mmCIF write: support 'relModel' keyword

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-17)
Description
Want save command keyword "relModel" for saving mmCIF format so a fit atomic model in a density map can be saved relative to the density map coordinates.  This keyword is available for saving PDB format but not mmCIF format.


Log:
UCSF ChimeraX version: 0.91 (2019-06-17)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs format session

opened ChimeraX session  

> toolshed show "Segment Map"

Segmenting 1080, density threshold 1.015837  
Showing 1080.seg - 0 regions, 0 surfaces  
Showing 28 region surfaces  
428 watershed regions, grouped to 28 regions  
Smoothing and grouping, standard deviation 5 voxels  
No new groups smoothing 5 voxels  
Showing 14 region surfaces  
Got 14 regions after smoothing 6 voxels.  
Simulating map res 8.000, grid 2.000  

> molmap #3 8.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Top score: 0.90530, z-score: 13.66756 (avg: 0.8212, stdev: 0.0062)  

> save /Users/goddard/Desktop/1grl_fit.cif models #3 relModel #1

got an unexpected keyword argument 'rel_model'  
got an unexpected keyword argument 'rel_model'  

> usage save

save filename [models] [format format] [includeMaps true or false] [width
width] [height height] [supersample supersample] [pixelSize a number]
[transparentBackground true or false] [quality quality] [center center] [size
a number] [shortVertexIndices true or false] [floatColors true or false]
[preserveTransparency true or false] [selectedOnly true or false]
[displayedOnly true or false] [allCoordsets true or false] [pqr true or false]
[relModel a model specifier] [serialNumbering serialNumbering] [atoms atoms]
[anchor anchor] [sybylHydNaming true or false] [combineModels true or false]
[skipAtoms skipAtoms] [resNum true or false] [gaffType true or false]
[alignment alignment] [region map region] [step 1 or 3 integers] [maskZone
true or false] [chunkShapes chunkShapes] [append true or false] [compress true
or false] [baseIndex an integer]  
— save data to various file formats  
filename: name of a file to save/write  
format: one of aln, bmp, cmap, dcd, dsn6, fasta, gif, gltf, jpeg, markers,
mmcif, mol2, mrc, obj, pdb, pir, png, ppm, pseudobonds, segger, session, stl,
tiff, or x3d  
width: an integer ≥ 1  
height: an integer ≥ 1  
supersample: an integer ≥ 1  
quality: an integer ≥ 0 and ≤ 100  
center: some numbers  
serialNumbering: one of amber or h36  
atoms: an atoms specifier  
anchor: an atoms specifier  
skipAtoms: an atoms specifier  
alignment: alignment-id  
chunkShapes: a collection of one of xyz, xzy, yxz, yzx, zxy, or zyx

save formats  
— report formats that can be saved

save image filename [format format] [width width] [height height] [supersample
supersample] [pixelSize a number] [transparentBackground true or false]
[quality quality]  
— save image  
filename: name of a file to save/write  
format: one of bmp, gif, jpeg, png, ppm, or tiff  
width: an integer ≥ 1  
height: an integer ≥ 1  
supersample: an integer ≥ 1  
quality: an integer ≥ 0 and ≤ 100

save map filename [models] [format format] [region map region] [step 1 or 3
integers] [maskZone true or false] [chunkShapes chunkShapes] [append true or
false] [compress true or false] [baseIndex an integer]  
— save map  
filename: name of a file to save/write  
format: one of cmap, dsn6, mrc, or segger  
chunkShapes: a collection of one of xyz, xzy, yxz, yzx, zxy, or zyx

save session filename [includeMaps true or false]  
— save session  
filename: name of a file to save/write  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Greg Couch]

Fix checked in. Please double check.

[Greg Couch]

Checked and works.