<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yuhong,<div class=""><br class=""></div><div class=""> I agree with Eric that it would be good to figure out what is going on with your Macs.</div><div class=""><br class=""></div><div class=""> But the more usual way to save a session file would be</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>rc(“save /Users/smith/Desktop/some_session.py”)</div><div class=""><br class=""></div><div class="">or</div><div class=""><br class=""></div><div class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>rc(“save ~/Desktop/some_session.py”)</div><div class=""><br class=""></div><div class="">ie. giving a full path instead of attempting to change the current working directory.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 28, 2019, at 10:53 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yuhong,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>That is a weird problem, particularly that it happens on only one of two macs you have. It certainly doesn’t happen for me. If I open Chimera’s IDLE shell and type in similar commands to yours, they work fine. If I run the commands from a file (attached), they also work fine. So you should probably look at the saveSession() routine in SimpleSession/save.py and (on the problematic mac) make the same calls as it does and see what they return, namely:</div><div class=""><br class=""></div><div class="">what does os.path.dirname(“current_session.py”) return?</div><div class="">after your os.chdir(path), what does os.getcwd() return?</div><div class="">what does os.path.exists(path) return?</div><div class=""><br class=""></div><div class="">If those look okay, you probably should insert print statements in the saveSession() routine to get some kind of idea about what’s happening.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><div class=""><br class=""></div><div class=""></div></div><span id="cid:577975A2-C933-4DA9-ADB0-70A27CEA8CE9@cgl.ucsf.edu"><testsave.py></span><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""><div class="">
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 27, 2019, at 1:41 PM, Yuhong Zha <<a href="mailto:zha0@purdue.edu" class="">zha0@purdue.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""></div><div style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Dear Sir or Madam,</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">This is Yuhong Zha from the Kihara Bioinformatics Laboratory. We are currently developing a Chimera extension to implement our MAINMAST algorithm. However, we encountered a problem of using Chimera's command line "rc(<span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">"save current_session.py"</span>)" to save current session. This problem only happens in some Mac system.</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">In our extension, we want to save the whole session after open some files. So we first do "os.chdir(path)" to where we want to store the file. Then we use "rc("save current_session.py")" to save the current session info to a file. However, after we changed the current working directory correctly, <span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">"rc("save current_session.py")"<span class=""> still fails and displays error message of "Directory () does not exists". </span></span>I have attached the code and error we encounter. I checked the current working directory right before calling <span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">"rc("save current_session.py)" and I am sure the <span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">current working directory is correct and is not (). Is there any settings we missed that result in rc(command) only execute at directory ()? Or is there any way that we can specify which directory we want to save the session using rc(command)?</span></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">We tried it on 2 Mac but only one of them has this problem. I am thinking maybe some preference setup would cause this problem?</span></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class=""></span></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class=""><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">Also, we encountered a problem of "Access Denied" when modifying the files from Chimera. On one Mac, we updated to the latest version chimera. But when we run our extension, we get <span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">"Access Denied" error when <span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; background-color: rgb(255, 255, 255); display: inline !important;" class="">try to remove some files</span>. No such error occurs within the same Mac before updating the version. Do you have any clue why that happens.</span></span></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">If there is any question regarding our extension, please let me know! For more information about our lab, here is the link to our website: <a href="http://www.kiharalab.org/index.php" target="_blank" rel="noopener noreferrer" style="margin: 0px;" class="">http://www.kiharalab.org/index.php</a>.</div><div style="margin: 0px 0px 20px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; overflow: auto;" class=""><table style="background-color: white; width: 510.296875px; margin-top: 20px; padding-top: 20px; padding-bottom: 20px; border-top-width: 1px; border-top-style: dotted; border-top-color: rgb(200, 200, 200); border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: rgb(200, 200, 200); overflow: auto;" class=""><tbody class=""><tr style="border-spacing: 0px;" class=""><td colspan="2" style="vertical-align: top; display: table-cell;" class=""><div style="margin: 0px;" class=""></div><div style="margin: 0px; font-family: "Microsoft YaHei UI", "Microsoft YaHei", 微软雅黑, SimSun, 宋体, sans-serif, serif, EmojiFont; font-size: 21px; line-height: 21px; color: rgb(0, 120, 215); top: 0px;" class=""><a href="http://www.kiharalab.org/index.php" target="_blank" rel="noopener noreferrer" style="margin: 0px;" class="">Kihara Bioinformatics Laboratory, Purdue University</a></div><div style="margin: 10px 0px 16px; font-family: "Microsoft YaHei UI", "Microsoft YaHei", 微软雅黑, SimSun, 宋体, sans-serif, serif, EmojiFont; font-size: 14px; line-height: 14px; color: rgb(102, 102, 102);" class=""><a href="http://www.kiharalab.org/" class="">www.kiharalab.org</a></div><div style="margin: 0px; font-family: "Microsoft YaHei UI", "Microsoft YaHei", 微软雅黑, SimSun, 宋体, sans-serif, serif, EmojiFont; font-size: 14px; line-height: 20px; color: rgb(102, 102, 102); display: block; overflow: hidden; max-height: 100px;" class="">Area of Research Dr. Daisuke Kihara Principal Investigator. Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways.</div></td></tr></tbody></table></div><br style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Thank you in advance for your help and looking forward to your reply!</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Best,</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Yuhong Zha,</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Kihara Bioinformatics Laboratory,<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Department of Biological & Computer Science at Purdue University</div><br class=""></div><span id="cid:A74BA7D0-2F25-4344-8982-5809891F924F@cgl.ucsf.edu" class=""><PastedGraphic-5.png></span><span id="cid:4AEE14B0-53E7-43DE-9B62-A233110E448D@cgl.ucsf.edu" class=""><Screen Shot 2019-02-27 at 4.37.30 PM.png></span><span style="caret-color: rgb(0, 0, 0); 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