{"id":567,"date":"2022-01-27T10:36:49","date_gmt":"2022-01-27T15:36:49","guid":{"rendered":"http:\/\/pages.vassar.edu\/kmclaughlin\/?page_id=567"},"modified":"2024-11-27T08:49:47","modified_gmt":"2024-11-27T13:49:47","slug":"servers","status":"publish","type":"page","link":"https:\/\/pages.vassar.edu\/kmclaughlin\/servers\/","title":{"rendered":"Helpful Links"},"content":{"rendered":"\n<p class=\"has-large-font-size\"><strong>Installing Crystallography Software <\/strong><\/p>\n\n\n\n<p>CCP4 (includes Coot): <a href=\"https:\/\/www.ccp4.ac.uk\/download\/#os=macos\">https:\/\/www.ccp4.ac.uk\/download\/#os=macos<\/a><\/p>\n\n\n\n<p>Phenix: <a href=\"https:\/\/phenix-online.org\/download\">https:\/\/phenix-online.org\/download <\/a><\/p>\n\n\n\n<p class=\"has-large-font-size\"><strong>Tips For DNA Oligos <\/strong><\/p>\n\n\n\n<p>Resuspending DNA Oligos (IDT DNA Tips)<a href=\"https:\/\/www.idtdna.com\/pages\/education\/decoded\/article\/tips-for-resuspending-and-diluting-your-oligonucleotides\">https:\/\/www.idtdna.com\/pages\/education\/decoded\/article\/tips-for-resuspending-and-diluting-your-oligonucleotides<\/a><\/p>\n\n\n\n<p>DNA Oligo Resuspension Calculator: <a href=\"https:\/\/www.idtdna.com\/Calc\/resuspension\/\">https:\/\/www.idtdna.com\/Calc\/resuspension\/<\/a><\/p>\n\n\n\n<p>IDT DNA OligoAnalyzer (SS-structure, Tm, extinction coefficients etc.): <a href=\"https:\/\/www.idtdna.com\/calc\/analyzer\">https:\/\/www.idtdna.com\/calc\/analyzer<\/a><\/p>\n\n\n\n<p>DNA and RNA Molecular Weights and Conversions: <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/references\/ambion-tech-support\/rna-tools-and-calculators\/dna-and-rna-molecular-weights-and-conversions.html\">https:\/\/www.thermofisher.com\/us\/en\/home\/references\/ambion-tech-support\/rna-tools-and-calculators\/dna-and-rna-molecular-weights-and-conversions.html<\/a><\/p>\n\n\n\n<p>Promega Biomath Calculators: <a href=\"https:\/\/www.promega.com\/resources\/tools\/biomath\/\">https:\/\/www.promega.com\/resources\/tools\/biomath\/<\/a><\/p>\n\n\n\n<p class=\"has-large-font-size\"><strong>Crystallization Resources <\/strong><\/p>\n\n\n\n<p><span style=\"text-decoration: underline\">Beamline Guides (MiTeGen):<\/span><\/p>\n\n\n\n<p>All: <a href=\"https:\/\/www.mitegen.com\/learn\/beamline-guides\/\">https:\/\/www.mitegen.com\/learn\/beamline-guides\/ <\/a><\/p>\n\n\n\n<p>ALS 8.2.2: <a href=\"https:\/\/www.mitegen.com\/learn\/beamline-guides\/als-8-2-2\/\">https:\/\/www.mitegen.com\/learn\/beamline-guides\/als-8-2-2\/<\/a><\/p>\n\n\n\n<p>NSLS II\/AMX: <a href=\"https:\/\/www.mitegen.com\/learn\/beamline-guides\/nsls-ii-amx-17-id-1\/\">https:\/\/www.mitegen.com\/learn\/beamline-guides\/nsls-ii-amx-17-id-1\/<\/a><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><span style=\"text-decoration: underline\">Crystal Freezing<\/span><\/p>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/EGarman_Cryo-cooling.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of EGarman_Cryo-cooling.\"><\/object><a id=\"wp-block-file--media-1acb609d-f3d0-4a66-8fec-c3e20c7edebb\" href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/EGarman_Cryo-cooling.pdf\">EGarman_Cryo-cooling<\/a><a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/EGarman_Cryo-cooling.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-1acb609d-f3d0-4a66-8fec-c3e20c7edebb\">Download<\/a><\/div>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/f-71-00622.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of f-71-00622.\"><\/object><a id=\"wp-block-file--media-5164cdf5-d9c7-4679-9d69-8dce45eaa52d\" href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/f-71-00622.pdf\">f-71-00622<\/a><a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/f-71-00622.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-5164cdf5-d9c7-4679-9d69-8dce45eaa52d\">Download<\/a><\/div>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/crystals-12-00138-1.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of crystals-12-00138-1.\"><\/object><a id=\"wp-block-file--media-d191e8b4-4df3-41cd-81a1-f8339a6549f4\" href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/crystals-12-00138-1.pdf\">crystals-12-00138-1<\/a><a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/crystals-12-00138-1.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-d191e8b4-4df3-41cd-81a1-f8339a6549f4\">Download<\/a><\/div>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/Uni-puck_Directions.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of Uni-puck_Directions.\"><\/object><a id=\"wp-block-file--media-ba0edcbf-9de9-413f-8d64-2b4a9e079e8e\" href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/Uni-puck_Directions.pdf\">Uni-puck_Directions<\/a><a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/Uni-puck_Directions.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-ba0edcbf-9de9-413f-8d64-2b4a9e079e8e\">Download<\/a><\/div>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Preparing Crystal Mounts Using MiTeGen Reusable Bases for Crystallography\" width=\"640\" height=\"360\" src=\"https:\/\/www.youtube.com\/embed\/ikiGH8otMXk?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/Cryoprotectants-typicalranges.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of Cryoprotectants-typicalranges.\"><\/object><a id=\"wp-block-file--media-f29f5747-987f-4833-a9b0-7a756faaaa93\" href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/Cryoprotectants-typicalranges.pdf\">Cryoprotectants-typicalranges<\/a><a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/Cryoprotectants-typicalranges.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-f29f5747-987f-4833-a9b0-7a756faaaa93\">Download<\/a><\/div>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/2-Protein-XRD-Protocols-Soaking-Mounting-and-Freezing-Protein-Crystals.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of 2-Protein-XRD-Protocols-Soaking-Mounting-and-Freezing-Protein-Crystals.\"><\/object><a id=\"wp-block-file--media-cdafa70c-14e3-44dc-899d-e8e848663c0e\" href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/2-Protein-XRD-Protocols-Soaking-Mounting-and-Freezing-Protein-Crystals.pdf\">2-Protein-XRD-Protocols-Soaking-Mounting-and-Freezing-Protein-Crystals<\/a><a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/files\/2024\/04\/2-Protein-XRD-Protocols-Soaking-Mounting-and-Freezing-Protein-Crystals.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-cdafa70c-14e3-44dc-899d-e8e848663c0e\">Download<\/a><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<p class=\"has-large-font-size\"><strong>Servers:<\/strong><\/p>\n\n\n\n<p><strong>ProtParam-<\/strong>&nbsp;<a href=\"https:\/\/web.expasy.org\/protparam\/\">https:\/\/web.expasy.org\/protparam\/<\/a><\/p>\n\n\n\n<p><em>A tool which allows the computation of various physical and chemical parameters for a given protein. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, and extinction coefficient.&nbsp;<\/em><\/p>\n\n\n\n<p><strong>JANE- Journal Author Name Estimator <\/strong>&#8211;&nbsp;<a href=\"https:\/\/jane.biosemantics.org\/index.php\">https:\/\/jane.biosemantics.org\/index.php<\/a><\/p>\n\n\n\n<p><em>Enter the title and\/or abstract of your potential paper in the box, and Jane will compare it to find the best matching journals, authors or articles to help choose a place for submission.<\/em><\/p>\n\n\n\n<p><strong>PDBePISA (Proteins, Interfaces, Structures and Assemblies)<\/strong>&#8211;&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/msd-srv\/prot_int\/pistart.html\">https:\/\/www.ebi.ac.uk\/msd-srv\/prot_int\/pistart.html<\/a><\/p>\n\n\n\n<p><em>Results include: <\/em><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><em>Structural and chemical properties of macromolecular surfaces and interfaces<\/em><\/li>\n\n\n\n<li><em>probable quaternary structures (assemblies), their structural and chemical properties and probable dissociation pattern<\/em><\/li>\n<\/ul>\n\n\n\n<p><strong>PDBeFold-<\/strong>&nbsp;<a href=\"https:\/\/www.ebi.ac.uk\/msd-srv\/ssm\/\">https:\/\/www.ebi.ac.uk\/msd-srv\/ssm\/<\/a><\/p>\n\n\n\n<p><em>A comparison with other protein matching services.&nbsp;PDBeFold&nbsp;is used as a structure search engine in PDBePISA.&nbsp;<\/em><\/p>\n\n\n\n<p><strong>Dali &#8211;<\/strong>&nbsp;<a href=\"http:\/\/ekhidna2.biocenter.helsinki.fi\/dali\/\">http:\/\/ekhidna2.biocenter.helsinki.fi\/dali\/<\/a><\/p>\n\n\n\n<p><em>The Dali server is a network service for comparing protein structures in 3D.&nbsp;<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Installing Crystallography Software CCP4 (includes Coot): https:\/\/www.ccp4.ac.uk\/download\/#os=macos Phenix: https:\/\/phenix-online.org\/download Tips For DNA Oligos Resuspending DNA Oligos (IDT DNA Tips)https:\/\/www.idtdna.com\/pages\/education\/decoded\/article\/tips-for-resuspending-and-diluting-your-oligonucleotides DNA Oligo Resuspension Calculator: https:\/\/www.idtdna.com\/Calc\/resuspension\/ IDT DNA OligoAnalyzer (SS-structure, Tm, extinction coefficients etc.): https:\/\/www.idtdna.com\/calc\/analyzer DNA and RNA Molecular Weights and Conversions: https:\/\/www.thermofisher.com\/us\/en\/home\/references\/ambion-tech-support\/rna-tools-and-calculators\/dna-and-rna-molecular-weights-and-conversions.html Promega Biomath Calculators: https:\/\/www.promega.com\/resources\/tools\/biomath\/ Crystallization Resources Beamline Guides (MiTeGen): All: https:\/\/www.mitegen.com\/learn\/beamline-guides\/ ALS 8.2.2: https:\/\/www.mitegen.com\/learn\/beamline-guides\/als-8-2-2\/ <a href=\"https:\/\/pages.vassar.edu\/kmclaughlin\/servers\/\" rel=\"nofollow\"><span class=\"sr-only\">Read more about Helpful Links<\/span>[&#8230;]<\/a><\/p>\n","protected":false},"author":7374,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-567","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/pages\/567","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/users\/7374"}],"replies":[{"embeddable":true,"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/comments?post=567"}],"version-history":[{"count":11,"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/pages\/567\/revisions"}],"predecessor-version":[{"id":959,"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/pages\/567\/revisions\/959"}],"wp:attachment":[{"href":"https:\/\/pages.vassar.edu\/kmclaughlin\/wp-json\/wp\/v2\/media?parent=567"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}