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hi Eric, thanks for letting me know. I am sorry if i bothered you too much for this. i have both chimerax versions on my machine bur the chimerax 1.25 is the one still pinned to the task bar and was not aware that i was using it.
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
hi Eric,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
thanks for letting me know. I am sorry if i bothered you too much for this.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
i have both chimerax versions on my machine bur the chimerax 1.25 is the one still pinned to the task bar and was not aware that i was using it.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
thanks again for your time,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
best</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
amith</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size: 11pt;"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, February 14, 2022 3:38 PM<br>
<b>To:</b> Rangarajan, Amith <Amith.Rangarajan@ucsf.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] error with open :: 'foreach' has no suffix</font>
<div> </div>
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<div class="" style="word-wrap:break-word; line-break:after-white-space"><span class="x_pfptPreheader" style="visibility: hidden; font-size: 1px; color: rgb(255, 255, 255); line-height: 1px; max-height: 0px; max-width: 0px; opacity: 0; overflow: hidden; display: none !important;">Yes,
that was quite helpful. The 'foreach' option only became available starting with the 1.3 release. You are running 1.2.5, so you need to upgrade. --Eric On Feb 14, 2022, at 3:35 PM, Rangarajan, Amith <Amith.Rangarajan@ucsf.edu
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Yes, that was quite helpful. The 'foreach' option only became available starting with the 1.3 release. You are running 1.2.5, so you need to upgrade.
<div class=""><br class="">
</div>
<div class="">--Eric<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 14, 2022, at 3:35 PM, Rangarajan, Amith <<a href="mailto:Amith.Rangarajan@ucsf.edu" class="">Amith.Rangarajan@ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
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This Message Is From an External Sender</div>
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This message came from outside your organization.</div>
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hi Eric,</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<br class="">
</div>
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i have submitted a bug report </div>
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</div>
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thanks</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
amith</div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Monday, February 14, 2022 3:15 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Rangarajan, Amith <<a href="mailto:Amith.Rangarajan@ucsf.edu" class="">Amith.Rangarajan@ucsf.edu</a>><br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [chimerax-users] error with open :: 'foreach' has no suffix</font>
<div class=""> </div>
</div>
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This Message Is From an External Sender<span class="x_Apple-converted-space"> </span></div>
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This message came from outside your organization.<span class="x_Apple-converted-space"> </span></div>
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Hi Amith,
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>I don't care so much about the contents of your script per se — I'd like to see the contents of the log when the error occurs. Do this: run the command that generates the "'foreach'
has no suffix" error and then use Help→Report A Bug and submit a bug report. That will include the contents of the log, which is what I need to see. Thanks!</div>
<div class=""><br class="">
</div>
<div class="">--Eric<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 10, 2022, at 4:52 AM, Rangarajan, Amith <<a href="mailto:Amith.Rangarajan@ucsf.edu" class="">Amith.Rangarajan@ucsf.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
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This Message Is From an External Sender</div>
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This message came from outside your organization.</div>
</div>
</div>
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Dear Tom and Eric,</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
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</div>
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I used notepad ++ to make sure that the cxc file was not a .txt ( i am on windows) and i am still getting the error ( foreach has no suffix) . i have attached my .cxc script .</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
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</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
I am trying to read a set of .mae files and write a log file with RMSD and some distance measurements.</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
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</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
I am new to chimera and would benefit a lot from your review of my script and possible fixes for this issue.</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
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</div>
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thank a lot for your time.</div>
<div class="" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<br class="">
</div>
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best regards,</div>
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amith</div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_x_Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<b class="">Sent:</b><span class="x_x_Apple-converted-space"> </span>Tuesday, February 8, 2022 10:36 AM<br class="">
<b class="">To:</b><span class="x_x_Apple-converted-space"> </span>PETTERSEN, ERIC <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Cc:</b><span class="x_x_Apple-converted-space"> </span>Rangarajan, Amith <<a href="mailto:Amith.Rangarajan@ucsf.edu" class="">Amith.Rangarajan@ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_x_Apple-converted-space"> </span>Re: [chimerax-users] error with open :: 'foreach' has no suffix</font>
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<div class="">Hi Eric,</div>
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<div class=""> Not quite sure I understand your theory abut Amith's error. In current ChimeraX daily build using non-existent files with open command</div>
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<span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>open something.cxc foreach somethingelse.py
<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>> No such file/path: something.cxc</div>
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<div class="">gives a very sensible error message and does not try to interpret "foreach" as a file name.</div>
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<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class="">On Feb 8, 2022, at 9:40 AM, Eric Pettersen via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<div class=""><span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Hi
Amith,</span>
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<span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>That error message indicates to me that the first file name (script.cxc) isn't being recognized as a ChimeraX command script file. So take a hard look at the command you typed and make sure
that the suffix for that file is ".cxc" and not something mistyped like ".cxs" or whatnot.</div>
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<div class="">--Eric</div>
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<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_x_x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Feb 8, 2022, at 6:25 AM, Rangarajan, Amith via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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This Message Is From an External Sender</div>
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This message came from outside your organization.</div>
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Hi,</div>
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I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory.</div>
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I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix""</div>
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I am not able to figure out how to debug this. </div>
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I am using the latest build of chimerax.</div>
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I will highly appreciate your suggestions on fixing this.</div>
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best</div>
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amith</div>
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">ChimeraX-users
mailing list</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Manage
subscription:</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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<span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">ChimeraX-users
mailing list</span><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Manage
subscription:</span><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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<span id="x_x_cid:593A2161-C3C9-4B95-8F86-59688584E848" class=""><RMSD-distance-final.cxc></span></div>
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