Re: [ccp4bb] iMosflm bug? - SOLVED
Hi I've just installed a Plain vanilla copy of Ubuntu 13.0.4 (aka rastafarian reefer or somesuch) with iMosflm 1.0.7 and CCP4 6.3.0 and found that Roger's suggestions were all that was needed (but I did log out and in again to use them) - sudo apt-get install ttf-mscorefonts-installer # installs microsoft fonts sudo apt-get install xfs xfstt xfonts-75dpi xfonts-100dpi # installs xfonts and xfont server Curiously, although Thomas found that the mscorefonts were installed by default, they weren't on my system. For those of you with time to spare, the Unity desktop that comes with Ubuntu is interesting and may reward further investigation... On 26 Jun 2013, at Wed26 Jun 06:21, Thomas Cleveland wrote: Hi everyone, Thanks again for the help. As several people suggested, it seems to have been a fonts package that was needed. I'm not sure if there is a single particular package that would have solved the problem, but I installed the following combination: t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi xfs xfstt (ttf-mscorefonts-installer was already installed by default) Everything is working fine now. Thanks again. -Thomas On Tue, Jun 25, 2013 at 10:23 AM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Hi everyone, Thanks for all your responses. I will try working on the fonts when I get back to my computer and report back when I find a working solution. I'm using a fresh installation of Ubuntu 13.04 amd64, so hopefully it will be relevant to other users of newer Ubuntu releases. Harry, I could drag the lower right corner to make the window *smaller*, but it would not let me make it any bigger. Reginald, I'll take a look at that. Thanks, Thomas On Mon, Jun 24, 2013 at 10:46 PM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] iMosflm bug?
This might be a problem with fonts. On my laptop the menu items use a sans serif font and that particular window is just wide enough to fit all the items. The font also looks more attractive and readable than your screenshot. I'm guessing (from your desktop background!) that you also use Ubuntu. Unfortunately I can't remember how I set fonts up on my machine, but it may help to: 1) install the ttf-mscorefonts-installer package 2) ensure the package gsfonts-x11 is *not* installed (this causes an incorrect mapping of unicode symbols so you get things like the registered trademark symbol appearing - an effect apparently known as mojibake...) Cheers -- David On 25 June 2013 03:46, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland
Re: [ccp4bb] iMosflm bug?
Hi As David suggests, this is certainly a problem with fonts - you're getting a large variant of Courier; the default font in iMosflm is Helvetica, and it looks like your X-display isn't finding it for some reason. You should be able to re-size the window by dragging out the bottom right hand corner of the Processing options window, even if there's no visible handle. Ubuntu has been becoming less good at having normal Linux things installed by default over the last few years - I'm sure Canonical has very good reasons for this, but it has put me off recommending it. On 25 Jun 2013, at 10:08, David Waterman wrote: This might be a problem with fonts. On my laptop the menu items use a sans serif font and that particular window is just wide enough to fit all the items. The font also looks more attractive and readable than your screenshot. I'm guessing (from your desktop background!) that you also use Ubuntu. Unfortunately I can't remember how I set fonts up on my machine, but it may help to: 1) install the ttf-mscorefonts-installer package 2) ensure the package gsfonts-x11 is *not* installed (this causes an incorrect mapping of unicode symbols so you get things like the registered trademark symbol appearing - an effect apparently known as mojibake...) Cheers -- David On 25 June 2013 03:46, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] iMosflm bug?
Hi, I have seen this before. I would also check the screen resolution (size) used by the terminal to launch the program matches the largest size capable by your monitor. You can check and change this with the xrandr command. Type man xrandr for info. Cheers, Reginald McNulty On Jun 25, 2013, at 2:35 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Hi As David suggests, this is certainly a problem with fonts - you're getting a large variant of Courier; the default font in iMosflm is Helvetica, and it looks like your X-display isn't finding it for some reason. You should be able to re-size the window by dragging out the bottom right hand corner of the Processing options window, even if there's no visible handle. Ubuntu has been becoming less good at having normal Linux things installed by default over the last few years - I'm sure Canonical has very good reasons for this, but it has put me off recommending it. On 25 Jun 2013, at 10:08, David Waterman wrote: This might be a problem with fonts. On my laptop the menu items use a sans serif font and that particular window is just wide enough to fit all the items. The font also looks more attractive and readable than your screenshot. I'm guessing (from your desktop background!) that you also use Ubuntu. Unfortunately I can't remember how I set fonts up on my machine, but it may help to: 1) install the ttf-mscorefonts-installer package 2) ensure the package gsfonts-x11 is *not* installed (this causes an incorrect mapping of unicode symbols so you get things like the registered trademark symbol appearing - an effect apparently known as mojibake...) Cheers -- David On 25 June 2013 03:46, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] iMosflm bug?
Hi everyone, Thanks for all your responses. I will try working on the fonts when I get back to my computer and report back when I find a working solution. I'm using a fresh installation of Ubuntu 13.04 amd64, so hopefully it will be relevant to other users of newer Ubuntu releases. Harry, I could drag the lower right corner to make the window *smaller*, but it would not let me make it any bigger. Reginald, I'll take a look at that. Thanks, Thomas On Mon, Jun 24, 2013 at 10:46 PM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland
Re: [ccp4bb] iMosflm bug?
This may no longer apply to the current version, but in older versions of imosflm and mosflm, I needed to install some xfonts to get the windows to display text properly. These xfonts are also required for ccp4i to fit the fonts properly into the windows unless you like tweaking the install. In any event, these fonts will probably not harm anything. The microsoft fonts may also be desirable. sudo apt-get install ttf-mscorefonts-installer # installs microsoft fonts sudo apt-get install xfs xfstt xfonts-75dpi xfonts-100dpi # installs xfonts and xfont server Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 6/25/2013 8:58 AM, Reginald McNulty wrote: Hi, I have seen this before. I would also check the screen resolution (size) used by the terminal to launch the program matches the largest size capable by your monitor. You can check and change this with the xrandr command. Type man xrandr for info. Cheers, Reginald McNulty On Jun 25, 2013, at 2:35 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk mailto:ha...@mrc-lmb.cam.ac.uk wrote: Hi As David suggests, this is certainly a problem with fonts - you're getting a large variant of Courier; the default font in iMosflm is Helvetica, and it looks like your X-display isn't finding it for some reason. You should be able to re-size the window by dragging out the bottom right hand corner of the Processing options window, even if there's no visible handle. Ubuntu has been becoming less good at having normal Linux things installed by default over the last few years - I'm sure Canonical has very good reasons for this, but it has put me off recommending it. On 25 Jun 2013, at 10:08, David Waterman wrote: This might be a problem with fonts. On my laptop the menu items use a sans serif font and that particular window is just wide enough to fit all the items. The font also looks more attractive and readable than your screenshot. I'm guessing (from your desktop background!) that you also use Ubuntu. Unfortunately I can't remember how I set fonts up on my machine, but it may help to: 1) install the ttf-mscorefonts-installer package 2) ensure the package gsfonts-x11 is *not* installed (this causes an incorrect mapping of unicode symbols so you get things like the registered trademark symbol appearing - an effect apparently known as mojibake...) Cheers -- David On 25 June 2013 03:46, Thomas Cleveland thomas.clevel...@gmail.com mailto:thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] iMosflm bug? - SOLVED
Hi everyone, Thanks again for the help. As several people suggested, it seems to have been a fonts package that was needed. I'm not sure if there is a single particular package that would have solved the problem, but I installed the following combination: t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi xfs xfstt (ttf-mscorefonts-installer was already installed by default) Everything is working fine now. Thanks again. -Thomas On Tue, Jun 25, 2013 at 10:23 AM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Hi everyone, Thanks for all your responses. I will try working on the fonts when I get back to my computer and report back when I find a working solution. I'm using a fresh installation of Ubuntu 13.04 amd64, so hopefully it will be relevant to other users of newer Ubuntu releases. Harry, I could drag the lower right corner to make the window *smaller*, but it would not let me make it any bigger. Reginald, I'll take a look at that. Thanks, Thomas On Mon, Jun 24, 2013 at 10:46 PM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland
[ccp4bb] iMosflm bug?
Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland
[ccp4bb] imosflm bug for Mar 225 (3x3) detectors
There is a bug in the latest imosflm (v0.5.2) which prevents the
correct direct beam coordinates being read from the image header for
Mar 3x3 tiled CCDs (225mm square, as installed on ID23-1 and BM14 at
ESRF for example). This is the ONLY detector affected by this bug.
When the program cannot read the direct beam position, it sets it to
the physical centre of the detector. This generates a warning message
(an exclamation mark will appear in the bottom right corner of the
GUI, click on the exclamation mark to list the warning). The direct
beam coordinates will be set to 112.43, 112.43 (or values very close
to this).
The physical centre of the image can be several mm from the true
direct beam position and this will almost certainly cause the indexing
to fail !
The fix is very simple, and requires a change to the file session.tcl.
The original code reads:
# Only set beam position if image is from reliable detector
set header_beam_x [$a_dom selectNodes normalize-space(//beam_x)]
set header_beam_y [$a_dom selectNodes normalize-space(//beam_y)]
if {[lsearch [list QUAD Q210 Q315 Q420 SAPPHIRE JUPITER SATURN
MERCURY MARCCD MARMOSAIC MOSAIC4] $detector_model] -1 ||
$detector_manufacturer == CBF } {
updateSetting beam_x $header_beam_x 1 1 Images
updateSetting beam_y $header_beam_y 1 1 Images
updateSetting backstop_x $header_beam_x 1 1 Images
updateSetting backstop_y $header_beam_y 1 1 Images
} else {
The required change is to replace MARMOSAIC with MOSAIC3.
This is the ONLY change required.
As this is part of the Tcl for the GUI, NO recompilation is required.
If you do not have access to the source code, a (messy) workaround is
to read an image into ipmosflm (which will read the direct beam
coordinates correctly), make a note of the values, then enter these
values into imosflm (at the head of the Images page).
Andrew Leslie and Harry Powell
