From: Rajesh kumar
Dear All,
All the suggestions helped me to solve this problem on my unix server.
Earlier I had 1.9.4 downloaded from http://pilatus.web.psi.ch/datasets.htm.
untar gunzip yielded two file adxv and adxv.i686FC2_static and they were made xecutable.
I wrote the path to .bashrc.
So still had windows locking with out opening anything.
I updated now to 1.9.8 and it had only one file adxv.i686FC2.
Copied this file to the adxv folder and start opening the file with adxv.i686FC2 instead of adxv.
Its working with some font error. Running "adxv" gives same old error. I dont worry about this any more.
Since it works on Linux server, I could open on my windows laptop through XMING without any problem.
I want to thank Tim, Andrew, David, Ian, Andrzej, Mark, and Edward for their valubale time an dsuggestions.
I still have some error but I guess its font error. I downloaded the fonts to my working directory and tried adxv -fp fonts/ and adxv.i686FC2 -fp fonts/ and it didnt woked I guess.
But its not effecting my work so I dont worry.
In case any one wanted to know, here it is.
tmp]$ adxv.i686FC2 /home/rajesh/Download/ALS831_lyso_Gd_001.img
Adxv Version 1.9.8
Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation
Using 24-bit TrueColor visual
adxv: Can not open font: "-*-lucidatypewriter-medium-r-*-*-*-120-75-75-*-*-iso8859-1". Trying: "fixed"
adxv: Can not open font: "-*-lucida-bold-r-*-*-*-120-75-75-*-*-iso8859-1". Trying: "-urw-urw bookman l-bold-r-*-*-*-120-75-75-*-*-iso8859-1"
adxv: Can not open font: "-*-lucida-medium-r-*-*-*-120-75-75-*-*-iso8859-1". Trying: "fixed"
Warning: Cannot convert string "-*-lucida-bold-r-*-*-*-120-75-75-*-*-iso8859-1" to type FontStruct
Warning: Cannot convert string "-*-lucida-medium-r-*-*-*-120-75-75-*-*-iso8859-1" to type FontStruct
adxv: Can not open font: "-*-lucida-bold-r-*-*-*-180-75-75-*-*-iso8859-1". Trying: "fixed"
adxv: Unable to open font: "-*-lucidatypewriter-bold-r-*-*-*-180-75-75-m-*-iso8859-1" Trying: "-urw-urw bookman l-bold-r-*-*-*-180-75-75-*-*-iso8859-1"...
adxv: Unable to open font: "-*-lucidatypewriter-medium-r-*-*-*-100-75-75-*-*-iso8859-1" Trying: "-urw-urw bookman l-medium-r-*-*-*-100-75-75-*-*-iso8859-1"...
adxv: Unable to open font: "-*-lucidatypewriter-medium-r-*-*-*-80-75-75-*-*-iso8859-1" Trying: "-urw-urw bookman l-medium-r-*-*-*-80-75-75-*-*-iso8859-1"...
adxv: Unable to open font: "-*-lucidatypewriter-bold-r-*-*-*-120-75-75-*-*-iso8859-1" Trying: "-urw-urw bookman l-bold-r-*-*-*-120-75-75-*-*-iso8859-1"...
adxv: Unable to open font: "-*-lucidatypewriter-bold-r-*-*-*-140-75-75-*-*-iso8859-1" Trying: "-urw-urw bookman l-bold-r-*-*-*-140-75-75-*-*-iso8859-1"...
adxv: Unable to open font: "-*-lucidatypewriter-bold-r-*-*-*-140-75-75-*-*-iso8859-1" Trying: "-urw-urw bookman l-bold-r-*-*-*-140-75-75-*-*-iso8859-1"...
Loading /home/yogesha/Download/ALS831_lyso_Gd_001.img
3072 x 3072 pixels
Distance: 250 mm, Lambda: 0.979 A
MaxI: 32609, AvgI: 42
0 Overflows
Scale factor: 0.19
THANKS for the HELP
Warm regards,
rajesh
> Date: Tue, 22 Nov 2011 14:41:19 +0000
>
> Hi Rajesh,
>
> That is a very old version (1.9.4) of ADXV.
>
> Try the current version from here
>
> http://www.scripps.edu/~arvai/adxv/
>
> version 1.9.8 works fine for us and opens Pilatus data without modifying
> the files.
>
> Hope this helps.
>
> Andrew Purkiss
>
> --
> X-ray Laboratory Manager,
> London Research Institute,
> Cancer Research UK.
>
> On Tue, 2011-11-22 at 09:30 -0500, Rajesh kumar wrote:
> > Hi Andrzej,
> >
> >
> > I used exactly what you have suggested.
> > Downloaded file adxv.i686FC2.tgz from some place.
> > untar Gunzip so I get a folder adxv.1686FC2 which has adxv and
> > adxv.1686FC2_static files.
> > I made both executable using chmod.
> > I put the PATH in .bashrc
> > If I run this command in the folder where images are then
> > it opens with "Windows open but the file selection dialogue is locked
> > and the selection pattern is 0.*."
> >
> >
> > But not functional and get the error I posted recently
> >
> >
> > pin8]$ adxv pin8_1_144.img
> > (standard_in) 1: parse error
> > (standard_in) 1: parse error
> > (standard_in) 1: parse error
> > beam_center x = pixels , mm
> > beam_center y = pixels , mm
> > distance = mm
> > overload = counts
> > pixelsize = 0.172 mm
> > wavelength = Angstroem
> >
> >
> > Adxv Version 1.9.4-beta
> > Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems
> > Corporation
> > Using 24-bit TrueColor visual
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > ManagerParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfBeginLine
> > Warning: ... found while parsing ':<Key>osfBeginLine:
> > ManagerGadgetTraverseHome()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name: osfHelp
> > Warning: ... found while parsing ':<Key>osfHelp:
> > ManagerGadgetHelp()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > ManagerParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > PrimitiveParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name: osfHelp
> > Warning: ... found while parsing ':<Key>osfHelp:
> > Help()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > PrimitiveParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfCancel
> > Warning: ... found while parsing ':<Key>osfCancel: MenuEscape()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfSelect
> > Warning: ... found while parsing ':<Key>osfSelect:
> > ArmAndActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > PrimitiveParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: Locale not supported for XmbTextListToTextProperty
> > Warning: Cannot convert XmString to compound text
> > Warning: translation table syntax error: Unknown keysym name:
> > osfPrimaryPaste
> > Warning: ... found while parsing ':m
> > <Key>osfPrimaryPaste:cut-primary()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > PrimitiveParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > PrimitiveParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfSelect
> > Warning: ... found while parsing ':<Key>osfSelect:
> > ArmAndActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfPrimaryPaste
> > Warning: ... found while parsing ':m
> > <Key>osfPrimaryPaste:cut-primary()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfSelect
> > Warning: ... found while parsing ':<Key>osfSelect:
> > ManagerGadgetSelect()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfSelect
> > Warning: ... found while parsing ':<Key>osfSelect:
> > MenuBarGadgetSelect()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > ManagerParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name: osfHelp
> > Warning: ... found while parsing ':<Key>osfHelp:
> > MenuHelp()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > PrimitiveParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfActivate
> > Warning: ... found while parsing ':<Key>osfActivate:
> > DrawingAreaInput() ManagerParentActivate()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name: osfUp
> > Warning: ... found while parsing ':<Key>osfUp:
> > DrawingAreaInput() ManagerGadgetTraverseUp()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfSelect
> > Warning: ... found while parsing ':<Key>osfSelect: KeySelect()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfSelect
> > Warning: ... found while parsing ':<Key>osfSelect: KeySelect()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfCancel
> > Warning: ... found while parsing '<Key>osfCancel:
> > MenuEscape()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfBeginLine
> > Warning: ... found while parsing ':s c <Key>osfBeginLine:
> > ListBeginDataExtend()'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: translation table syntax error: Unknown keysym name:
> > osfBeginLine
> > Warning: ... found while parsing ':c <Key>osfBeginLine:
> > ActionGrab(SWTopLine)'
> > Warning: String to TranslationTable conversion encountered errors
> > Warning: Locale not supported for XmbTextListToTextProperty
> > Warning: Cannot convert XmString to compound text
> > Warning: Locale not supported for XmbTextListToTextProperty
> > Warning: Cannot convert XmString to compound text
> > No such file: 0.172
> >
> >
> > Loading predictions from: -wavelength
> > error: can not open: -wavelength
> >
> >
> >
> >
> > Thanks
> > Rajesh
> >
> > >
> > >
> > > Rajesh,
> > >
> > > I think there is a simpler explanation to your problems but we need
> > to
> > > go back to the installation of adxv on your linux machine.
> > >
> > > How did you extract adxv binary from the *.gz file?
> > >
> > > I've actually learned yesterday that if you use graphic tools to
> > > extract the binary the resulting file will not be fully functional!
> > > Windows open but the file selection dialogue is locked and the
> > selection
> > > pattern is 0.*.
> > >
> > > Use command line 'gunzip' to extract the binary.
> > > Don't forget to 'chmod +x' on the resulting file and you should have
> > a
> > > working adxv.
> > >
> > > Andrzej
> > >
> > > On 11/22/11 3:07 PM, Ian Tickle wrote:
> > > > Rajesh
> > > >
> > > > I use adxv (as well as xemacs, xdsview, imosflm, hklview, ipdisp
> > etc)
> > > > over ssh/Cygwin X11 from Windows XP to a Centos (like RedHat)
> > server
> > > > with no problems at all.
> > > >
> > > > I suspect your xming either just doesn't have the requisite X11
> > libs
> > > > or somehow they have not gotten installed on your system. Can you
> > try
> > > > Cygwin/X11, it's very easy to install.
> > > >
> > > > Cheers
> > > >
> > > > -- Ian
> > > >
> > > > On 22 November 2011 13:49, Rajesh kumar
> > wrote:
> > > >> Dear Tim,
> > > >> Yes, I have windows 7 computer and use ccp4 and phenix through
> > xming/putty
> > > >> and I run them over linux lab computer.
> > > >> Sorry if I have confused you all with insufficient information.
> > > >> On the lab linux system, I installed everything you suggested in
> > BASH and
> > > >> it works but not completely.
> > > >> Core manager kind of not interested to look in to it and I dont
> > know much to
> > > >> understand everything you nice people saying here.
> > > >> So instead I used idiffdisp and it opens the image. But wanted
> > adxv to work
> > > >> thats all.
> > > >> Thanks
> > > >> Raj
> > > >>> Date: Tue, 22 Nov 2011 14:41:00 +0100
> > > >>>
> > > >>> Dear Rajesh,
> > > >>>
> > > >>> are you saying that the computer you are sitting in front of is
> > a
> > > >>> windows computer?
> > > >>> Are you sure you have been using CCP4 and phenix through an
> > > >>> ssh-connection and not the respective windows-binaries?
> > > >>>
> > > >>> I am not familiar with windows and the possible existence of
> > > >>> X11-clients, but I would think that most suggestions to you
> > assumed that
> > > >>> your client computer was also a linux-machine.
> > > >>>
> > > >>> Cheers,
> > > >>> Tim
> > > >>>
> > > >>> On 11/22/2011 02:27 PM, Rajesh kumar wrote:
> > > >>>>
> > > >>>> I don't know if I need that installed on my windows computer
> > terminal.On
> > > >>>> the server also I could run adxv. Thought of using other ccp4
> > utilities.
> > > >>>> Thanks for everyone for the help. I give up.
> > > >>>> Regards,Rajesh
> > > >>>>
> > > >>>>> Date: Mon, 21 Nov 2011 11:36:14 -0500
> > > >>>>> From:
> > > >>>>>
> > > >>>>> yum install lesstif ?
> > > >>>>>
> > > >>>>> but wouldn't the motif stuff be required for the X-server,
> > i.e. your
> > > >>>>> terminal, not for the
> > > >>>>> server running adxv?
> > > >>>>>
> > > >>>>> Rajesh kumar wrote:
> > > >>>>>> Dear Mark,
> > > >>>>>>
> > > >>>>>> $ locate XKeysymDB - didnt come with any thing suggests
> > probably
> > > >>>>>> openmotif lib is not
> > > >>>>>> installed.
> > > >>>>>> I linux server has Fedora and I am using latest version of
> > Adxv so
> > > >>>>>> details on the sbgrid
> > > >>>>>> suggest its same problem.
> > > >>>>>>
> > > >>>>>> So how would I fix this.
> > > >>>>>>
> > > >>>>>> Thanks for your time.
> > > >>>>>>
> > > >>>>>> Regards
> > > >>>>>> Rajesh
> > > >>>>>>
> > > >>>>>>
> --
>
----------
From: Ian Tickle
Date: 22 November 2011 15:57
Hi Rajesh
The fonts have to be installed where they are needed, i.e. where the
display of the GUI is happening, on the X server (e.g. your Windows
PC), not on the compute server (your Linux box). I had problems with
missing fonts in Cygwin when I first installed it. Cygwin doesn't
install all the fonts by default, I had to specifically ask for them
(I just installed all the fonts I could find in the Cygwin software
installation menu). Can't help you with xming though, I've no idea if
it has all the fonts that adxv is asking for.
According to Wikipedia "xming is described as simple and easier to
install though less configurable than other popular free choices like
Cygwin/X" so it may not be fully functional.
Cheers
-- Ian
----------
From: Pius Padayatti
Date: 22 November 2011 22:04
Rajesh,
The fonts error please follow the guidelines from following link
http://www.scripps.edu/~arvai/adxv.html
see relevant parts under the heading questions
it did solve issues for me
cheers
psp
--
Pius S Padayatti,PhD,
Phone: 216-658-4528
----------
From: Ian Tickle
OK the fonts you need are the ones mentioned above (in
http://www.scripps.edu/~arvai/adxv/fonts.tar.gz), BUT the installation
instructions there are for an X server running on Linux. It won't do
you any good to install them on the Linux system disk, unless it
happens to be mounted on your Windows PC (possible though unlikely).
The logical place to install them is with the Xming X server on your
Windows PC (or you could put them on any disk that's mounted from your
Windows PC). For that you need to follow these instructions:
http://www.straightrunning.com/XmingNotes/fonts.php
Cheers
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