ClampFit on MacOSX

Posted on Jan 4, 2011

This is instructions to use the ClampFit from the pClamp suite for ion channel analysis on the Mac.  The system this write-up is based on is OSX 10.6 (Snow Leopard), pClamp 10, and uses Winebottler 1.1.44.

By way of introduction, Wine is the general open-source solution for running Windows-based software on UNIX-like systems (for example, Linux and OSX) by providing a compatibility layer underneath the application.  Specific implementations for different platforms and applications exist; e.g., CrossOver, Darwine, and Bordeaux.  This is advantageous to running pClamp in Bootcamp as you can simultaneously run your OSX software; it is better than running pClamp in Parallels Desktop as it does not require booting up a separate operating system for a single application — not to mention the high combined cost of both the WinOS and Parallels.

As mentioned above, a number of Wine-related apps are available for OSX, some of which are known to be incompatible with pClamp (e.g., CorssOver 8 and 9).  Winebottler worked marvelously for me and I’d like to share the procedure.  You will need your pClamp installer (it should be named pClamp-10_0_0_79.exe)

(i) Download and launch the .dmg

(ii) Drag both Wine and Winebottler to applications (optional).

(iii) Run Winebottler, and select “Create Custom Prefixes” (ion channels isn’t exactly a household name ;) )

(iv) Select a file (A), decide if you want Wine to be encapsulated (B), check silent install (C), and Install (D).  This will launch first a prompt for the location/name to store the result, then the pClamp installer.

(v)  Pick a “destination folder” – this does not matter.

(vi) You will see a pair of device driver errors.  Ignore them.  pClamp suite of software uses a security dongle for verification and the dongle is not supported in Wine.  This does not affect ClampFit.

(vii)  In the dialog box, select ClampFit.exe as what should be running in the application.

At this point you should have an app at the location you specified in step (iv).  Treat this as any native OSX app – just double click it, and ClampFit should launch:

Congratulations!  Now you get to analyse your traces in OSX instead of having to boot up a Windows partition.  If you have trouble locating your data files, head all the way up to the desktop first, then go back down into the Users folder.

Comments and feedback are welcome.

  • legal service

    Nice solution for Winebottler. Thanks!

  • Hanoch Kaphzan

    I downloaded clampfit and wine and winebottler. clampfit was opened but the fonts were just squares, and I was unable to read the properties of the signal. That made the whole thing not worthy. I would be glad if anyone can let me know how can this be corrected.

    • [This is some combinations of wine/winebottler configuration that we resolved by using the .app from my machine.]

  • Mark Bellingham

    Thanks a lot! As a recent PC to Mac transitioner, I was dreading the thought of leaving Clampfit analysis behind and learning something new, such as Axograph. This procedure worked perfectly for me, and I had Clampfit up and was analyzing data within 30 minutes. I did get a screen of goobledegook when I tried to look at the results page, but unchecking the Clampex-style Statistics Display box in the Statistics dialog seems to fix that. WINE has come a long way over the years…..

    • I’ve made a similar PC->Mac transition two years ago, and have not booted up the Windows partition for a year now. All hail the open source community!

  • Rob

    How do you do this from the pClamp install disc? I’ve run the setup.exe using the pClamp install disc and the installation appears to work successfully. However, when I launch clampfit and try to scroll along my traces, the scroll bar does not work. Any help would be much appreciated.

    • Jon

      Hi Robert – I have the same problem with the scroll-bars, so you’re not alone here. As I tend to use the [zoom out -> blow up range], I did not try to solve it. You may want to file this with the folks at Wine. Regards, Jon

  • Marcelo

    Nice Jon. The only one problem is that I can’t move across my recording, so I just have to zoom in and out to see different areas. Do you have any idea about how to fix it?
    Thanks

    • Jon

      Hi Marcelo – I had the same problem, and while I was using Clampfit I’d do the zooming thing. I looked briefly but didn’t find a solution. I have since wrote an application to work with ABF files, and Clampfit was sorta off the radar. Sorry to be not much of help. Jon

  • Jeremy

    hi! I am trying to export data from clampfit into microsoft excel. I can’t copy and paste data from Winebottled clampfit into any ordinary OS programs. Further, I am unable to open .rlt files using clampfit on a regular PC. Is there any way around this? thanks

    • Jon

      It’s been a while for me, but I remember copy and paste worked alright. Note, however, that once in the simulated environment, the keyboard short-cuts is different – instead of the usual [cmd-C], it’s [ctrl-C] for copy.

      Failing that, you could always save as a comma-separated plain-text document, and let Excel suck that in.

  • Jeremy

    right ignore that last comment. I saved the results sheet as an .atf file, which both Excel and regular PC clampfit was happy to open

    • Jon

      Ah good. Incidentally — I’m curious — how come you’re bringing things from Clampfit into Excel? When I did use CF 10 I’ve always found that its data analysis excellent (certainly better than Excel).

  • Calcium

    Hi,

    1.) Thank you for helping the novice users out there. But I was wondering if this works on OS 10.7(lion) does it also work on this?
    2.) Also I was wondering if you have the pClamp-10_0_0_79.exe file ? I can try on OS Lion and see but I don’t have the software and I am unable to download it from Molecular devices, as it requires a serial # during registration which I do not have access. Your help is sincerely appreciated.

    • Jon

      Hi – I’ve been using this in OSX 10.5 (Leopard) and 10.6 (Snow Leopard). I don’t have Lion yet, so I can’t tell you if it works on that.

      As for (2) – while I do have said file tucked away somewhere, it’s technically property of my grad school supervisor and I’m not at liberty to be passing it along (which is why the bottled app is not available on this page either). What I can tell you is that (ahem!) the “update files” on Molecular Devices used to be the full software, and that only require registration on MD to access…

  • Phil

    Is it possible to copy-paste from the layout window with winebottler? With Fusion4 running Clampfit 9 under windows xp, graphs don’t transfer from the windows clipboard to the mac clipboard. It’s possible to transfer text, but graphics never make it.

    • Jon

      Hi Phil – I did not know that you could directly copy-paste the layout window at all!

      I’m not sure what you need here, but I’m assuming you want the traces into some OSX application. In the last two years I worked with voltage-clamp expts., I wrote custom code to deal with the plotting and exporting. Prior to that, I’ve either worked with (1) saving as PDF and subsequently re-opening in (vector) OSX applications, or (2) screenshot (shift-ctrl-cmd-4) and drop it into (raster) OSX application. Both of these modes should be accessible to Fusion4 emulations.

      • Phil

        Thanks for the help. Until recently I had to resort to pdf printing because screenshot drops the quality of the tracing to much. I just discovered that if I transfer the trace (Edit / Transfer traces) to the graph window, then the trace can be copied under Windows and pasted into Adobe Illustrator (CS4) under the mac. Works perfectly. It should also work under winebottler.

  • MCT

    Thanks for the awesome solution. I used to use clampfit on lab PC and axograph on my MBP. I love some features that clampfit has in handling traces that axograph falls short of. I have been always wanting to get clampfit on my Mac but I don’t want to pay for parallel destop/VMfusion as well as windows OS just for it. Finally I find your post. Just wanna say my install works w/ the following version: snow leopard, winebottler 1.2.5, pclamp_10_3_1_4. Thanks again.

  • It seems that with the new version of BottleWiner (1.2.5) this doesn’t work. I have a running copy on my MB with OS 10.8 but it’s almost impossible tu run it on my iMac. I’m able to install it with many errors but, once launched, the program just shut down.

    The OS in both machine is OS 10.8 (Mountain Lion)
    The pClamp version in 10.3.1.4
    The XQuartz version is 2.7.4

    The Bottlewiner version on the MB is the 1.2.3, while on the iMac 1.2.5

  • STill not able to install pCLAMP on my macbook because the CDrom i have with the installation packages only has the setup.exe not the pCLAMP.exe What can i do?

    • basically the problem is that as i follow the steps you have provided above, the step regarding the selection of startfile does not appear at all!

  • Rebecca

    This is wonderful and made my day thank you so much!!

  • Jenny

    Using Winebottler version 1.6.1 and Clampfit.exe from pCLAMP10 version 10.3.2.1 clampfit quits immediately as its opened. =/