SEQCROW: trouble reading .out files

[2529108683@…]

  I used ORCA software to calculate the VCD profiles of propylene oxide and diclofenac separately and got .out files for both.However, when I use the ChimeraX software to try to open the .out file to visualize the profile data, only the propylene oxide file can be opened in ChomeraX, and the output file of diclofenac cannot be opened.
  The output files of propylene oxide and diclofenac are provided in the attachment, and there is a specific error in the Word document, please help me check what the error is and give a specific solution.
  Please don't just send me a bunch of code, I'm not a professional and can't read the code. Thank you!


赵辰
2529108683@qq.com



 




------------------ 原始邮件 ------------------
发件人:                                                                                                                        "ChimeraX-bugs"                                                                                    <ChimeraX-bugs-admin@cgl.ucsf.edu&gt;;
发送时间:&nbsp;2024年10月14日(星期一) 上午8:40
收件人:&nbsp;"赵辰"<2529108683@qq.com&gt;;"pett"<pett@cgl.ucsf.edu&gt;;

主题:&nbsp;Re: [ChimeraX] #16126: Unknown problem



#16126: Unknown problem
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Reporter:&nbsp; 2529108683@…&nbsp; |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Owner:&nbsp; pett
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Type:&nbsp; defect&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp;&nbsp;&nbsp; Status:&nbsp; feedback
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Priority:&nbsp; normal&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp; Milestone:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Component:&nbsp; Core&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp;&nbsp; Version:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Resolution:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp; Keywords:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Blocked By:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp; Blocking:
Notify when closed:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp; Platform:&nbsp; all
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Project:&nbsp; ChimeraX&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |
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Changes (by pett):

&nbsp;* status:&nbsp; accepted =&gt; feedback

Comment:

&nbsp;Sorry, but what problem are you having exactly?
-- 
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16126#comment:2&gt;
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/&gt;
ChimeraX Issue Tracker

[Eric Pettersen]

Apparent follow-up to #16126 and possibly/probably #16095

[Eric Pettersen]

Had to add the attachments by hand, probably because the Subject line had Chinese characters in it and didn't get automatically recognized by Trac

[Eric Pettersen]

The comment that went with the attachments was "The attachment contains the output files of epichlorohydrin and diclofenac, as well as specific error codes."

[Tony Schaefer]

This is related to #16125 (
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16125#comment:2). The
"diclofenac" job has multiple imaginary vibrational frequencies, which are
displayed as negative numbers in the ".out" file. The ORCA output parser
currently cannot handle VCD with imaginary frequencies. I will fix that
soon. However, I would like to note that I don't think frequency
computations are not valid unless the structure is at a stationary point. I
encourage the user to optimize their structure at the same level of theory
they are using to compute the frequencies and VCD.

Best,

Tony

On Fri, Oct 18, 2024 at 5:36 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>

[Eric Pettersen]

Again, the user's mailer's munging of the subject line prevented the reply from going to this ticket, but from #16143:

"I understand now. Thank you very much for your reply!"