{"id":18,"date":"2017-07-12T14:15:34","date_gmt":"2017-07-12T19:15:34","guid":{"rendered":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/?page_id=18"},"modified":"2024-09-18T08:23:09","modified_gmt":"2024-09-18T13:23:09","slug":"group-wisdom","status":"publish","type":"page","link":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/group-wisdom\/","title":{"rendered":"Group Wisdom"},"content":{"rendered":"<p>Our \u2018wisdom\u2019 pages are written protocols and &#8220;tips and tricks&#8221; documents used to help newcomers to the lab.\u00a0 In addition, these electronic collections are searchable (great for digging up badly indexed facts), they can be shared with the world at large (we are scientists and thus part of a culture where sharing is still a virtue), and web-based collections of data.<\/p>\n<p>Disclaimer: We believe that all information contained herein is accurate, but we do not provide any guarantees.\u00a0 In particular, this is a cumulative storage point, so some of the information may be out of date.<\/p>\n<p>&nbsp;<\/p>\n<map id=\"barMap\" name=\"barMap\">\n<area alt=\"Research Description\" coords=\"2,2,130,21\" shape=\"rect\" href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/work.html\" \/>\n<area alt=\"Publications\" coords=\"145,2,222,21\" shape=\"rect\" href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/publication\/\" \/>\n<area alt=\"Calcium-Binding Protein Database\" coords=\"232,2,363,21\" shape=\"rect\" href=\"https:\/\/structbio.vanderbilt.edu\/cabp_database\/cabp.html\" \/>\n<area alt=\"Group Wisdom\" coords=\"378,2,429,21\" shape=\"rect\" href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/\" \/>\n<area alt=\"Search\" coords=\"441,2,489,21\" shape=\"rect\" href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/search.html\" \/>\n<area alt=\"Vanderbilt University Homepage\" coords=\"501,2,607,21\" shape=\"rect\" href=\"https:\/\/www.vanderbilt.edu\/\" \/> <\/map>\n<table border=\"0\" width=\"100%\" cellspacing=\"0\" cellpadding=\"0\" align=\"center\" bgcolor=\"#ffffff\">\n<tbody>\n<tr>\n<td bgcolor=\"#ffffff\" width=\"73\"><\/td>\n<td bgcolor=\"#ffffff\">\n<table border=\"0\">\n<tbody>\n<tr valign=\"top\">\n<td colspan=\"2\">\n<h2>Our Stocks<\/h2>\n<\/td>\n<\/tr>\n<tr valign=\"top\">\n<td valign=\"top\" width=\"50%\">\n<h3>Our Proteins<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/annexin.xi.html\">Annexin XI stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/calbindin.proteins.html\">Calbindin stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/calcyclin.proteins.html\">Calcyclin stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/CaM.TnC.proteins.html#Calmodulin\">Calmodulin stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/Caltractin.proteins.html\">Caltractin stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/MRP.proteins.html\">MRP8\/14 stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/s100a2.proteins.html\">S100A2 Stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/CaM.TnC.proteins.html#Stellacyanin\">Stellacyanin stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/CaM.TnC.proteins.html#Troponin%20C\">Troponin C stocks<\/a><\/li>\n<\/ul>\n<\/td>\n<td valign=\"top\" width=\"50%\">\n<h3>Other Stocks<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/cell.stocks.html\">Cell stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/Plasmids.html\">Plasmid stocks<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/protected\/kuznicki_dnas.html\">DNA from Kuznicki lab<\/a><\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<tr valign=\"top\">\n<td colspan=\"2\">\n<hr \/>\n<h2>Laboratory Procedures<\/h2>\n<h3><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/template.html\">Protocol template file<\/a><\/h3>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"50%\">\n<h3>General Procedures<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/stdcellprep.html\">Standard Cell Prep<\/a><\/li>\n<li><a href=\"wisdom\/protected\/competent_cells.pdf\">Preparation of Competent Cells<\/a> <a href=\"wisdom\/protected\/competentcells.html\">(old)<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/sequenceDNA.html\">Getting DNA sequenced<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/inclusion.html\">Isolating Inclusion Bodies<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/protected\/competentcells.html\">Making Competent Cells<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/maldiproto.html\">MALDI<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/AAAprotocol.html\">Amino Acid Analysis<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/M9.html\">Minimal Media Recipe<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/sterile.html\">Sterile Technique<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/thrombin.html\">Thrombin Cleavage<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/Western_Blotting.html\">Western Blotting and Immunostaining<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/proteolysis.html\">Limited proteolysis<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/CDthermal_melt.html\">Thermal melt using CD<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/denaturants.html\">Calculating denaturant concentration by r.i.<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/kdcalc.htm\">Theoretical simulations and considerations for Kd measurement and calculation<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/minimal_medium.pdf\">Protocol for growing labeled protein<\/a><\/li>\n<\/ul>\n<h3>DNA Processing Assemblies<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/rpaAB-purifl.html\">RPA-AB Purification<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/t-ag-protocol.html\">T-Antigen Purification<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/primase-purif.html\">DNA primase Exp. \/ Purification<\/a><\/li>\n<\/ul>\n<\/td>\n<td valign=\"top\" width=\"50%\">\n<h3>Calcium-Binding Proteins<\/h3>\n<ul>\n<\/ul>\n<ul>\n<a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/Standard.html\">Standard Lab Practices<\/a> <\/ul>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/labguide.html\">Lab Guidelines<\/a>\n<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/batchproto.html\">Bradford Assay<\/a> <\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/protected\/calbindin_expr_pure.html\">Calbindin D<sub>9k<\/sub> Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/clb_purif.pdf\">updated Calbindin D<sub>9k<\/sub> Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/calmodulin.html\">Calmodulin Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/S100A2_purification.html\">S100A2 Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/S100A6_purification.html\">S100A6 Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/S100B_purification.html\">S100B Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/s100a8a9_purification.doc\">S100A8\/A9 Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/CBMprotocol.html\">Production of Calbindomodulin Mutants<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/Centrin.htm\">Centrin Prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/protected\/hcen2.html\">Purification Protocol for HCentrin2<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/CDPKexp.html\">CDPK prep<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/ca_titr_new.html\">Competitive Chelator Method for Calcium-Binding Constants (Updated version)<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/phenylproto.html\">Phenyl Sepharose Binding Assay for Calbindin Mutants<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/chelex.html\">Preparing Chelexed water<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/labpro\/NMR_EDTA.html\">Walter&#8217;s notes about NMR with EDTA<\/a><\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<tr valign=\"top\">\n<td colspan=\"2\">\n<hr \/>\n<h2>NMR and Computational Wisdom<\/h2>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"50%\">\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/xwinnmr.html\">Beginner&#8217;s guide to data collection on Bruker instruments using xwinnmr<\/a><\/li>\n<\/ul>\n<h3>FELIX<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/felix_intro.html\">Introduction to Felix<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/undocumented.html\">Useful<br \/>\nbut undocumented Felix97 commands<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/biomagresbank.html\">BioMagResBank<br \/>\ninfo<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/script\/grad2.html\">Grad2<\/a>&#8211;<br \/>\nShuffle gradient echo\/antiecho data into sine-cosine (States) format<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/sshift.html\">sshift<\/a><br \/>\n&#8211; Calculate secondary chemical shifts&nbsp;<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/felix-to-genxpk.html\">Automation<br \/>\nof GENXPK tasks from within Felix<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/genxpkass.html\">Assigning<br \/>\ncrosspeaks with GENXPK<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/felix-menus.html\">Customizing<br \/>\nthe Felix &#8220;right-click&#8221; menu<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/lpx-do.html\">Linear<br \/>\nprediction do&#8217;s and don&#8217;ts<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/lpx.html\">Linear<br \/>\nprediction parameters<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/felix-hotkeys.html\">Programming<br \/>\nFelix95 hotkeys<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/felix-keypad.html\">Enabling keypad<br \/>\nnavigation in Felix95 on SUN computers<\/a><\/li>\n<\/ul>\n<h3>Other NMR Data Processing<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/drxB.html\">Removing<br \/>\noff-resonance water line<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/drxB.html#13c_edge\">Handling<br \/>\n<sup>13<\/sup>C resonances at spectrum edge<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/modelfree.tips.html\">Tips<br \/>\non getting Modelfree up and running<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/overlay.html\">Overlaying<br \/>\nmultiple spectra in colors<\/a><\/li>\n<li><a style=\"margin-top: 0;margin-bottom: 0\" href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/ppg.html\">Summary<br \/>\nof common commands used in Bruker pulse programming<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/automated.html\">Description<br \/>\nof some automated backbone and NOE assignment packages<\/a><\/li>\n<\/ul>\n<h3>Calculating Structures<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/struct_howto.html\">Chazin Lab &#8220;how to&#8221;<\/a><\/li>\n<\/ul>\n<h3>Analysis and Comparison of Structures<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/ketchemr_insightii.html\">Randy&#8217;s InsightII Tips<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/elec_surf.html\">Electrostatic Surface calculation<\/a> with UHBD and display with AVS<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/cmap_instruct.html\">Contact maps with CHARMM<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/ddm_instruct.html\">Distance difference matrices with DISCOM<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/chazin\/wisdom\/ketchemr_discom.html\">Randy&#8217;s DISCOM Tips<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/interhel.html\">Calculating Interhelical Angles with signs using Interhlx<\/a>, a program written by Kyoko Yap<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/iupac.pdf\">Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids<\/a>-PDF format<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/dino_surface.html\">Displaying Protein Surfaces With Dino<\/a><\/li>\n<\/ul>\n<\/td>\n<td valign=\"top\" width=\"50%\">\n<h3>UNIX and Other Computing Topics<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/unix.html\">UNIX Tips<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/ketchemr_unix.html\">Randy&#8217;s UNIX Tips<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/psql_howto.html\">Basic procedures in PostgreSQL<\/a>, a database management system<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/dbi_howto.html\">Using the DBI and DBD:Pg Perl modules<\/a> to access PostgreSQL databases<\/li>\n<\/ul>\n<h3>Software Manuals<\/h3>\n<ul>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/comp\/soft\/accelrys\/doc\">MSI Online Docs<\/a> (Vandy only)<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/facelift_doc\/facelift_manual.html\">Facelift<\/a> &#8211; multidimensional baseline correction<\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/facelift_doc\/gif\/facelift_exp.html\">Our own experience<\/a><\/li>\n<li><a href=\"https:\/\/www.scripps.edu\/case\/nab5\/NAB.html\">NAB<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/xv-3.10a\/index.html\">xv<\/a><\/li>\n<li><a href=\"https:\/\/www.fkem2.lth.se\/~garry\/programs.html\">Garry Gippert&#8217;s programs<\/a><\/li>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/acegr\/ACEgr.html\">ACE\/gr<\/a>-also known as xmgr or xvgr<\/li>\n<\/ul>\n<h3>Javascript and Perl Utilities<\/h3>\n<ul>\n<a href=\"https:\/\/www.scripps.edu\/~mjhunter\/jsframes.html\">Mike&#8217;s JavaScripts<\/a><br \/>\n&#8211; for labeled\/unlabeled protein and DNA mass determination and DNA extinction coefficients&nbsp;<\/p>\n<p><a href=\"https:\/\/www.scripps.edu\/~mjhunter\/perlprogs.html\">Mike&#8217;s Perl Programs<\/a><br \/>\n&#8211; for extracting acquisition parameters from bruker acquisition<br \/>\nfiles, determining least squares fit of data, and least squares fit, molar<br \/>\nellipticity, and percent helical content of CD data.&nbsp;<\/p>\n<p><a href=\"https:\/\/www.scripps.edu\/~lenam\/things.html\">Lena&#8217;s Perl Programs<\/a><br \/>\nPrograms to convert felix cross peaks to a structure calculation constraint<br \/>\nlist (Randy&#8217;s program) and to analyze torsion angles.&nbsp; &#8211;&gt;<\/p>\n<li><a href=\"https:\/\/structbio.vanderbilt.edu\/wisdom\/struct_scripts.html\">Perl scripts for use in structure calculations<\/a><\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<address>\u00a0<\/address>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"<p>Our \u2018wisdom\u2019 pages are written protocols and &#8220;tips and tricks&#8221; documents used to help newcomers to the lab.\u00a0 In addition, these electronic collections are searchable (great for digging up badly indexed facts), they can be shared with the world at large (we are scientists and thus part of a culture where sharing is still a&#8230;<\/p>\n","protected":false},"author":6793,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"tags":[],"class_list":["post-18","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/pages\/18","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/users\/6793"}],"replies":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":8,"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":915,"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/pages\/18\/revisions\/915"}],"wp:attachment":[{"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/media?parent=18"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/chazinlab\/wp-json\/wp\/v2\/tags?post=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}