Phenix.refine in WinXP?
Now that Phenix has a nice GUI and all that, will there ever be a Windows version? And a similar question: has anyone managed to get phenix.refine from cci_apps for Win32 distribution running? I can't seem to make it run: 1. Installer says run \cci_apps_build\setpaths.bat The script produces an error: ******************************************* Fatal Error: Incomplete libtbx environment\! ******************************************* Please re-run the libtbx/configure.py command. 2. configure.py is found in two places: \cci_apps_sources\libtbx\configure.py \cci_apps_sources\libtbx\command_line\configure.py When I run either of them with command python configure.py I get an error "ImportError: No module named libtbx.env_config" 3. There is no file libtbx.env_config anywhere in the installation. There is file \cci_apps_build\libtbx_env. Placing it in the same directory with configure.py does not help. Even renaming libtbx_env. to libtbx.env_config and running "python configure.py" still gives an error "No module named libtbx.env_config" (?) 4. If I just run phenix.refine executable from its directory, it stops with en error: File "c:\cci_apps_sources\mmtbx\secondary_structure.py", line 941, in run_ksdssp_direct raise RuntimeError, "KSDSSP not available" RuntimeError: KSDSSP not available Thanks in advance for any help! I am comfortable setting any environmental variables manually - just need to know what they should be. Dima
On Wed, Apr 21, 2010 at 1:10 PM, Dima Klenchin
Now that Phenix has a nice GUI and all that, will there ever be a Windows version?
Short answer: probably better than 50% odds of this happening, but we don't have a timeline for it. Since Python and wxPython are cross-platform and we have some support for Windows anyway, once Ralf drives a stake through the heart of FORTRAN it will be much easier, but Windows has so little in common with Mac and Linux that it will still require a substantial amount of effort to create something complete and bug-free (and automated - this is the really hard part). I'd estimate at least several months' work between Ralf and me, and we both have many other more urgent items on our to-do lists. 4. If I just run phenix.refine executable from its directory, it stops with
en error: File "c:\cci_apps_sources\mmtbx\secondary_structure.py", line 941, in run_ksdssp_direct raise RuntimeError, "KSDSSP not available" RuntimeError: KSDSSP not available
This is my fault. I'd recommend using the latest nightly build (the ones I released are relatively stable). -Nat
4. If I just run phenix.refine executable from its directory, it stops with en error: File "c:\cci_apps_sources\mmtbx\secondary_structure.py", line 941, in run_ksdssp_direct raise RuntimeError, "KSDSSP not available" RuntimeError: KSDSSP not available
This is my fault. I'd recommend using the latest nightly build (the ones I released are relatively stable).
Thanks, that [almost] did it. setpaths.bat now runs without an error but evidently still does not set any paths. (At least none new is shown when I use SET command to display them). If, however, I provide path to phenix.refine.exe explicitly, it seems to run fine. If, say, I only use phenix.refine.exe, do I need to manually set any other paths besides this executable? Dima
Hi Dima,
Thanks, that [almost] did it. setpaths.bat now runs without an error but evidently still does not set any paths. (At least none new is shown when I use SET command to display them).
If you just run path do you see "cci_apps" in the output? setpaths.bat is supposed to add one entry to the beginning of PATH (that's all it does). You need to repeat this in each new cmd.exe (unless you are an expert and you somehow setup cmd.exe to execute cci_apps setpaths.bat automatically).
If, however, I provide path to phenix.refine.exe explicitly, it seems to run fine.
That's a good sign.
If, say, I only use phenix.refine.exe, do I need to manually set any other paths besides this executable?
No, each of the commands in the "bin" directory updates all required environment variables before launching the actual command doing the work. Ralf
Ralf W. Grosse-Kunstleve wrote:
You need to repeat this in each new cmd.exe (unless you are an expert and you somehow setup cmd.exe to execute cci_apps setpaths.bat automatically).
Not a windows expert, but one or the other of these might serve: 1. right-click on desktop, new shortcut, enter for the command: c:\windows\system32\cmd.exe /K "D:\path to script which sets environment.bat" set startup directory, fullscreen or regular window, close on exit, select a suggestive icon for the shortcut "OK" until you get back to the desktop, double click this icon every time you want to run with this environment. (If "new shortcut" brings up a wizard, enter the above command in the textbox "type the location of the item" and finish. Then rightclick on the shortcut, properties, set anything else you need) or: 2. right-click on "my computer", properties, advanced tab, "environment" add any new variables and their value to your list, edit the %path% variable under "system variables" (separator is semicolon).
You could, of course, always install virtualbox
(http://www.virtualbox.org/) for free and then run phenix (etc) from
within a Linux virtual machine. I do the reverse (WinXP virtual
machine under Ubuntu) for running the few Windows programs for which
there is no good Linux equivalent - it is brilliant.
Cheers,
Stephen
P.S. Perhaps it would be easier for the phenix dev team to make and
distribute a Linux virtual image with phenix pre-installed, rather
than try to support Windows natively?
On 21 April 2010 21:10, Dima Klenchin
Now that Phenix has a nice GUI and all that, will there ever be a Windows version?
And a similar question: has anyone managed to get phenix.refine from cci_apps for Win32 distribution running? I can't seem to make it run:
1. Installer says run \cci_apps_build\setpaths.bat The script produces an error: ******************************************* Fatal Error: Incomplete libtbx environment\! ******************************************* Please re-run the libtbx/configure.py command.
2. configure.py is found in two places: \cci_apps_sources\libtbx\configure.py \cci_apps_sources\libtbx\command_line\configure.py When I run either of them with command python configure.py I get an error "ImportError: No module named libtbx.env_config"
3. There is no file libtbx.env_config anywhere in the installation. There is file \cci_apps_build\libtbx_env. Placing it in the same directory with configure.py does not help. Even renaming libtbx_env. to libtbx.env_config and running "python configure.py" still gives an error "No module named libtbx.env_config" (?)
4. If I just run phenix.refine executable from its directory, it stops with en error: File "c:\cci_apps_sources\mmtbx\secondary_structure.py", line 941, in run_ksdssp_direct raise RuntimeError, "KSDSSP not available" RuntimeError: KSDSSP not available
Thanks in advance for any help! I am comfortable setting any environmental variables manually - just need to know what they should be.
Dima
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-- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638
On Thu, Apr 22, 2010 at 2:11 AM, Stephen Graham
P.S. Perhaps it would be easier for the phenix dev team to make and distribute a Linux virtual image with phenix pre-installed, rather than try to support Windows natively?
Not really - then we'd be expected to support the virtual Linux system too. My experience with virtual machines is that they're not particularly stable or reliable, and the only person I know who runs Phenix this way has reported issues with the GUI freezing, apparently unrelated to the networking issues some other people have had. I still don't know what's causing that. Running the most processor-intensive programs on a virtual machine seems like a waste of time anyway. For now, I would still recommend that crystallographers either buy computers from companies that specifically support Linux on their hardware and will pre-install it, or buy Macs. -Nat
participants (5)
-
Dima Klenchin -
Edward A. Berry -
Nathaniel Echols -
Ralf W. Grosse-Kunstleve -
Stephen Graham