Follow up to: SEQCROW: trouble reading .out files

[2529108683@…]

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




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19日(星期六) 上午9:24
收件人:&nbsp;"tony.schaefer.chem"<tony.schaefer.chem@gmail.com&gt;;"赵辰"<2529108683@qq.com&gt;;
抄送:&nbsp;"pett"<pett@cgl.ucsf.edu&gt;;
主题:&nbsp;Re: [ChimeraX] #16131: SEQCROW: trouble reading .out files



#16131: SEQCROW: trouble reading .out files
-----------------------------------+---------------------------
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Reporter:&nbsp; 2529108683@…&nbsp; |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Owner:&nbsp; Tony Schaefer
&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; assigned
&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; Third Party&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; |
-----------------------------------+---------------------------
Comment (by Tony Schaefer):

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

&nbsp;Best,

&nbsp;Tony

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

&nbsp;&gt;
&nbsp;&gt;
&nbsp;}}}
-- 
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16131#comment:4&gt;
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/&gt;
ChimeraX Issue Tracker

[Eric Pettersen]

Intended as follow up to #16131