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It covers required VNMR preprocessing choices, locating and transferring the procpar and phasefile inputs, and running vnmr2ucsf on Sun and Windows. It also explains setting contour levels, zoom shortcuts, TMS/DSS referencing, saving views or projects, and overlaying multi-dimensional NMR datasets for peak assignment support, especially COSY, TOCSY, and NOESY workflows.",{"@graph":63,"@context":122},[64,80,101],{"@type":65,"itemListElement":66},"BreadcrumbList",[67,71,74,77],{"item":68,"name":69,"@type":70,"position":9},"https://docshare.wps.com","Home","ListItem",{"item":72,"name":10,"@type":70,"position":73},"https://docshare.wps.com/template/",2,{"item":75,"name":11,"@type":70,"position":76},"https://docshare.wps.com/template/presentations/",3,{"item":78,"name":59,"@type":70,"position":79},"https://docshare.wps.com/template/sparky-cheat-sheet-brief-instructions-for-creating-sparky-formatted-data/572170/",4,{"url":78,"name":59,"@type":81,"image":82,"author":87,"headline":59,"publisher":90,"fileFormat":93,"inLanguage":57,"description":61,"dateModified":94,"datePublished":95,"encodingFormat":93,"isAccessibleForFree":96,"interactionStatistic":97},"DigitalDocument",{"url":83,"@type":84,"width":85,"height":86},"https://docshare.wps.com/thumbnails/sparky-cheat-sheet-brief-instructions-for-creating-sparky-formatted-data/572170.png","ImageObject",442,249,{"name":88,"@type":89},"Asher","Person",{"url":68,"name":91,"@type":92},"DocShare","Organization","application/pdf","2026-10-22","2026-10-13",true,{"@type":98,"interactionType":99,"userInteractionCount":73},"InteractionCounter",{"@type":100},"ViewAction",{"@type":102,"mainEntity":103},"FAQPage",[104,110,114,118],{"name":105,"@type":106,"acceptedAnswer":107},"What VNMR preprocessing steps are required before converting to Sparky format?","Question",{"text":108,"@type":109},"Process the VNMR data using appropriate apodization, zero filling, and linear prediction, then ensure the full spectrum is displayed and that trace='f1' is set for the indirect dimension on the x-axis.","Answer",{"name":111,"@type":106,"acceptedAnswer":112},"Which two VNMR files are needed for the conversion?",{"text":113,"@type":109},"You need the procpar file from /babylon6/hf/rgroup/user(=path)/vnmrsys/exp#/procpar and the phasefile from (path)/vnmrsys/exp#/datdir/phasefile.",{"name":115,"@type":106,"acceptedAnswer":116},"How do you set contour levels and zoom in Sparky?",{"text":117,"@type":109},"Use 'ct' to adjust the lowest contour, number of contours, multiplier, and color. Zoom using mouse-drawn boxes or shortcuts like 'zi' (zoom in), 'zo' (zoom out), 'zp' (zoom previous), and 'zf' (zoom full).",{"name":119,"@type":106,"acceptedAnswer":120},"How are overlay and referencing used for peak assignments?",{"text":121,"@type":109},"Overlay COSY and TOCSY onto NOESY to simplify assignments. For referencing, zoom to the TMS peak, ensure sufficient contours to find the center, place the cursor at the center, and type 'xO'.","https://schema.org",{"og:url":78,"og:type":124,"og:title":59,"og:site_name":91,"og:description":61},"article",{"robots":126,"canonical":78},"index,follow",{"doc_id":128,"site_id":56},572170,1792635634,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":88,"user_avatar":133,"doc_module":9,"category_id":8,"category_name":11,"doc_title":59,"doc_description":61,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":73,"is_deleted":4,"is_public":9,"is_downloadable":9,"audit_status":9,"page_count":79,"language":139,"language_code":57,"site_id":56,"html_lang":57,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":61,"update_tm":143,"read_time":73},687197207639,"https://ap-avatar.wpscdn.com/davatar_a8503ba1806abce46bf441b54a3ca4cd","Sparky Cheat Sheet  \nBy Monika Ivancic, last updated March 13th, 2009  \nYou may download the program Sparky from its website:  \n[http://www.cgl.ucsf.edu/home/sparky/](http://www.cgl.ucsf.edu/home/sparky/)  \nThe download files and installation instructions are on the main page towards the bottom. Thereis also an online manual, which is quite good and you should be using that in addition to this‘cheat sheet’. This ‘cheat sheet’ is intended for brief instructions in creating Sparky formatted data, for assignments of mainly 2D 1H data, for volume integrations and restraint list generation.  \nI. Converting VNMR data to Sparky format:  \nPreparing VNMR data: (Whether you use Sparky on the Sun to convert or on Windows to convert, you’ll need to do the following.)  \nIn VNMR on Sun:  \n•process the data as desired (using appropriate apodization, zero filling and linear prediction), then make sure that the full spectrum is displayed (f full dconi) and that trace=’f1’(indirect dimension on the horizontal – x – axis) .  \n•then type ‘flush’ in the line command (this updates the exp\\#/datdir/phasefile)  \n•take note of which experiment number you’re in, you will need 2 files:  \n1. /babylon6/hf/rgroup/user(=path)/vnmrsys/exp\\#/procpar  \n2. (path)/vnmrsys/exp\\#/datdir/phasefile  \nA. On the Sun stations (unix): use the ‘vnmr2ucsf.exe’command in the following way:  \nin Sparky directory: cd to ‘bin’(/babylon6/hf/cic/ivancic/sparky/bin for now)  \nthen type the conversion command at % prompt:  \n%vnmr2ucsf (path)/vnmrsys/exp\\#/procpar (path)vnmrsys/exp\\#/datdir/phasefile newfilename.ucsf H H (enter) 1st H is nucleus in f1, 2nd H is nucleus in f2 (change to corresponding nucleus)  \n•this creates a newfilename.ucsf file, which then can be opened in Sparky. (Move into afolder in which you want to keep your sparky spectra.)  \nB. On Windows computers:  \n•open up the C:ProgramFiles/Sparky/bin directory  \n•make a subdirectory in which you’ll put the procpar and phasefile (you may want to use the type of experiment as a name, ie. gcosy if you ran a gcosy)  \n•ftp the above mentioned procpar and phasefile from apollo (or gaim if need it immediately) into this subdirectory  \n•open the command prompt (Start-> All Programs-> Accessories-> Command Prompt)  \n•maneuver to the Sparky/bin directory, using ‘cd ..’ to go up one directory and ‘cd Sparky’ to go into a directory. The prompt will tell you if you’re in the correct directory.(C:\\Program Files\\sparky\\bin>)  \n•type the following at prompt>  \nvnmr2ucsf subdirectory/procpar subdirectory/phasefile newfilename.ucsf H H (1st H is nucleus in f1, 2nd H is nucleus in f2, change appropriately)  \n(for example: vnmr2ucsf gcosy/procpar gcosy/phasefile newfilename.ucsf H H)  \n•this will create a ‘newfilename.ucsf’ file, which you should move into the subdirectory (ie. gcosy), then move this subdirectory to a desired directory in your file system  \nII. Setting up your data views in Sparky:  \nA. Open Sparky by clicking on it the sparky.bat icon in the sparky/bin subdirectory, OR on the shortcut that you created on your desktop (shortcut to Sparky)  \nB. Once opened, you’ll see 3 windows: a DOS command type window (which you don’t use), a pointer mode window (tells you what mode the mouse cursor is in, by default in‘zoom’), and the main Sparky 3.114 with a menu that you will be using to manipulate your data  \nC. Open up your data file from the Sparky 3.114 command window: File-> Open and find the file that you just created and placed in your file system (newfilename.ucsf) OR use the two letter shortcut ‘fo’ to get the ‘open file’ window to pop up; Note: Sparky keeps track of your file system and where the file (newfilename.ucsf) is located, if you move your file/folder later there will be some difficulty in re-setting this in Sparky (doable, but may be complicated) .  \nD. The easiest way to set the contour levels is to use ‘ct’ and play with the lowest level contour, the number of contours and the multiplier, which sets each nex","cbCaipMnN64hEqIA","https://ap.wps.com/l/cbCaipMnN64hEqIA","pdf",103085,"English","# Converting VNMR data to Sparky format\n## Preparing VNMR data and required files\n## Converting on Sun stations (unix)\n## Converting on Windows computers\n# Setting up data views in Sparky\n## Opening Sparky and loading data\n## Contour levels, zooming, and referencing\n## Saving settings and projects\n# Assignments in Sparky\n## Overlaying multiple datasets for assignments","[{\"question\":\"What VNMR preprocessing steps are required before converting to Sparky format?\",\"answer\":\"Process the VNMR data using appropriate apodization, zero filling, and linear prediction, then ensure the full spectrum is displayed and that trace='f1' is set for the indirect dimension on the x-axis.\"},{\"question\":\"Which two VNMR files are needed for the conversion?\",\"answer\":\"You need the procpar file from /babylon6/hf/rgroup/user(=path)/vnmrsys/exp#/procpar and the phasefile from (path)/vnmrsys/exp#/datdir/phasefile.\"},{\"question\":\"How do you set contour levels and zoom in Sparky?\",\"answer\":\"Use 'ct' to adjust the lowest contour, number of contours, multiplier, and color. Zoom using mouse-drawn boxes or shortcuts like 'zi' (zoom in), 'zo' (zoom out), 'zp' (zoom previous), and 'zf' (zoom full).\"},{\"question\":\"How are overlay and referencing used for peak assignments?\",\"answer\":\"Overlay COSY and TOCSY onto NOESY to simplify assignments. For referencing, zoom to the TMS peak, ensure sufficient contours to find the center, place the cursor at the center, and type 'xO'.\"}]","Sparky Cheat Sheet - Brief instructions for creating Sparky formatted data | PDF",1791925911]