If the only thing you need ChimeraX for is to read/parse mmCIF files, we do package that part as a separate library: GitHub - RBVI/readcif: A fast C++ CIF and mmCIF parser https://github.com/RBVI/readcif

--Eric

Eric Pettersen UCSF Computer Graphics Lab

On Jul 6, 2021, at 11:01 AM, Tom Goddard via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi James,

The ChimeraX Python modules have not been packaged to be used outside the ChimeraX application. I have tried making a chimerax module that can be installed in any Python (with the right version for binary compatibility) where all its Python capabilities can be used without needing the application user interface. But we have not distributed that, it has lots of problems. We have put it into two grant proposals to get funding for it but one proposal was not funded and the other we are still waiting to hear about.

In theory it shouldn't be hard to reuse specific parts of ChimeraX, for instance reading mmCIF files. That is in the mmcif ChimeraX Python module.

https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif

But that needs various other ChimeraX modules (atomstruct, element, pyinstance, pdbconnect, readcif, logger, arrays) listed in the mmcif bundle_info.xml file

https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.... https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml

and those in turn require some other ChimeraX Python modules. ChimeraX contains hundreds of Python modules, so how will you figure out which ones you need? The easy solution is to take them all. But there are more problems, because the ChimeraX application initializes many of the modules, for instance, letting the atomic data structures module know where the residue template files are located. So you also need to figure that out. These many obstacles are why we proposed funding to make the code more usable without running the ChimeraX application -- it will be a good bit of work.

So the standard solution is instead to just run your processing scripts with the ChimeraX application from the command-line

chimerax --nogui myscript.py

For compiling ChimeraX you must be using old ChimeraX source code (your example is fetching Python 3.7 but ChimeraX has used Python 3.8 for the last 9 months). The current ChimeraX build does not fetch third party libraries with rsync, it uses https and curl and does not need a password. So use the current ChimeraX source from github and you should not have that problem.

https://github.com/RBVI/ChimeraX https://github.com/RBVI/ChimeraX

Tom

...

On Jul 3, 2021, at 5:51 AM, James Loy via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hello!

Thank you for creating such an amazing piece of software!

I'm trying to use portions of ChimeraX for part of a CIF file processing pipeline. In order to automate the process, I'm building a docker image that has ChimeraX installed. Ideally, we would like to use the pieces of ChimeraX we need by importing the relevant python modules. Is this possible? If so, must I build ChimeraX from source?

Additionally, I have tried several times to build v1.1.1 from source and I have not been able to. I am always prompted for a password when trying to rsync the dependencies: /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu:/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz user@plato.cgl.ucsf.edu mailto:user@plato.cgl.ucsf.edu's password: In order to build from source, do I need to register somewhere to get credentials?

Just to be clear, this CIF file processing pipeline is for academic (UT Austin) use, not commercial.

Thanks in advance! James -- James Loy, Ph. D. 614.915.9792 LinkedIn https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

---

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If you want to install additional PyPi packages into the ChimeraX Python use

chimerax -m pip install <NameOfPyPiPackage>

as discussed in this message

https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002000.html

If you don't have permission to modify ChimeraX where you might need to use the --user option to pip install. On windows you probably need to use the chimerax-console.exe executable.

Tom

On Jul 6, 2021, at 11:29 AM, James Loy via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Tom, Eric--

Thanks for the responses!

We'd certainly like to read the cif files, but in addition, we'd like to add hydrogens to the protein as well. For an MVP, I was just going to have some script that calls the chimerax CLI. Something like this (in python):

for code in pdb_codes: subprocess.run(f"chimerax --nogui --cmd 'load {code}.cif; addh; save {code}.addh.cif; exit'"

This will likely be okay. But, if I am able to call a python script using chimera basically as the interpreter then that might work better. My only question would be how could I utilize other third party libraries? Say, if I were to use chimerax as the interpreter for the entire cif processing pipeline, then I would need to utilize a few outside modules.

Thanks again for your help-- I really appreciate it! -James

On Tue, Jul 6, 2021 at 1:07 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: If the only thing you need ChimeraX for is to read/parse mmCIF files, we do package that part as a separate library: GitHub - RBVI/readcif: A fast C++ CIF and mmCIF parser https://github.com/RBVI/readcif

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Jul 6, 2021, at 11:01 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hi James,

The ChimeraX Python modules have not been packaged to be used outside the ChimeraX application. I have tried making a chimerax module that can be installed in any Python (with the right version for binary compatibility) where all its Python capabilities can be used without needing the application user interface. But we have not distributed that, it has lots of problems. We have put it into two grant proposals to get funding for it but one proposal was not funded and the other we are still waiting to hear about.

In theory it shouldn't be hard to reuse specific parts of ChimeraX, for instance reading mmCIF files. That is in the mmcif ChimeraX Python module.

https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif

But that needs various other ChimeraX modules (atomstruct, element, pyinstance, pdbconnect, readcif, logger, arrays) listed in the mmcif bundle_info.xml file

https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.... https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml

and those in turn require some other ChimeraX Python modules. ChimeraX contains hundreds of Python modules, so how will you figure out which ones you need? The easy solution is to take them all. But there are more problems, because the ChimeraX application initializes many of the modules, for instance, letting the atomic data structures module know where the residue template files are located. So you also need to figure that out. These many obstacles are why we proposed funding to make the code more usable without running the ChimeraX application -- it will be a good bit of work.

So the standard solution is instead to just run your processing scripts with the ChimeraX application from the command-line

chimerax --nogui myscript.py

For compiling ChimeraX you must be using old ChimeraX source code (your example is fetching Python 3.7 but ChimeraX has used Python 3.8 for the last 9 months). The current ChimeraX build does not fetch third party libraries with rsync, it uses https and curl and does not need a password. So use the current ChimeraX source from github and you should not have that problem.

https://github.com/RBVI/ChimeraX https://github.com/RBVI/ChimeraX

Tom

...

On Jul 3, 2021, at 5:51 AM, James Loy via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hello!

Thank you for creating such an amazing piece of software!

I'm trying to use portions of ChimeraX for part of a CIF file processing pipeline. In order to automate the process, I'm building a docker image that has ChimeraX installed. Ideally, we would like to use the pieces of ChimeraX we need by importing the relevant python modules. Is this possible? If so, must I build ChimeraX from source?

Additionally, I have tried several times to build v1.1.1 from source and I have not been able to. I am always prompted for a password when trying to rsync the dependencies: /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu http://plato.cgl.ucsf.edu/:/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz user@plato.cgl.ucsf.edu mailto:user@plato.cgl.ucsf.edu's password: In order to build from source, do I need to register somewhere to get credentials?

Just to be clear, this CIF file processing pipeline is for academic (UT Austin) use, not commercial.

Thanks in advance! James -- James Loy, Ph. D. 614.915.9792 LinkedIn https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

---

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-- James Loy, Ph. D. 614.915.9792 LinkedIn https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Here's a bit more info on installing a PyPi package in ChimeraX on Windows

https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002304.html https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002304.html

And if you are still interested in compiling ChimeraX there is info about that in the programming manual

https://www.cgl.ucsf.edu/chimerax/docs/devel/building.html https://www.cgl.ucsf.edu/chimerax/docs/devel/building.html

Tom

On Jul 6, 2021, at 12:21 PM, Tom Goddard goddard@sonic.net wrote:

If you want to install additional PyPi packages into the ChimeraX Python use

chimerax -m pip install <NameOfPyPiPackage>

as discussed in this message

https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002000.html https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002000.html

If you don't have permission to modify ChimeraX where you might need to use the --user option to pip install. On windows you probably need to use the chimerax-console.exe executable.

Tom

...

On Jul 6, 2021, at 11:29 AM, James Loy via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Tom, Eric--

Thanks for the responses!

We'd certainly like to read the cif files, but in addition, we'd like to add hydrogens to the protein as well. For an MVP, I was just going to have some script that calls the chimerax CLI. Something like this (in python):

for code in pdb_codes: subprocess.run(f"chimerax --nogui --cmd 'load {code}.cif; addh; save {code}.addh.cif; exit'"

This will likely be okay. But, if I am able to call a python script using chimera basically as the interpreter then that might work better. My only question would be how could I utilize other third party libraries? Say, if I were to use chimerax as the interpreter for the entire cif processing pipeline, then I would need to utilize a few outside modules.

Thanks again for your help-- I really appreciate it! -James

On Tue, Jul 6, 2021 at 1:07 PM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: If the only thing you need ChimeraX for is to read/parse mmCIF files, we do package that part as a separate library: GitHub - RBVI/readcif: A fast C++ CIF and mmCIF parser https://github.com/RBVI/readcif

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Jul 6, 2021, at 11:01 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hi James,

The ChimeraX Python modules have not been packaged to be used outside the ChimeraX application. I have tried making a chimerax module that can be installed in any Python (with the right version for binary compatibility) where all its Python capabilities can be used without needing the application user interface. But we have not distributed that, it has lots of problems. We have put it into two grant proposals to get funding for it but one proposal was not funded and the other we are still waiting to hear about.

In theory it shouldn't be hard to reuse specific parts of ChimeraX, for instance reading mmCIF files. That is in the mmcif ChimeraX Python module.

https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif

But that needs various other ChimeraX modules (atomstruct, element, pyinstance, pdbconnect, readcif, logger, arrays) listed in the mmcif bundle_info.xml file

https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.... https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml

and those in turn require some other ChimeraX Python modules. ChimeraX contains hundreds of Python modules, so how will you figure out which ones you need? The easy solution is to take them all. But there are more problems, because the ChimeraX application initializes many of the modules, for instance, letting the atomic data structures module know where the residue template files are located. So you also need to figure that out. These many obstacles are why we proposed funding to make the code more usable without running the ChimeraX application -- it will be a good bit of work.

So the standard solution is instead to just run your processing scripts with the ChimeraX application from the command-line

chimerax --nogui myscript.py

For compiling ChimeraX you must be using old ChimeraX source code (your example is fetching Python 3.7 but ChimeraX has used Python 3.8 for the last 9 months). The current ChimeraX build does not fetch third party libraries with rsync, it uses https and curl and does not need a password. So use the current ChimeraX source from github and you should not have that problem.

https://github.com/RBVI/ChimeraX https://github.com/RBVI/ChimeraX

Tom

...

On Jul 3, 2021, at 5:51 AM, James Loy via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hello!

Thank you for creating such an amazing piece of software!

I'm trying to use portions of ChimeraX for part of a CIF file processing pipeline. In order to automate the process, I'm building a docker image that has ChimeraX installed. Ideally, we would like to use the pieces of ChimeraX we need by importing the relevant python modules. Is this possible? If so, must I build ChimeraX from source?

Additionally, I have tried several times to build v1.1.1 from source and I have not been able to. I am always prompted for a password when trying to rsync the dependencies: /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu http://plato.cgl.ucsf.edu/:/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz user@plato.cgl.ucsf.edu mailto:user@plato.cgl.ucsf.edu's password: In order to build from source, do I need to register somewhere to get credentials?

Just to be clear, this CIF file processing pipeline is for academic (UT Austin) use, not commercial.

Thanks in advance! James -- James Loy, Ph. D. 614.915.9792 LinkedIn https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

---

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-- James Loy, Ph. D. 614.915.9792 LinkedIn https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

FYI, readcif doesn't build the molecular data structures, it just parses (mm)CIF files quickly.  That is, it's the foundation that you would need to build a mmCIF reader.

-- Greg

On 7/6/2021 11:07 AM, Eric Pettersen via ChimeraX-users wrote:

If the /only/ thing you need ChimeraX for is to read/parse mmCIF files, we do package that part as a separate library: GitHub - RBVI/readcif: A fast C++ CIF and mmCIF parser https://github.com/RBVI/readcif

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Jul 6, 2021, at 11:01 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hi James,

The ChimeraX Python modules have not been packaged to be used outside the ChimeraX application.  I have tried making a chimerax module that can be installed in any Python (with the right version for binary compatibility) where all its Python capabilities can be used without needing the application user interface.  But we have not distributed that, it has lots of problems.  We have put it into two grant proposals to get funding for it but one proposal was not funded and the other we are still waiting to hear about.

In theory it shouldn't be hard to reuse specific parts of ChimeraX, for instance reading mmCIF files.  That is in the mmcif ChimeraX Python module.

https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif

But that needs various other ChimeraX modules (atomstruct, element, pyinstance, pdbconnect, readcif, logger, arrays) listed in the mmcif bundle_info.xml file

https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.... https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml

and those in turn require some other ChimeraX Python modules.  ChimeraX contains hundreds of Python modules, so how will you figure out which ones you need?  The easy solution is to take them all.  But there are more problems, because the ChimeraX application initializes many of the modules, for instance, letting the atomic data structures module know where the residue template files are located.  So you also need to figure that out.  These many obstacles are why we proposed funding to make the code more usable without running the ChimeraX application -- it will be a good bit of work.

So the standard solution is instead to just run your processing scripts with the ChimeraX application from the command-line

chimerax --nogui myscript.py

For compiling ChimeraX you must be using old ChimeraX source code (your example is fetching Python 3.7 but ChimeraX has used Python 3.8 for the last 9 months).  The current ChimeraX build does not fetch third party libraries with rsync, it uses https and curl and does not need a password.  So use the current ChimeraX source from github and  you should not have that problem.

https://github.com/RBVI/ChimeraX https://github.com/RBVI/ChimeraX

Tom

...

On Jul 3, 2021, at 5:51 AM, James Loy via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Hello!

Thank you for creating such an amazing piece of software!

I'm trying to use portions of ChimeraX for part of a CIF file processing pipeline. In order to automate the process, I'm building a docker image that has ChimeraX installed. Ideally, we would like to use the pieces of ChimeraX we need by importing the relevant python modules. Is this possible? If so, must I build ChimeraX from source?

Additionally, I have tried several times to build v1.1.1 from source and I have not been able to. I am always prompted for a password when trying to rsync the dependencies: /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu http://plato.cgl.ucsf.edu:/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz user@plato.cgl.ucsf.edu mailto:user@plato.cgl.ucsf.edu's password: In order to build from source, do I need to register somewhere to get credentials?

Just to be clear, this CIF file processing pipeline is for academic (UT Austin) use, not commercial.

Thanks in advance! James -- James Loy, Ph. D. 614.915.9792 LinkedIn https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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