<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="">Put “cofr fixed” between your two open commands.<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 27, 2019, at 2:32 PM, 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="">Are you using ‘open’ or ’source’ to process the command file? Those should work AFAIK. If you use ‘read’ though, it will not wait for the ‘move cofr’ to finish before going on to the ‘write’ command, so nothing will have moved. Seems unlikely you’re using ‘read’ though…<div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jun 27, 2019, at 9:56 AM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="">ryanharlich@hotmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div lang="EN-US" link="blue" vlink="#954F72" style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div class="x_WordSection1"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am still having some trouble. It was working last night but this morning my script started having trouble again.</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">'open ' + paths['input'] + '\n'</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">'open ' + paths['test'] + '\n'</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">move cofr mod #1\n'</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">'write relative #0 #1 ' + paths['centered_test'] + '\n'</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">'open ' + paths['centered_test'] + '\n</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The objective is to have ‘test’ in line with ‘input’, but when I check the save file it never got moved and is still offset. What is strange is last night it was working fine.</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Ryan</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sent from<span class="Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">Mail</a><span class="Apple-converted-space"> </span>for Windows 10</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p></div><hr tabindex="-1" style="display: inline-block; width: 525.265625px;" class=""><div id="x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">meng@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, June 26, 2019 12:40:37 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Ryan Harlich<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Saving .pdb file in location of .mrc file</font><div class=""> </div></div></div><font size="2" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; 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;" class=""><span style="font-size: 11pt;" class=""><div class="PlainText">Yes, that is explained in the link in my previous message.<br class=""><br class="">Elaine<br class=""><br class="">> On Jun 26, 2019, at 9:23 AM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ryanharlich@hotmail.com</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.<br class="">> <span class="Apple-converted-space"> </span><br class="">> Sent from Mail for Windows 10<br class="">> <span class="Apple-converted-space"> </span><br class="">> From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">meng@cgl.ucsf.edu</a>><br class="">> Sent: Wednesday, June 26, 2019 9:20:21 AM<br class="">> To: Ryan Harlich<br class="">> Cc:<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><br class="">> Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file<br class="">> <span class="Apple-converted-space"> </span><br class="">> For the others on the list,<br class="">> although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):<br class="">><span class="Apple-converted-space"> </span><br class="">> <<a href="https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html%23afterfitting&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409359477&sdata=FnFgKvNsF1uTW3hV5nIkwJdGLKzzFsHlrZm0U3Ra90c%3D&reserved=0" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html%23afterfitting&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409359477&sdata=FnFgKvNsF1uTW3hV5nIkwJdGLKzzFsHlrZm0U3Ra90c%3D&reserved=0</a>><br class="">><span class="Apple-converted-space"> </span><br class="">> Elaine<br class="">> -----<br class="">> Elaine C. Meng, Ph.D.<br class="">> UCSF Chimera(X) team<br class="">> Department of Pharmaceutical Chemistry<br class="">> University of California, San Francisco<br class="">><span class="Apple-converted-space"> </span><br class="">> > On Jun 25, 2019, at 6:49 PM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ryanharlich@hotmail.com</a>> wrote:<br class="">> ><span class="Apple-converted-space"> </span><br class="">> > Hi Chimera,<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > I was able to figure this out after several hours. You can disregard the below email.<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > Best,<br class="">> > Ryan Harlich<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > Sent from Mail for Windows 10<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > From: Ryan Harlich<br class="">> > Sent: Tuesday, June 25, 2019 4:46:11 PM<br class="">> > To:<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><br class="">> > Subject: Saving .pdb file in location of .mrc file<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > Hi Chimera,<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > Best,<br class="">> > Ryan Harlich<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > Sent from Mail for Windows 10<br class="">> > <span class="Apple-converted-space"> </span><br class="">> > _______________________________________________<br class="">> > Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">Chimera-users@cgl.ucsf.edu</a><br class="">> > Manage subscription:<span class="Apple-converted-space"> </span><a href="https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409369482&sdata=CovI3tPrPnKG0QSl%2BhN2g52Z2JIrwPO%2BiXpAvOfxTI0%3D&reserved=0" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409369482&sdata=CovI3tPrPnKG0QSl%2BhN2g52Z2JIrwPO%2BiXpAvOfxTI0%3D&reserved=0</a><br class="">><span class="Apple-converted-space"> </span><br class="">> _______________________________________________<br class="">> Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">Chimera-users@cgl.ucsf.edu</a><br class="">> Manage subscription:<span class="Apple-converted-space"> </span><a href="https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409369482&sdata=CovI3tPrPnKG0QSl%2BhN2g52Z2JIrwPO%2BiXpAvOfxTI0%3D&reserved=0" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409369482&sdata=CovI3tPrPnKG0QSl%2BhN2g52Z2JIrwPO%2BiXpAvOfxTI0%3D&reserved=0</a><br class=""><br class=""></div></span></font><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>