SEQCROW: could not convert string to float: 'TITLE'

[2529108683@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I can't open the experimental data,how can I do?

Log:
Boltzmann population of VCD-out-1.out: 19.6%  
Boltzmann population of VCD-out-2.out: 43.9%  
Boltzmann population of VCD-out-3.out: 24.5%  
Boltzmann population of VCD-out-4.out: 2.9%  
Boltzmann population of VCD-out-5.out: 6.4%  
Boltzmann population of VCD-out-6.out: 1.6%  
Boltzmann population of VCD-out-7.out: 1.0%  
Boltzmann population of VCD-out-1.out: 53.5%  
Boltzmann population of VCD-out-2.out: 20.7%  
Boltzmann population of VCD-out-3.out: 21.7%  
Boltzmann population of VCD-out-4.out: 1.9%  
Boltzmann population of VCD-out-5.out: 1.3%  
anharmonic frequencies requested on the 'plot settings' tab, but anharmonic
data was not parsed from VCD-out-4.out  
ValueError: could not convert string to float: 'TITLE'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\25291\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1338, in load_data  
data = np.loadtxt(filename, delimiter=",", skiprows=self.skip_lines.value())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1373, in
loadtxt  
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string 'TITLE' to float64 at row 0, column 1.  
  
ValueError: could not convert string 'TITLE' to float64 at row 0, column 1.  
  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
ValueError: could not convert string to float: 'LASTX'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\25291\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1338, in load_data  
data = np.loadtxt(filename, delimiter=",", skiprows=self.skip_lines.value())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1373, in
loadtxt  
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string 'LASTX' to float64 at row 0, column 1.  
  
ValueError: could not convert string 'LASTX' to float64 at row 0, column 1.  
  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
saved to E:/data/2024/计算图谱/L-Ala-solid-VCD/L-Ala.csv  
ValueError: could not convert string to float: 'frequency (cm^-1)'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\25291\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1338, in load_data  
data = np.loadtxt(filename, delimiter=",", skiprows=self.skip_lines.value())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1373, in
loadtxt  
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string 'frequency (cm^-1)' to float64 at row 0,
column 1.  
  
ValueError: could not convert string 'frequency (cm^-1)' to float64 at row 0,
column 1.  
  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
ValueError: could not convert string to float: 'TITLE'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\25291\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1338, in load_data  
data = np.loadtxt(filename, delimiter=",", skiprows=self.skip_lines.value())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1373, in
loadtxt  
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string 'TITLE' to float64 at row 0, column 1.  
  
ValueError: could not convert string 'TITLE' to float64 at row 0, column 1.  
  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open https://comp.chem.umn.edu/freqscale/index.html

Opened https://comp.chem.umn.edu/freqscale/index.html  
ValueError: could not convert string to float: 'TITLE'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\25291\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1338, in load_data  
data = np.loadtxt(filename, delimiter=",", skiprows=self.skip_lines.value())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1373, in
loadtxt  
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string 'TITLE' to float64 at row 0, column 1.  
  
ValueError: could not convert string 'TITLE' to float64 at row 0, column 1.  
  
File "D:\ChimeraX 1.9\bin\Lib\site-packages\numpy\lib\npyio.py", line 1016, in
_read  
arr = _load_from_filelike(  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.6078
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 14 Plus 7430
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 16,849,256,448
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i7-13620H
OSLanguage: zh-CN

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File attachment: 曲线校正-solid-L-Ala-KBr-0.15-5000-1.csv

曲线校正-solid-L-Ala-KBr-0.15-5000-1.csv​

[2529108683@…]

Added by email2trac

[Eric Pettersen]

Reported by Zhaochen

[2529108683@…]

How should I proceed? Delete all strings? Keep only numbers?



---Original---
From: "ChimeraX"<ChimeraX-bugs-admin@cgl.ucsf.edu&gt;
Date: Tue, Jan 7, 2025 03:03 AM
To: "tony.schaefer.chem"<tony.schaefer.chem@gmail.com&gt;;"2529108683"<2529108683@qq.com&gt;;
Subject: Re: [ChimeraX] #16559: SEQCROW: could not convert string to float:'TITLE' (was: ChimeraX bug report submission)


#16559: SEQCROW: could not convert string to float: 'TITLE'
-----------------------------------+---------------------------
          Reporter:  2529108683@…  |      Owner:  Tony Schaefer
              Type:  defect        |     Status:  assigned
          Priority:  normal        |  Milestone:
         Component:  Third Party   |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+---------------------------
Changes (by pett):

 * component:  Unassigned =&gt; Third Party
 * owner:  (none) =&gt; Tony Schaefer
 * platform:   =&gt; all
 * project:   =&gt; ChimeraX
 * status:  new =&gt; assigned
 * summary:  ChimeraX bug report submission =&gt; SEQCROW: could not convert
     string to float: 'TITLE'

Comment:

 Reported by Zhaochen

[Tony Schaefer]

Zhao Chen,

The IR plot tool is unfortunately only able to read very simple CSV files.
The first column should contain wavenumbers, and subsequent columns would
have the corresponding intensity. Some rows in the CSV file can be skipped,
so that title data can be skipped.

This file looks like it has other data at both the top and bottom of the
file that could probably be used by some other plotting software. You could
keep everything in the file above "XYDATA" as long as you have "skip first
lines" set to 21, as the data starts at line 22. You will probably need to
remove the text at the bottom of the file as well.

It looks like the file also has two columns for the uncertainty in the
absorbance values. The IR plot tool will interpret those as other spectra
instead of error bars, so the plot will have two lines just above zero
unless you delete these columns as well.

Let me know if this works.

Best,

Tony

On Mon, Jan 6, 2025 at 1:06 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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