MFP3D FAQ |
How do I set up a Mac to run the MFP3D software?
How do I fit force plots with the WLC model. 1) Find the force plot you what to fit. 2) Plot it as Force Vs. Sep (Sep is short for tip - sample separation). The X axis is controlled with the popup menu beneath the Y axis data type list, on the Display tab. 3) You need to define where 0,0 is. To set the offsets you can either right click on the graph to offset X and Y, so that the force is zeroed, and the tip hits the surface at zero separation, or go to the Mod tab, and click on "Y offset" and "Raw (X) offset". 4) Go to the cursor tab, select that you only want cursors on Ret (short for retract). 5) Shift + left click on the graph to define the stretching regions. You want to define the error region of the fitting function, so pick one point where the polymer ruptures its attachment to the tip, and pick the other point at the lowest extension as the data looks like it will be fit. You can fit multiple stretching events in a single force plot. If you want to do that, pick two "locks" (cursors) to define each stretching event (the software calls polymer stretching events hitches). 6) Go to the WLC tab. Make sure that the initial state of the parameters is close to the data; the fitting function often throws up its hands in despair if the initial guess is too far from the data. The Pers is the persistence length; it is basically a measure of the polymer's stiffness. Lower persistence lengths have much more non-linear responses. The extension ratio is the fraction of the contour length that the polymer chain is extended. The fit parameter is the extension ratio where the polymer chain ruptures its attachment to the tip (max extension ratio). So you can get the contour length of the chain from the rupture length divided by the max extension ratio. 7) Once you have your fit parameters fairly close to the data, you can then click Fit. 8) If you have multiple hitches in a force plot that you want to fit, then there are two questions you have to answer. A) Is the observed response due to one chain with domains or loops; or is each hitch the result of stretching a separate chain? If you think you have a single chain, then you want to unselect Multi Chain (upper left corner). If you think that each hitch is from a separate chain, then select Multi Chain. B) Do you think that each hitch should have the same persistence length? Generally this is the case, but isn't required by the fitting function. If you want to fit each hitch to a single persistence length, then select Single Pers; if you want each hitch to have its own persistence length parameter, then unselect it. 9) You can also hold and constrain each of the fit parameters using the hold and constrain checkboxes. Hold means that the fitting function will hold that parameter constant and not fit it. Constrain means that it will keep the fit parameter between the upper and lower limits (the limit controls show up after you constrain one of the parameters. I have to admit that the constrain option does not work well with this fitting function. 10) Once you like the fit, you can show the individual responses by clicking on the "Show Individual Stretches" checkbox. Then you can label the contour length of each response with the Tag Stretches checkbox. 11) You can also tweak your fit with the Max Iterations and Fit Tolerance controls. And finally you can specify the temperature at which the stretching was done with the temperature control. How do I export my data in ASCII format? You can export any wave in Igor. 90% of the battle is finding the wave. New Quick and dirty way in Igor 6 1) This way makes a table of the trace, and you can copy and paste that into your spread sheet or notepad. It is a fairly good way to get force plot data exported, since it grabs the X data with it. But it depends, in the offline, it will only grab 1 section at a time, extend, retract, or a dwell. In the realtime force, it will grab the entire force plot, so there are options. 1) Right click on the trace you want to export. 2) Select Edit 3) Right click on the Table. 4) Select Digits, then select the highest number there (16 at the moment). 5) Hit Ctrl + A, to select the entire table 6) Hit Ctrl + C to copy the contents of the table to the clipboard. 7) Paste your ascii data into your preferred format. Older-slower-more-general-way for more precision 1) Double click on the wave. You get a modify trace dialog. 2) *Hold Down* the left mouse button on the name of the wave that looks like the correct wave. The box below then shows the data folder that is holding that wave. 2b) A different way to find the folder (which I just learned myself) is to hit Shift + F1, then click on the trace. This brings up a tooltip type box with the names of the waves, and the data folders. 3) Go to the Data -> Data Browser menu. 4) Go to the Data -> Save Waves -> Save Delimited Text menu. 5) Click Do it. Then select where you want to save that .dat file. 6) Note images are layered waves, 3 dimensional. Ascii can only handle 2D waves, so the layers are stacked in the rows. EX: • Make/N=(3,4,2) LayeredImageWave • LayeredImageWave = P+Q*10+R*100 • Save/J/M="\r\n" LayeredImageWave as "LayeredImageWave.txt" 0 10 20 30 So you can either deal with all the data in 1 wave, pulling the layers out that you want. What is InVOLS and how do I use it? InVOLS stands for the Inverse Optical Lever Sensitivity. Most AFMs use the optical lever detection method, where light is bounced off of the end of the cantilever, and is reflected to a segmented photodiode. By looking at the voltage on the various segments of the photodiode, we can determine how far the cantilever is deflected. To do this, you make the assumption that the voltage difference between the top two segments and the bottom two segments is linear with deflection. This is, in general, a valid assumption, particularly in the smaller the voltage ranges, and the closer you are to zero volts difference between the top two segments and the bottom two. To get rid of the black fit line on your data graph, right click on it and select Remove fit_deflection. Customer instructions for leaving files on our FTP site We have a new method of sending us files, which is still in development. This page requires java 1.5, which you can download from here:
How do I setup a second copy of Igor on my MFP3D computer? To make another copy of Igor on your MFP3D computer, go to: Now you are all set to install or update either Igor. Using the original Igor will be fairly straight forward. It will be registered with windows as the default Igor, so if you double click on any Igor file (pxp, pxt, ibw, etc.) then the OS will try to launch the original Igor and pass it the file you double clicked. The trick is if you want to open up the file with Igor copy. To do this you will have to first launch the Igor copy by double clicking on the Igor.exe executable in You can also make a shortcut to the Igor copy executable to make your life easier. Once the Igor copy is launched, then when you double click on a Igor file, the OS will pass that file to the running Igor. Another option we often use the file -> Recent Experiments menu in Igor to open up experiments in the Igor copy. Having multiple copies of Igor on your computer can be a little confusing to work with at first. One thing to be careful of is to not to click on the original Igor Pro Folder's MFP3D template.pxt when the Igor copy is running. Weird things happen since it is loading the template for the original Igor, but using the Igor copy and the MFP3D code installed in Freds Igor Pro Folder. Other than that it works quite well. Another thing to be aware of is that installing Igor to the copy's location will register that Igor as the default Igor. Then the tables are turned and when you double click on a Igor file without any Igor open, windows will launch the copy of Igor, and pass the file to that Igor. Once you reach this state it is always safer to open the Igor executable you want, and then start bringing in files (i.e. the MFP3D template.pxt) to that Igor. How do I setup Igor 6 on my MFP3D computer? How to setup a second MFP3D Computer? First off, Install a new license of Igor as outlined in Igor 6. When you start up the software, it will bring forward the parm panel showing that a number of calibration constants are red, meaning that there is a discrepancy between the hardware and software values. This is because you don't have software parm values on your computer yet. So when that panel comes up, click on Move all under hardware, then click on the Use the "use This" Values button at the bottom. That will enable the Save the "Use This" Values to software button. Clicking on that button will save the calibration constants to the harddrive, so you won't have to deal with this dialog again (until there is a real problem). How to setup an offline rig? But make sure your Igor pro is updated to the latest version from wavemetrics, see also Igor Update. Then you need to install the MFP3D software. For offline rigs, it is best to use the same version as the real time rig. To get the version number of the MFP3D software on your real time computer see versions. Do NOT update to beta versions of Igor. These versions often do not get along with the MFP3D software. Make sure that the web page you download the Igor update says release, and not beta. Many MFP3D software updates will require you to update Igor as well, as we use the new features of Igor. The easiest way to do this is to open Igor and go to the Help-> Updates for Igor 6.0.x.x menu item. This will take you to a web page on the Wavemetrics site that will tell you if you can update Igor or not. If your MFP3D computer is NOT connected to the network, then you have to do some more work. You can download standalone updates for Igor from the support page. OK, so you have some force plots and you want to get a histogram of adhesion values, here's how to do that. 1) Load your data into the Force review panel, which is started from the MFP IP -> Force Display Panel Menu. 2) Go to the analyze tab. 3) Make sure that first popup is adhesion. 3.1) If you only want to look at a subset of the data, check your limits (Start index and Stop Index). 3.2) Note that these are indexes, Not suffixes, so use the values for the indexes on the display tab. For example you want to look at the adhesion values for data from ForcePlot0010 to ForcePlot0078. Go to the display tab, select ForcePlot0010, record the value listed in the Index control, and enter that value in Start Index on the analyze tab. Then go back to the display tab and select ForcePlot0078, record the index and enter it in Stop Index on the analyze tab. 4) Check the Histogram checkbox. 5) Yeah it is that easy. So what are you looking at? It is the difference between the lowest point in the retract deflection data and the average of the last 5 points of the retract deflection data. So if you are stretching molecules, this value may or may not be the stretching events. If the adhesion for a force plot is stronger than the stretching events, then the adhesion will be recorded for that force plot. If the stretching events for a force plot are stronger than the adhesion, then the strongest rupture will be recorded. Another handy tool is the edit button on the histogram. This puts up a table of the adhesion values, with labels for the force plot from which those values were obtained. This way you can go through the values, and see which force plots are giving your which adhesion values. How write code to click on buttons? One of the easiest ways to get started writing Igor code is to write something that simply clicks on Asylum buttons in a certain order. Here is how to get started with that. 1) Bring up the panel that has the button you want to click on. 2) Hit Ctrl + T to bring up the tools for the panel. 3) Click on the second button on the left that now shows. 4) Double Click on the button you want to use. 5) For buttons there are 2 things you need to get from this dialog. The Control name (First field of the control dialog), and the function the button calls (listed in the procedure popup in the control dialog). You can click on the edit button, and then copy the function's name. So from this you need to get that the name is DoScan_0, and the function is DoScanFunc. Since this is a button (Checkboxes, popups, etc are all different), the function has 1 argument, and it is probably a string. OK This is where things get a little complicated. Since Igor 5 we have 2 ways we can write control functions, either with a structure or with the classical input arguments. Most of our controls use the classical input arguments, but if you click on edit in the control dialog and see something like this: Which is the function dialog for the little "3D" buttons on the offline image graphs. How to determine your MFP3D Software Version? Now for the old way, for those of you that have software version < 050811. 1) The MFP3D Software Version number. This is probably the most useful version number for you. It is a 6 digit number of the date (YYMMDD) that it was made. On versions ( > 050603) this number is also on the titlebar. 2) The MFP3D Xop Version. This is a number such as 24 up 2. It describes the build number of the xop that runs the controller. On older versions of the MFP3D Software (< 050603) this number was also on the titlebar. Newer versions this number is on the status bar (on the bottom of Igor). 3) Argyle Version number. This is a standard 4 number version such as 1.0.0.12. This Version number describes the build number of the Argyle xop that does the 3D open GL rendering. 4) Utilities version number. This is another standard 4 number version such as 1.0.0.12. This Version number describes the build number of the utilities xop that does various things. 5) The Igor version number, shown in the title bar, as well as from the Help -> About Igor Pro menu. |
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Mac Setup
