Saturday 21 January 2012

adxv

From: Rajesh kumar
Date: 19 November 2011 16:53


Dear All,

I have connected to unix server of the  lab through ssh/xming/x11. I can run open phenix and CCP4 GUI.

I am trying to adxv to see images but I am unable to do so.
 
I have got two files adxv and adxv.i686FC2 sitting in my work/adxv/.

when i run adxv in bash
bash: adxv: command not found



when i run ./adxv  in bash
$ ./adxv /home/raj/work/wen/pin8/pin8_1_001.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: line 39: adxv.i686FC2_static: command not found

when i do
$ ./adxv.i686FC2_static /home/raj/work/wen/pin8/pin8_1_001.img

-X11TransSocketINETConnect() cnat get address for loaclhost:6011: name or service not known
error: cannot open display

I cant use Nxclient.

Thanks
Raj

----------
From: Tim Gruene 

 Dear Raj,

your first two error messages are because your 'current working
directory' is not part of your bash's PATH variable. As you login, type
       export PATH=$PATH:/full/path/to/your/work/adxv
then run adxv.

I am not sure whether this will prevent the last error to occur, but
since you can run other graphical programs there is a fair chance.

Cheers,
Tim
- --
Dr Tim Gruene

----------
From: Rajesh kumar

Dear Tim,

Thanks. Your suggestion of adding to PATH  works and its not completely functional may be due to the Ximg/ssh or some thing to do with display.
All three windows opened but couldn't open any image as it didn't display in the list of autoload window. Pattern shows *.0.

$adxv pin8_1_180.img
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


----------
From: Mark Brooks


Dear Rajesh,
                  Are you using the Openmotif library? If so, do you
have an XKeysymDB file installed?
In as shell, issue:
$ locate XKeysymDB
You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
elsewhere [1].
I suspect you're not the only one to have seen this [2].

I hope this helps.

Mark
[1] ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt
[2] http://sbgrid.org/news/newsletters/2009/06 (search for the string "adxv")

----------
From: Rajesh kumar


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: Edward A. Berry


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?

----------
From: Rajesh kumar


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

----------
From: Tim Gruene

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


----------
From: Rajesh kumar


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

----------
From: Ian Tickle

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

----------
From: AFL


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

----------
From: Rajesh kumar


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
Loading predictions from: -wavelength
error: can not open: -wavelength


Thanks
Rajesh


----------
From: David Waterman


Hi Rajesh,

A simple thing I would try first is to try to open a different image. I'm a bit suspicious about yours given the error messages you sent. Is this from a Pilatus detector? The line "pixelsize = 0.172 mm" suggests this is so, but at the bottom below all the warnings it looks like this value is being treated as a file: "No such file: 0.172".

ADXV can be used to open Pilatus images, in CBF format, but as I remember you need a special start up script to do it. To rule out the X display stuff as the source of your problems, perhaps try opening some images that we know should work with ADXV. Harry has a set of images as part of the iMosflm tutorial that would do:

Cheers

-- David

----------
From: Andrew Purkiss


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.
--

----------
From: David Waterman


In addition, perhaps a safer test of ADXV than the set of Mar IP frames I suggested is by using a file from an ADSC detector, such as this one (thanks to James Holton):


I have no reason to believe the image plate frames shouldn't work with ADXV other than that I haven't tested it. I would be extremely surprised however if the ADSC image doesn't work with a properly functioning ADXV.

-- David

----------
From: stacy William

Dear All...
I am new user for Phenix. I am right now working with SAD data. I had run Ausol in GUI interface with my SAD anamolous data. but when i am using the output file  for my autobuild program it is giving problems with Resolve... n terminating with  an error message suggesting to check resolve file. Do i need to change some parameters in Autosol to produce right output files which in turn can work as input files for Autobuild program 
Thanks 
Stacy

----------
From: Tom Terwilliger


Hi Stacy,
I'll answer you on the phenix bb!
-Tom T

Thomas C. Terwilliger



----------
From: Navraj S. Pannu


Hi Stacy,

If you give the CCP4 program crank a try, I can give you advice, if needed.  It can work with SAD data.

Best wishes,
Raj

On Thu, 8 Dec 2011, stacy William wrote:

Dear All...I am new user for Phenix. I am right now working with SAD data. I


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