Hi Tom, let me explain the case.

I'm pablo (Scipion developer). We Integrate many cryo-em (not only cryoem) software and ChimeraX is among them. We tipically work and develop in native Linux OS.

Recently users, are using WLS2 to install Scipion and companions and in this case ChimeraX wasn't an option to be installed in WSL2. So we though, "Ok, let's use windows native chimeraX from WSL2".

And here is the "stupid problem":

We in scipion know the location of many cryoem/pdb files form the "WSL2 perspactive". e.g.: */home/pablo/*mymap.mrc.

Now, ChimeraX as a command is launchable from Scipion as long as we know the path (something that can be configured in Scipion). e.g.: */mnt/c/*Program\ Files/ChimeraX/bin

Note that there are here 2 perpectives for the paths: WSL2 and Windows.

So, when scipion launches ChimeraX (in the simplest way, we also create more complex cxc files) it can do something like: */mnt/c/*Program\ Files/ChimeraX/bin/ChimeraX */home/pablo/*mymap.mrc

These are valid paths from WSL2 perspective, but */home/pablo/*mymap.mrc is NOT valid from Windows perspective.

When ChimeraX is launched (as a windows app) it does not recognize */home/pablo/*mymap.mrc as a valid path, since it "technically does not exist".

It is actually: *\wsl.localhost\Ubuntu-22.04*\home\pconesa\mymap.mrc

There is a command on WLS2:

wslpath wslpath: Invalid argument Usage:     -a    force result to absolute path format     -u    translate from a Windows path to a WSL path (default)     -w    translate from a WSL path to a Windows path     -m    translate from a WSL path to a Windows path, with '/' instead of ''

EX: wslpath 'c:\users'

This might help us to "translate our path to the right windows one" (this would be on our side). But when looking into this issue we though that maybe you "ChimeraX" would like to be aware o this error and maybe ( this is a wild guess) it is a low hanging fruit for you to tolerate this paths.. .or maybe not! I do not know and this is why Dmitry was asking.

Note that this is not just a fix for Scipion (we probably can correct this on our side) but a "feature" that will facilitate any*ChimeraX usage from WSL2* (not being ChimeraX on WSL2 installed but on windows).

All the best, Pablo

El 24/10/2023 a las 20:35, Tom Goddard escribió:

Hi Dmitry,

Zach in our lab has tried ChimeraX on an Ubuntu 22 WSL installation about 2 months ago and said it worked but ran slowly compared to running ChimeraX natively on Windows.  Also Zach suggested that ChimeraX run under Windows could read and write the data files on the Windows System for Linux (WSL) virtual machine file system.

So could you explain what your use case is?  We recommend not using ChimeraX on virtual machines because performance may be poor and problems often arise getting hardware accelerated graphics to work.

Tom

...

On Oct 20, 2023, at 7:22 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Dear Elaine and Eric,

Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX?

Thank you

Kind regards,

Dmitry

---

ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Pablo,

I would start with a different approach.

What if you would try/catch a "am I on WSL" test in Scipion like 'wsl.exe --status' or 'wsl.exe --list' and if yes put the ScipionUserData folder instead of /home/user/ScipionUserData to /mnt/c/Users/user/ScipionUserData

or if not enough space on c: the user could modify scipion.conf to SCIPION_USER_DATA = /mnt/d/ScipionUserData /mnt/d could then also be not only an internal drive, but an external harddisk. Maybe due space reasons the CryoEM movies are already there for the import and motion correction steps.

Then you must only replace /mnt/c to C: and the / to \ (or \) in your call of Chimerax.exe from WSL2.

In addition I think Windows user would appreciate it to browse the Scipion project via the Windows filebrowser and look at files e.g. in the extra folder by double-clicking on them. Also backing up the project is easier from Windows than using commandline tools like rsync, scp, ...

Cheers, Wolfgang

From: "Tom Goddard via ChimeraX-users" chimerax-users@cgl.ucsf.edu To: "Pablo Conesa" pconesa@cnb.csic.es Cc: "Dmitry Semchonok" semchonok@gmail.com, "chimerax-users" chimerax-users@cgl.ucsf.edu Sent: Wednesday, 25 October, 2023 20:30:17 Subject: [EXT] [chimerax-users] Re: ChimeraX for WSL: release request

Hi Pablo, Thanks for the clarification. As I said in my email, one of our developers (Zach) claims ChimeraX can be installed on WSL. I didn't realize there is a WSL2, but Zach probably tested with that since WSL2 came out in 2019. The second point is Zach said performance of ChimeraX on WSL was significantly worse, so that is probably not desirable. As for Scipion launching ChimeraX to open a map file, it seems like Scipion of course has to know whether it is launching a WSL ChimeraX that uses a file path /home/pablo/mymap.mrc or Windows ChimeraX which requires a path like \wsl.localhost\Ubuntu-22.04\home\pconesa\mymap.mrc. I don't think ChimeraX can help automatically correct paths that were specified for a different operating system. Scipion has to give a legal path for the ChimeraX it is invoking. A Windows ChimeraX would have no idea that Scipion on WSL2 launched it.

So I still have not heard of anything that ChimeraX developers could or should do to help WSL2 users, except maybe to advise them that running ChimeraX on WSL2 will give poorer performance than running on Windows natively.

Tom

On Oct 25, 2023, at 12:43 AM, Pablo Conesa Mingo pconesa@cnb.csic.es wrote:

Hi Tom, let me explain the case.

I'm pablo (Scipion developer). We Integrate many cryo-em (not only cryoem) software and ChimeraX is among them. We tipically work and develop in native Linux OS.

Recently users, are using WLS2 to install Scipion and companions and in this case ChimeraX wasn't an option to be installed in WSL2. So we though, "Ok, let's use windows native chimeraX from WSL2".

And here is the "stupid problem":

We in scipion know the location of many cryoem/pdb files form the "WSL2 perspactive". e.g.: /home/pablo/ mymap.mrc.

Now, ChimeraX as a command is launchable from Scipion as long as we know the path (something that can be configured in Scipion). e.g.: /mnt/c/ Program\ Files/ChimeraX/bin

Note that there are here 2 perpectives for the paths: WSL2 and Windows.

So, when scipion launches ChimeraX (in the simplest way, we also create more complex cxc files) it can do something like: /mnt/c/ Program\ Files/ChimeraX/bin/ChimeraX /home/pablo/ mymap.mrc

These are valid paths from WSL2 perspective, but /home/pablo/ mymap.mrc is NOT valid from Windows perspective.

When ChimeraX is launched (as a windows app) it does not recognize /home/pablo/ mymap.mrc as a valid path, since it "technically does not exist".

It is actually: \wsl.localhost\Ubuntu-22.04 \home\pconesa\mymap.mrc

There is a command on WLS2:

wslpath wslpath: Invalid argument Usage: -a force result to absolute path format -u translate from a Windows path to a WSL path (default) -w translate from a WSL path to a Windows path -m translate from a WSL path to a Windows path, with '/' instead of ''

EX: wslpath 'c:\users'

This might help us to "translate our path to the right windows one" (this would be on our side). But when looking into this issue we though that maybe you "ChimeraX" would like to be aware o this error and maybe ( this is a wild guess) it is a low hanging fruit for you to tolerate this paths.. .or maybe not! I do not know and this is why Dmitry was asking. Note that this is not just a fix for Scipion (we probably can correct this on our side) but a "feature" that will facilitate any ChimeraX usage from WSL2 (not being ChimeraX on WSL2 installed but on windows).

All the best, Pablo

El 24/10/2023 a las 20:35, Tom Goddard escribió:

BQ_BEGIN Hi Dmitry,

Zach in our lab has tried ChimeraX on an Ubuntu 22 WSL installation about 2 months ago and said it worked but ran slowly compared to running ChimeraX natively on Windows. Also Zach suggested that ChimeraX run under Windows could read and write the data files on the Windows System for Linux (WSL) virtual machine file system.

So could you explain what your use case is? We recommend not using ChimeraX on virtual machines because performance may be poor and problems often arise getting hardware accelerated graphics to work.

Tom

BQ_BEGIN

On Oct 20, 2023, at 7:22 AM, Dmitry Semchonok via ChimeraX-users [ mailto:chimerax-users@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] wrote:

Dear Elaine and Eric,

Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX?

Thank you

Kind regards,

Dmitry

_______________________________________________ ChimeraX-users mailing list -- [ mailto:chimerax-users@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] To unsubscribe send an email to [ mailto:chimerax-users-leave@cgl.ucsf.edu | chimerax-users-leave@cgl.ucsf.edu ] Archives: [ https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ | https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ ]

BQ_END

Let me reply in line

El 26/10/2023 a las 11:45, Lugmayr, Wolfgang escribió:

Hi Pablo,

I would start with a different approach.

What if you would try/catch a "am I on WSL" test in Scipion like 'wsl.exe --status' or 'wsl.exe --list' and if yes put the ScipionUserData folder instead of /home/user/ScipionUserData to /mnt/c/Users/user/ScipionUserData

Not sure how safe is this but I've seen in my WSL env I got "WSL_DISTRO_NAME" I'm using it existence to "mark" Scipion is running on WSL (how weak is this.... we'll see).

or if not enough space on c: the user could modify scipion.conf to SCIPION_USER_DATA = /mnt/d/ScipionUserData /mnt/d could then also be not only an internal drive, but an external harddisk. Maybe due space reasons the CryoEM movies are already there for the import and motion correction steps.

Then you must only replace  /mnt/c to C: and the / to \ (or \) in your call of Chimerax.exe from WSL2.

In addition I think Windows user would appreciate it to browse the Scipion project via the Windows filebrowser and look at files e.g. in the extra folder by double-clicking on them. Also backing up the project is easier from Windows than using commandline tools like rsync, scp, ...

umm! Nice idea... not sure if we can make a "FileHandler" to launch windows filebrowser, but will make a note.

Cheers, Wolfgang

---

*From: *"Tom Goddard via ChimeraX-users" chimerax-users@cgl.ucsf.edu *To: *"Pablo Conesa" pconesa@cnb.csic.es *Cc: *"Dmitry Semchonok" semchonok@gmail.com, "chimerax-users" chimerax-users@cgl.ucsf.edu *Sent: *Wednesday, 25 October, 2023 20:30:17 *Subject: *[EXT] [chimerax-users] Re: ChimeraX for WSL: release request

Hi Pablo,   Thanks for the clarification.  As I said in my email, one of our developers (Zach) claims ChimeraX can be installed on WSL.  I didn't realize there is a WSL2, but Zach probably tested with that since WSL2 came out in 2019.  The second point is Zach said performance of ChimeraX on WSL was significantly worse, so that is probably not desirable.  As for Scipion launching ChimeraX to open a map file, it seems like Scipion of course has to know whether it is launching a WSL ChimeraX that uses a file path /home/pablo/mymap.mrc or Windows ChimeraX which requires a path like \wsl.localhost\Ubuntu-22.04\home\pconesa\mymap.mrc.  I don't think ChimeraX can help automatically correct paths that were specified for a different operating system.  Scipion has to give a legal path for the ChimeraX it is invoking.  A Windows ChimeraX would have no idea that Scipion on WSL2 launched it.

So I still have not heard of anything that ChimeraX developers could or should do to help WSL2 users, except maybe to advise them that running ChimeraX on WSL2 will give poorer performance than running on Windows natively.

Tom

On Oct 25, 2023, at 12:43 AM, Pablo Conesa Mingo
<pconesa@cnb.csic.es> wrote:

Hi Tom, let me explain the case.

I'm pablo (Scipion developer). We Integrate many cryo-em (not only
cryoem) software and ChimeraX is among them. We tipically work and
develop in native Linux OS.

Recently users, are using WLS2 to install Scipion and companions
and in this case ChimeraX wasn't an option to be installed in
WSL2. So we though, "Ok, let's use windows native chimeraX from WSL2".

And here is the "stupid problem":

We in scipion know the location of many cryoem/pdb files form the
"WSL2 perspactive". e.g.: */home/pablo/*mymap.mrc.

Now, ChimeraX as a command is launchable from Scipion as long as
we know the path (something that can be configured in Scipion).
e.g.: */mnt/c/*Program\ Files/ChimeraX/bin

Note that there are here 2 perpectives for the paths: WSL2 and
Windows.

So, when scipion launches ChimeraX (in the simplest way, we also
create more complex cxc files) it can do something like:
*/mnt/c/*Program\ Files/ChimeraX/bin/ChimeraX */home/pablo/*mymap.mrc

These are valid paths from WSL2 perspective, but
*/home/pablo/*mymap.mrc is NOT valid from Windows perspective.

When ChimeraX is launched (as a windows app) it does not recognize
*/home/pablo/*mymap.mrc as a valid path, since it "technically
does not exist".

It is actually: *\\wsl.localhost\Ubuntu-22.04*\home\pconesa\mymap.mrc

There is a command on WLS2:

wslpath
wslpath: Invalid argument
Usage:
    -a    force result to absolute path format
    -u    translate from a Windows path to a WSL path (default)
    -w    translate from a WSL path to a Windows path
    -m    translate from a WSL path to a Windows path, with '/'
instead of '\'

EX: wslpath 'c:\users'

This might help us to "translate our path to the right windows
one" (this would be on our side). But when looking into this issue
we though that maybe you "ChimeraX" would like to be aware o this
error and maybe ( this is a wild guess) it is a low hanging fruit
for you to tolerate this paths.. .or maybe not! I do not know and
this is why Dmitry was asking.

Note that this is not just a fix for Scipion (we probably can
correct this on our side) but a "feature" that will facilitate
any*ChimeraX usage from WSL2* (not being ChimeraX on WSL2
installed but on windows).

All the best, Pablo

El 24/10/2023 a las 20:35, Tom Goddard escribió:

    Hi Dmitry,

      Zach in our lab has tried ChimeraX on an Ubuntu 22 WSL
    installation about 2 months ago and said it worked but ran
    slowly compared to running ChimeraX natively on Windows.  Also
    Zach suggested that ChimeraX run under Windows could read and
    write the data files on the Windows System for Linux (WSL)
    virtual machine file system.

      So could you explain what your use case is?  We recommend
    not using ChimeraX on virtual machines because performance may
    be poor and problems often arise getting hardware accelerated
    graphics to work.

    Tom


        On Oct 20, 2023, at 7:22 AM, Dmitry Semchonok via
        ChimeraX-users <chimerax-users@cgl.ucsf.edu>
        <mailto:chimerax-users@cgl.ucsf.edu> wrote:

        Dear Elaine and Eric,

        Since the number of Windows WSL systems is increasing do
        you consider releasing the compatible version of ChimeraX?

        Thank you


        Kind regards,

        Dmitry


        _______________________________________________
        ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu
        To unsubscribe send an email
        tochimerax-users-leave@cgl.ucsf.edu
        Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/


-- 
Pablo Conesa *Scipion <http://scipipon.i2pc.es/> cryo-em workflow
engine developer at Madrid, among many others.*

---

ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Thanks Tom! This is a nice advice and very likely our cxc can contain relative paths that will save a lot of hassle otherwise.

Scipion generates cxc files for visualizing volumes with axis reference (cilinders + cones on top on eech axis) or even more complex ones like local resolution visualization or "refinement angular distribution plots"

Thanks, Pablo.

El 26/10/2023 a las 19:46, Tom Goddard escribió:

Hi Pablo,

I see.  I didn't know there were many ChimeraX scripts containing file paths.  Did you know that when ChimeraX opens a script (.cxc) file it changes directory to the directory containing the script so you can open files in the same directory or subdirectories with a relative path, for example, "open mymap.mrc" instead of "open /home/pablo/mymap.mrc".  So if you keep the scripts with the data files and use relative paths then you don't need to worry about where they are on the file system.  This is especially useful when you end up moving your project directory -- the scripts then still all work.

Tom

...

On Oct 26, 2023, at 7:49 AM, Pablo Conesa Mingo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Thanks Tom,

For me the actual burden, would be to adapt paths not only from the command line but from all the scripts (cxc files) created from linux software that in cryoem is majority.

But I managed to do the translation in Scipion at leaast for command line calls not cxc files yet.

El 25/10/2023 a las 20:30, Tom Goddard escribió:

...

Hi Pablo,

Thanks for the clarification.  As I said in my email, one of our developers (Zach) claims ChimeraX can be installed on WSL.  I didn't realize there is a WSL2, but Zach probably tested with that since WSL2 came out in 2019.  The second point is Zach said performance of ChimeraX on WSL was significantly worse, so that is probably not desirable.  As for Scipion launching ChimeraX to open a map file, it seems like Scipion of course has to know whether it is launching a WSL ChimeraX that uses a file path /home/pablo/mymap.mrc or Windows ChimeraX which requires a path like \wsl.localhost\Ubuntu-22.04\home\pconesa\mymap.mrc.  I don't think ChimeraX can help automatically correct paths that were specified for a different operating system.  Scipion has to give a legal path for the ChimeraX it is invoking.  A Windows ChimeraX would have no idea that Scipion on WSL2 launched it.

So I still have not heard of anything that ChimeraX developers could or should do to help WSL2 users, except maybe to advise them that running ChimeraX on WSL2 will give poorer performance than running on Windows natively.

Tom

...

On Oct 25, 2023, at 12:43 AM, Pablo Conesa Mingo pconesa@cnb.csic.es wrote:

Hi Tom, let me explain the case.

I'm pablo (Scipion developer). We Integrate many cryo-em (not only cryoem) software and ChimeraX is among them. We tipically work and develop in native Linux OS.

Recently users, are using WLS2 to install Scipion and companions and in this case ChimeraX wasn't an option to be installed in WSL2. So we though, "Ok, let's use windows native chimeraX from WSL2".

And here is the "stupid problem":

We in scipion know the location of many cryoem/pdb files form the "WSL2 perspactive". e.g.: */home/pablo/*mymap.mrc.

Now, ChimeraX as a command is launchable from Scipion as long as we know the path (something that can be configured in Scipion). e.g.: */mnt/c/*Program\ Files/ChimeraX/bin

Note that there are here 2 perpectives for the paths: WSL2 and Windows.

So, when scipion launches ChimeraX (in the simplest way, we also create more complex cxc files) it can do something like: */mnt/c/*Program\ Files/ChimeraX/bin/ChimeraX */home/pablo/*mymap.mrc

These are valid paths from WSL2 perspective, but */home/pablo/*mymap.mrc is NOT valid from Windows perspective.

When ChimeraX is launched (as a windows app) it does not recognize */home/pablo/*mymap.mrc as a valid path, since it "technically does not exist".

It is actually: *\wsl.localhost\Ubuntu-22.04*\home\pconesa\mymap.mrc

There is a command on WLS2:

wslpath wslpath: Invalid argument Usage:     -a    force result to absolute path format     -u    translate from a Windows path to a WSL path (default)     -w    translate from a WSL path to a Windows path     -m    translate from a WSL path to a Windows path, with '/' instead of ''

EX: wslpath 'c:\users'

This might help us to "translate our path to the right windows one" (this would be on our side). But when looking into this issue we though that maybe you "ChimeraX" would like to be aware o this error and maybe ( this is a wild guess) it is a low hanging fruit for you to tolerate this paths.. .or maybe not! I do not know and this is why Dmitry was asking.

Note that this is not just a fix for Scipion (we probably can correct this on our side) but a "feature" that will facilitate any*ChimeraX usage from WSL2* (not being ChimeraX on WSL2 installed but on windows).

All the best, Pablo

El 24/10/2023 a las 20:35, Tom Goddard escribió:

...

Hi Dmitry,

Zach in our lab has tried ChimeraX on an Ubuntu 22 WSL installation about 2 months ago and said it worked but ran slowly compared to running ChimeraX natively on Windows.  Also Zach suggested that ChimeraX run under Windows could read and write the data files on the Windows System for Linux (WSL) virtual machine file system.

So could you explain what your use case is?  We recommend not using ChimeraX on virtual machines because performance may be poor and problems often arise getting hardware accelerated graphics to work.

Tom

...

On Oct 20, 2023, at 7:22 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Dear Elaine and Eric,

Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX?

Thank you

Kind regards,

Dmitry

---

ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

-- Pablo Conesa *Scipion http://scipipon.i2pc.es/ cryo-em workflow engine developer at Madrid, among many others.*

-- Pablo Conesa *Scipion http://scipipon.i2pc.es/ cryo-em workflow engine developer at Madrid, among many others.* _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/