error. How I can exclude a bad wedge in the middle of my data from within scala without going through the split and sort route in mtzutils. I have attached the com file generated by ccp4i and the error text below Thanks for your help Hari Jayaram Postdoc , Miller Lab Brandeis University - The error I get is - 13714715716 717718719720 Run 2 has not been assigned to a dataset *** * Information from CCP4Interface script *** The program run with command: scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/hari/aps_feb08/p2-2/p2_2_12_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_correlplot.xmgr" has failed with error message Scala: * Error in input * *** In the GUI and the com file I can see that Run 2 has been correctly assigned to the correct dataset , i.e the same as Run 1 , but I still see this error - The ccp4i generated com files is attached here *** /tmp/hari/p2_2_12_3_com.tmp *** title Scala anon and deleted batches 200_400b try with two run definitions run 1 - INCLUDE batch 1 to 200 run 2 - INCLUDE batch 400 to 720 RUN 1 reference name run 1 project p2_2 crystal p2-2_A1_1 dataset p2_2 name run 2 project p2_2 crystal p2-2_A1_1 dataset p2_2 exclude EMAX - 10.0 exclude batch - 400 to 540 partials - check - test 0.95 1.05 - nogap intensities PROFILE - PARTIALS final PARTIALS scales - rotation SPACING 5 - secondary 6 - bfactor ON - BROTATION SPACING 20 UNFIX V FIX A0 UNFIX A1 initial MEAN tie surface 0.001 tie bfactor 0.3 cycles 10 converge 0.3 reject 2 anomalous on output AVERAGE print cycles nooverlap RSIZE 80 ## This script run with the command ## # scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/hari/aps_feb08/p2-2/p2_2_12_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_correlplot.xmgr"
Re: [ccp4bb] exclude range within data in scala , discontinuous run in scala problem
Hi. Based on your explanation it looks like you want to remove your "RUN 1 REFERENCE" and "EXCLUDE BATCH 400 TO 500" lines from your script. You might also want to try without the NAME lines on the off chance that the harvesting stuff is causing the problems. My best guess is that the "RUN 1 REFERENCE" is conflicting with assigning both runs the same dataset name, but that's only a guess. Good luck, Pete -Original Message- From: CCP4 bulletin board on behalf of hari jayaram Sent: Fri 3/14/2008 1:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] exclude range within data in scala , discontinuous run in scala problem Hi I am trying to exclude a bad wedge of data during scaling in scala in the newest ccp4 ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so they should be version 6) The batches I need are 1 to 200 and 400-720 I have clicked the "Override automatic definition of runs to mark discontinuities in data" button as well as created two runs to contain the required data But I get a "Run 2 has not been assigned to a dataset" error. How I can exclude a bad wedge in the middle of my data from within scala without going through the split and sort route in mtzutils. I have attached the com file generated by ccp4i and the error text below Thanks for your help Hari Jayaram Postdoc , Miller Lab Brandeis University - The error I get is - 13714715716 717718719720 Run 2 has not been assigned to a dataset *** * Information from CCP4Interface script *** The program run with command: scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/hari/aps_feb08/p2-2/p2_2_12_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_correlplot.xmgr" has failed with error message Scala: * Error in input * *** In the GUI and the com file I can see that Run 2 has been correctly assigned to the correct dataset , i.e the same as Run 1 , but I still see this error - The ccp4i generated com files is attached here *** /tmp/hari/p2_2_12_3_com.tmp *** title Scala anon and deleted batches 200_400b try with two run definitions run 1 - INCLUDE batch 1 to 200 run 2 - INCLUDE batch 400 to 720 RUN 1 reference name run 1 project p2_2 crystal p2-2_A1_1 dataset p2_2 name run 2 project p2_2 crystal p2-2_A1_1 dataset p2_2 exclude EMAX - 10.0 exclude batch - 400 to 540 partials - check - test 0.95 1.05 - nogap intensities PROFILE - PARTIALS final PARTIALS scales - rotation SPACING 5 - secondary 6 - bfactor ON - BROTATION SPACING 20 UNFIX V FIX A0 UNFIX A1 initial MEAN tie surface 0.001 tie bfactor 0.3 cycles 10 converge 0.3 reject 2 anomalous on output AVERAGE print cycles nooverlap RSIZE 80 ## This script run with the command ## # scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/hari/aps_feb08/p2-2/p2_2_12_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/p2_2_12_correlplot.xmgr"
Re: [ccp4bb] exclude range within data in scala , discontinuous run in scala problem
In ccp4i Scala task, click to open the "Excluded data" panel, click on "Exclude selected batches" There you can define one or more ranges of batches or lists to exclude If you just want to exclude the last part you can define a range eg 301 to 999 You don't need to explicitly define runs Phil On 14 Mar 2008, at 18:57, hari jayaram wrote: Hi I am trying to exclude a bad wedge of data during scaling in scala in the newest ccp4 ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so they should be version 6) The batches I need are 1 to 200 and 400-720 I have clicked the "Override automatic definition of runs to mark discontinuities in data" button as well as created two runs to contain the required data But I get a "Run 2 has not been assigned to a dataset" error. How I can exclude a bad wedge in the middle of my data from within scala without going through the split and sort route in mtzutils. I have attached the com file generated by ccp4i and the error text below Thanks for your help Hari Jayaram Postdoc , Miller Lab Brandeis University - The error I get is - 13714715716 717718719720 Run 2 has not been assigned to a dataset *** * Information from CCP4Interface script *** The program run with command: scala HKLIN "/Users/hari/aps_feb08/ p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/ hari/aps_feb08/p2-2/p2_2_12_rogues.log" NORMPLOT "/Users/hari/ aps_feb08/p2-2/p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/ aps_feb08/p2-2/p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/ p2-2/p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/ p2-2/p2_2_12_correlplot.xmgr" has failed with error message Scala: * Error in input * *** In the GUI and the com file I can see that Run 2 has been correctly assigned to the correct dataset , i.e the same as Run 1 , but I still see this error - The ccp4i generated com files is attached here *** /tmp/hari/p2_2_12_3_com.tmp *** title Scala anon and deleted batches 200_400b try with two run definitions run 1 - INCLUDE batch 1 to 200 run 2 - INCLUDE batch 400 to 720 RUN 1 reference name run 1 project p2_2 crystal p2-2_A1_1 dataset p2_2 name run 2 project p2_2 crystal p2-2_A1_1 dataset p2_2 exclude EMAX - 10.0 exclude batch - 400 to 540 partials - check - test 0.95 1.05 - nogap intensities PROFILE - PARTIALS final PARTIALS scales - rotation SPACING 5 - secondary 6 - bfactor ON - BROTATION SPACING 20 UNFIX V FIX A0 UNFIX A1 initial MEAN tie surface 0.001 tie bfactor 0.3 cycles 10 converge 0.3 reject 2 anomalous on output AVERAGE print cycles nooverlap RSIZE 80 ## This script run with the command ## # scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/ p2-2/p2_2_12.scala" ROGUES "/Users/hari/aps_feb08/p2-2/ p2_2_12_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/ p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/ p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/ p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/ p2_2_12_correlplot.xmgr"
Re: [ccp4bb] exclude range within data in scala , discontinuous run in scala problem
Hi. I did try that beforehand when I tried excluding a "range" of batches with the ccp4i gui But I got an error Scala: *** Gap in "time" (rotation) *** Sorry...both versions of the protocol for handling a bad internal wedge are giving me either a "gap in rotation" error or a "Run 2 has not been assigned to a dataset" error I am still stuck. ( error and com file for the "exclude data" range option is attached below) Thanks for your help. Hari Jayaram Error --- Large gap in "time" (rotation) coordinate:3.5 See WARNING above Smoothed B-factor impossible *** * Information from CCP4Interface script *** The program run with command: scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_13_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_13.scala" ROGUES "/Users/hari/aps_feb08/p2-2/p2_2_13_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_correlplot.xmgr" has failed with error message Scala: *** Gap in "time" (rotation) *** *** #CCP4I TERMINATION STATUS 0 " Scala: *** Gap in "time" (rotation) ***" #CCP4I TERMINATION TIME 14 Mar 2008 17:38:34 #CCP4I TERMINATION OUTPUT_FILES /Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz p2_2 #CCP4I MESSAGE Task failed The com script was *** /tmp/hari/p2_2_13_3_com.tmp *** title Scala anon and deleted batches 200_400b try with two run definitions name project p2_2 crystal p2-2_A1_1 dataset p2_2 exclude EMAX - 10.0 exclude batch - 400 to 540 partials - check - test 0.95 1.05 - nogap intensities PROFILE - PARTIALS final PARTIALS scales - rotation SPACING 5 - secondary 6 - bfactor ON - BROTATION SPACING 20 UNFIX V FIX A0 UNFIX A1 initial MEAN tie surface 0.001 tie bfactor 0.3 cycles 10 converge 0.3 reject 2 anomalous on output AVERAGE print cycles nooverlap RSIZE 80 ## This script run with the command ## # scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_13_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/p2-2/p2_2_13.scala" ROGUES "/Users/hari/aps_feb08/p2-2/p2_2_13_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/p2_2_13_correlplot.xmgr" On Fri, Mar 14, 2008 at 5:11 PM, Phil Evans <[EMAIL PROTECTED]> wrote: > In ccp4i Scala task, click to open the "Excluded data" panel, click on > "Exclude selected batches" > > There you can define one or more ranges of batches or lists to exclude > > If you just want to exclude the last part you can define a range eg > 301 to 999 > > You don't need to explicitly define runs > > Phil > > On 14 Mar 2008, at 18:57, hari jayaram wrote: > > > Hi I am trying to exclude a bad wedge of data during scaling in > > scala in the newest ccp4 > > > > ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so > > they should be version 6) > > > > The batches I need are > > 1 to 200 and 400-720 > > I have clicked the "Override automatic definition of runs to mark > > discontinuities in data" button as well as created two runs to > > contain the required data > > > > But I get a "Run 2 has not been assigned to a dataset" error. > > How I can exclude a bad wedge in the middle of my data from within > > scala without going through the split and sort route in mtzutils. I > > have attached the com file generated by ccp4i and the error text below > > > > Thanks for your help > > Hari Jayaram > > Postdoc , Miller Lab > > Brandeis University > > > > > > - > > The error I get is > > - > > 13714715716 > > 717718719720 > > > > Run 2 has not been assigned to a dataset > > > > > *** > > * Information from CCP4Interface script > > > *** > > The program run with command: scala HKLIN "/Users/hari/aps_feb08/ > > p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" > > SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/ > > hari/aps_feb08/p2-2/p
[ccp4bb] Tricks to solubilize protein
Dear all, Sorry for this off-topic question. I am studying a peripheral membrane protein (13kDa) by liquid state NMR, which is stable at pH 9.0 (50mM CHES pH9.0, 150mM NaCl and 1mM DTT). It crashes when I lower pH of buffer. The addition of 50mM Arg + Glu works to stabilize the protein at low pH, but interfere with the interaction between protein and phosphatidylinositol mono-phosphate (PtdInsP1). I've already tried some other ways to stabilize the protein, like high salt concentration (400mM), detergents (NP40 and Triton X-100). None of them worked. Any input would be very helpful. All the best, Ju
