Hi Helge,

The underlying reason that it is hard or impossible to show your aligned maps in Coot without resampling is because the file formats like CCP4 and MRC and others for the maps don't include any header information about how the map should be rotated in the physical coordinate space. They do have some information about how it is shifted, but for instance with CCP4 format the shift can only be an integer number of grid points. So to show one map fit into another the software needs to be able to input the position information that it won't get from the file itself. I don't know if Coot can do that and you would need to ask in a Coot forum to figure that out.

Tom

On Jan 26, 2022, at 8:25 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Helge, As far as I know, you would have to resample in order to save one map relative to another and actually have the orientation saved in the file, as explained here: https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#afterfitting

Theoretically you could just save the rotation/translation information instead, but then every time you open the map file, you have to apply that rotation/translation in an additional step. See how to save/apply ChimeraX positions files: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html

See also "view matrix" and "measure rotation" https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation

The other alternative is to save the session, which will retain the relative orientations. https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session

I hope this helps, Elaine

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Jan 26, 2022, at 3:01 AM, Helge Paternoga via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi,

I would like to know if it is possible to save a .mrc map relative to another one. Basically, I would like to superpose two volumes and compare them outside of ChimeraX (i. e. using Coot) without resampling in ChimeraX, as it is my understanding that resampling changes the volume in question. I noticed that "fitmap" outputs the rotation etc. in the log, but I do not know if and how I can apply this to a map.

Many thanks in advance,

Helge

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Hi Helge,

As you can see in the MRC 2000 specification which ChimeraX tries to follow

https://www.ccpem.ac.uk/mrc_format/mrc2000.php https://www.ccpem.ac.uk/mrc_format/mrc2000.php

The "skew matrix" is in the space labeled "EXTRA" in the header and the comments below say "CCP4 uses words 25-37 for defining skew planes." CCP4 is a (slightly) different format than MRC. ChimeraX writes MRC not CCP4 and so does not write those skew matrix fields. ChimeraX reads CCP4 format maps but still ignores the skew matrix fields. In about 20 years of Chimera and ChimeraX reading CCP4 files no one has ever reported an alignment bug where skew matrix was used. So it has been my hunch that no one uses that. And so ChimeraX currently does not support it.

Tom

On Jan 28, 2022, at 7:01 AM, Helge Paternoga via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

I have asked in the Coot forum and it was mentioned that there is a feature called "skew transformation" that is defined in the MRC/CCP4 2000 specification.

See here for the comment: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2201&L=COOT&D=0...

It is mentioned that this is already used by Pymol, so I was wondering if this would be useful also for ChimeraX?

Best,

Helge

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The log uses HTML.  And displaying HTML is provided by the Qt user interface toolkit.  To check for missing shared libraries, first "cd CHIMERAX/lib/python3.9/site-packages/PyQt5/Qt/lib" where CHIMERAX is where you installed ChimeraX.  Then run ldd on libQt5WebEngineWidgets.so.5, libQt5WebEngineCore.so.5, and libQt5WebEngine.so.5.   For example: "ldd libQt5WebEngineCore.so.5".   That will show all of the shared libraries that are needed for the given shared library to work. There will probably be lines with "LIBRARY_NAME => not found" in them.  Those will be the missing libraries that you need to install.

There is a chance that the missing libraries will be older versions of libraries that are installed on your system.  In that case, you can try tricking the runtime loader by adding symbolic links in CHIMERAX/lib from the older name to the newer system version, e.g., "ln -s /usr/lib64/libpng15.so.20 CHIMERAX/lib/libpng15.so.15".  But it might not work.  An alternative would be to install the older version of the library along side the newer one.  Exactly how to do that on Manjaro is left to you.

HTH,

Greg

On 3/12/2022 12:25 PM, Helge Paternoga via ChimeraX-users wrote:

Hi,

I would like to ask for some help running the generic Linux version of ChimeraX.

I was running ChimeraX 1.3 without problems on my home machine with Manjaro Linux. But now I had to format my system drive and after installing the current Manjaro release, ChimeraX is not working 100%. One thing that is not working is the log dialog: It is just blank and when I perform actions (i. e. selecting residues in a model or switching the lighting settings) no commands are shown in the log, it just flashes white briefly. Also the toolshed does not seem to load.

As ChimeraX was running fine before the system re-install, I assume that I am missing some libraries that where installed before. I just do not remember installing anything specific for ChimeraX in the past, so I would like to ask if you have some idea which library could be amiss here? I am running ChimeraX from the terminal, but there was no output to point me in the correct direction.

Many regards,

Helge

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linux-vdso.so.1 is preloaded, so that is not an issue.  And LIBRARY_NAME is not literal, look for "not found".  If it is not one of those libraries, then try checking all of the other libraries in that directory.

This could also be a Wayland problem.  If Manjaro has switched to Wayland by default, you could fix this by switching back to X11. Another fix is to use the ChimeraX daily build if you can.  The current ChimeraX Linux daily builds have switched to Qt6, which has better Wayland support, but only for Ubuntu 20.04 and CentOS 8.  Ideally you would convert the Ubuntu 20.04 .deb or the CentOS 8 .rpm to a Manjaro package, and install that.  It is also possible to install the pypi versions of PyQt6 and PyQt6-WebEngine by hand to switch any daily build to PyQt6.  Assuming CHIMERAX is the directory where ChimeraX is installed:

sudo CHIMERAX/bin/python3.9 -m pip install PyQt6 PyQt6-WebEngine

Look at the chimerax symbolic link to see where it was installed.   CHIMERAX/bin should *not* be on your path.

-- Greg

On 3/17/22 14:33, Helge Paternoga via ChimeraX-users wrote:

Thanks for the tips Greg!

I ran "ldd" on the three files you mentioned, but I am not getting the "LIBRARY_NAME => not found" message for any of the libraries.

Most of them are found in "/usr/lib/", but many are also listed under "...ChimeraX/chimerax-1.3/lib/python3.9/site-packages/PyQt5/Qt/lib/". Then there is one where I am only getting the libary name with no path: "linux-vdso.so.1 (0x00007ffef85ca000)".

I realized that my system default for python has recently been switched to 3.10, could this be the reason for my issues? Also, the most recent system update included an update to Qt5 version 5.15.3...

Many regards,

Helge

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