Would it be possible to allow for *.allxyz trajectory files to be loaded? Currently I need to change the extension to *.xyz and they load perfectly fine, but it would be nice to directly load the *.allxyz file as is (for book keeping purposes). Using the *.allxyz extension would also allow for the coordset slider command to be automatically entered upon loading the file.

An additional request (which may take a bit more time to implement) is allowing for ORCA xyz trajectory files to be directly loaded. These are the same as all other xyz trajectory files, but each structure is separated by a line containing the character ">". So the format is: # atoms, title, coordinates, >, # atoms, title, etc...

Thanks a bunch for your time :)

Hello,

I am unable to get SEQCROW to work with ChimeraX 1.6.1 on macOS 13.3.1 - I am not sure if I am doing something wrong, or if support just hasn't been added yet?

Thanks a bunch,
Colton

Describe the bug
I cannot open a file containing a thorium atom.

To Reproduce
Open any Gaussian calculation with Th in it

Expected behavior
It should open!

Screenshots

It seems to be AaronTools based.

Analysing an NMR calculation from Orca in ChimeraX is nice. But i can not easily assign the isotropic schift values for specific atoms. In the fiile tool i find a table weith shift, element, intensity und ndx. But no explanation what ndx mean.
Can zou add a row with atom name like C2 or H5. This can be helpful for analysing NMR calculations.

Thanks for your nice work

I have ran a conformational search with crest externally, but when I open the crest_conformers.xyz file, I do not see any place to get an animation of all the conformers.

It would be great if there was an option to turn on pre-optimization for nudged elastic band calculations via the SEQROW GUI. It would make sense to have a yes/no option under "TS search options > algorithm options".

Basically any structure that I draw in ChimeraX for a NEB-TS job will require pre-optimization, especially when I'm manually manipulating a reactant structure into a product structure (to preserve atom numbering).

Traceback (most recent call last):
File "/home/deo/.local/share/ChimeraX/1.1/site-packages/SEQCROW/tools/normal_modes.py", line 449, in show_anim
Xf = geom.coords() + dX
TypeError: 'numpy.ndarray' object is not callable

TypeError: 'numpy.ndarray' object is not callable

File "/home/deo/.local/share/ChimeraX/1.1/site-packages/SEQCROW/tools/normal_modes.py", line 449, in show_anim
Xf = geom.coords() + dX

Describe the bug
When I trying to installing SEQCROW, there are always some problems reported

To Reproduce
Steps to reproduce the behavior:

1. Go to ChimeraX
2. Click on 'Tools'
3. Click on "More Tools"
4. Click on "SEQCROW"
5. Click on "Install"
6. The problems report

the problems are copyed here
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\users\lenovo\downloads\seqcrow-1.6.3-py3-none-any.whl
Requirement already satisfied: scipy in d:\chimerax\chimerax\bin\lib\site-packages (from SEQCROW==1.6.3) (1.9.3)
Requirement already satisfied: psutil in d:\chimerax\chimerax\bin\lib\site-packages (from SEQCROW==1.6.3) (5.9.4)
Requirement already satisfied: ChimeraX-Core=1.2 in d:\chimerax\chimerax\bin\lib\site-packages (from SEQCROW==1.6.3) (1.6.dev202303230759)
Could not fetch URL https://pypi.org/simple/basis-set-exchange/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/basis-set-exchange/ (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))) - skipping
Could not fetch URL https://cxtoolshed.rbvi.ucsf.edu/pypi/basis-set-exchange/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='cxtoolshed.rbvi.ucsf.edu', port=443): Max retries exceeded with url: /pypi/basis-set-exchange/ (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))) - skipping
Could not fetch URL https://pypi.org/simple/pip/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/pip/ (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))) - skipping
Could not fetch URL https://cxtoolshed.rbvi.ucsf.edu/pypi/pip/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='cxtoolshed.rbvi.ucsf.edu', port=443): Max retries exceeded with url: /pypi/pip/ (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))) - skipping
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/basis-set-exchange/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/basis-set-exchange/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/basis-set-exchange/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/basis-set-exchange/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/basis-set-exchange/
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /pypi/basis-set-exchange/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /pypi/basis-set-exchange/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /pypi/basis-set-exchange/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /pypi/basis-set-exchange/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /pypi/basis-set-exchange/
ERROR: Could not find a version that satisfies the requirement basis-set-exchange (from seqcrow) (from versions: none)
ERROR: No matching distribution found for basis-set-exchange

Hello, I have created a diazo ligand using 2D bulilder and added it to "add to personal libary" in SEQCROW. Afterwards, I selected the two N atoms coordinated to the metal atoms for the "swap ligand" operation, but the following error occurs "LookupError: could not determine best path between 2 N 1.520100 -0.935999 -0.373990 and 1 N -1.422200 -0.283099 0.406010 File "C:\Users\49347\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-packages\AaronTools\geometry.py", line 2083, in shortest_path raise LookupError( See log for complete Python traceback." How do I fix this, thank you very much!

When I try to run conformer generation, it says it did not find the path for crest. Where and how do I define it on chimera X (I am using macOS)

Thank you very much for this superb extension for ChimeraX. I wanted to use the QM Input Generator for xTB, to optimize my 2D drawn input (I prefer xTB over AM1, PM6 or any other semi empirical calculation, because of speed and accuracy.)

Describe the bug
When I use the QM Input Generator for xTB everything seems fine and the calculations also finish
successfully, but the problem I have, is that the output does not get opened up again after the calculation finsihed.

Here I tried to put all windows together that are needed to reproduce.

To Reproduce
Steps to reproduce the behavior:

1. Goto QM Inputer Generator
2. Use xTB for given strucuture and use GFN2-xTB
3. Set "open structure" for "when finished"
4. After successful "job" get error

Additional context
I am not sure if that is the problem, but when I look into the scratch folder I see that the folder containing my calculation has spaces in it of the form:
"Phosphan_test_opt Fri Sep 29 12.44.08 2023"

Could I be that the Python code does not support spaces in the path name for the folder? How can I change the folder name for the calculation?

It would be really useful to have a plot of energy vs conformer number pop up when a crest_conformers.xyz file is opened. The same structure as the plot that opens for geometry optimizations would be ideal (plotting energy vs conformer number).

The output would look something like this:

It would be useful to plot energy relative to the lowest energy structure rather than absolute energy.

Just like the plot for geometry optimizations, it would be great to have a second tab that just gives the conformer number and relative energy. I like to use this tab for scrolling through lists of geometries using the down arrow rather than clicking on each point in the plot.

Below is an example crest_conformers.xyz file. By default it contains geometries and energies, sorted from lowest energy structure to highest energy structure with energies in Hartree.

crest_conformers.txt

Hello,

Grimmes new QCG docking algorithm (https://doi.org/10.1021/acs.jctc.2c00239) produces an XYZ ensemble file (example attached below) where each structure has one more solvent molecule than the previous. To the best of my knowledge, there is currently no convenient way to load all of these structures. As such, I am just wondering if it would be possible to support loading this type of file? Maybe the extension 'growxyz' could be used to distinguish these files from other ensemble files?

Thanks a bunch,
Colton

qcg_grow.txt

I love the feature for constrained geometry searches that allows you to point and click at the bonds, angles, torsions to be constrained.

It would be amazing if there was a similar feature for pointing and clicking at the bonds, angles, torsions to be scanned in a constrained geometry optimization. (It is always a hiccup to go back and remember the syntax for scanning a particular geometric parameter).

It would also be awesome to have a gui option for defining the parameters of the scan (from x to y in z equal steps).