<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="">It sounds like you just want to resample a map at a new grid spacing. Chimera does not have such a feature. The vop resample command is intended make the grids of two different maps match each other.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 22, 2019, at 1:54 PM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="">ryanharlich@hotmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; 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;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Tom,</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I need the voxel size to be 1, so subdivideSurface and subdivisionLevel options won’t work. Also, vop new won’t work because I need it to have the same bounding box as the input surface.</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><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 Harlich</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><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><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><hr tabindex="-1" 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; display: inline-block; width: 784px;" 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=""></span><div id="divRplyFwdMsg" dir="ltr" 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=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="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="Apple-converted-space"> </span>Monday, July 22, 2019 1:49:38 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="">ryanharlich@hotmail.com</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Cannot resample to voxel size of 1</font><div class=""> </div></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="">Hi Ryan,<div class=""><br class=""></div><div class=""> Resampling only works on the grid of another map as you can see from the documentation so "vop new" allows you to make that map. If you just want to make the mesh of a surface depiction of a map finer then look at the volume command subdivideSurface and subdivisionLevel options.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23dispsurf&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835707622&sdata=X%2BgN1OYI3XC%2FfvqO6CxIAK4%2F7Mr94hAZg8LSjxVcgj4%3D&reserved=0" originalsrc="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf" shash="zs9oUliPfNvDKa3KxFcw8JVmiGP3Lh8SGSMKxgwVeJDATG3OYr2subZoD9xUCVbx/LxB8Jh+0cY63dBQDIQj5exJuYfO9LxHhXUfhO/OznAVnSU0qXXqGB9ikcYmrfS0hYDaPmtXags/hyAt8BaullmDj6PwdLujgBitIhmB38U=" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jul 22, 2019, at 12:03 PM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">ryanharlich@hotmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div lang="EN-US" link="blue" vlink="#954F72" class="" 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;"><div class="x_WordSection1"><div class="" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Hi Elaine,</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div class="" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">I think you missed the point. I am trying to take an existing surface and resample it to a grid Spacing of 1. I am not sure I see the point of making a new map.</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div class="" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Best,</div><div class="" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Ryan Harlich</div><p class="x_MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div class="" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Sent from<span class="Apple-converted-space"> </span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835717633&sdata=sKPYQqECuYa940LKtImp%2FevWeT%2BPg4iRNqUAmBSG1NQ%3D&reserved=0" originalsrc="https://go.microsoft.com/fwlink/?LinkId=550986" shash="FbUQp9z2SPKv6nzdcEmqD59Y9JQeQ2TJ6k/HhgY3FU2vcBF8KMNuDReTGIkmzCN2nJ9dphjV7QFmhUKyjMk1mTl/NzKNR2eqwdX/Hb4zsVhukaD9HdYBCmtP/c0NBJoX5WcLpv97bYja6+AF6f/lLBEwi+UmsJ9HjyFVNepW1Qo=" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">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" class="" style="display: inline-block; width: 784px;"><div id="x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">meng@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, July 22, 2019 11:59:06 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">ryanharlich@hotmail.com</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB <<a href="mailto:chimera-users@cgl.ucsf.edu" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Cannot resample to voxel size of 1</font><div class=""> </div></div></div><font size="2" class="" 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;"><span class="" style="font-size: 11pt;"><div class="PlainText">Hi Ryan,<br class="">You can make a new map of whatever grid spacing you want without any atoms using “vop new”:<br class=""><<a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvop.html%23new&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835727638&sdata=iGSe0Ft5vnC0N%2Bx7EOcwhwFhyMQPERz6bWMvQsosACo%3D&reserved=0" originalsrc="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new" shash="jXBSOvrJGOuFLXjWUC+3uQE/w9Wm6yUekwp23eUxSUo+BRYCb8DBMByRiHeB02sK/bM4XPkbnhIPPcO3rNw6Wi7WFuUalEI1FJ2XHaBROZt/JQO5BBZcFORWFLk8TrHbfg3y+nKThXjvnAWcw2hyjdNVf+qTV8/1QQvZ4RBsdXg=" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvop.html%23new&data=02%7C01%7C%7C0fae3f40d7504ce6f8a908d70ed6ac3d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994187477432851&sdata=pVKM4r3k6C%2Bd%2FNBnpxZOR8qwzr5Q6dUeqFXLvHkEwqE%3D&reserved=0</a>><br class=""><br class="">I hope this helps,<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=""><br class="">> On Jul 22, 2019, at 11:33 AM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="" style="color: rgb(149, 79, 114); text-decoration: underline;">ryanharlich@hotmail.com</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Hi Chimera Bug Team,<br class="">> <span class="Apple-converted-space"> </span><br class="">> I am unable to resample surface to a grid spacing of 1 to be 1 voxel.<br class="">> <span class="Apple-converted-space"> </span><br class="">> Currently I do this:<br class="">> 'molmap #2 6 gridSpacing 1\n'<span class="Apple-converted-space"> </span><br class="">> 'vop resample #3 onGrid #2.1\n'<br class="">> <span class="Apple-converted-space"> </span><br class="">> But this requires me to have a pdb structure. I would like to do this without a pdb structure.<br class="">> <span class="Apple-converted-space"> </span><br class="">> Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z.<br class="">> <span class="Apple-converted-space"> </span><br class="">> Any help would be much appreciated. Option 1 would be a much better approach.<br class="">> <span class="Apple-converted-space"> </span><br class="">> Best,<br class="">> Ryan Harlich<br class=""><br class=""></div></span></font><span class="" 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;"></span><span class="" 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;">_______________________________________________</span><br class="" 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;"><span class="" 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;">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Chimera-users@cgl.ucsf.edu</a><br class="" 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;"><span class="" 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;">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C470a6f16006d4c0c583208d70ee61f25%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636994253835737655&sdata=%2BTnlRD0kSODPesKdTjb2ypjj%2FrcjFiExD%2BD1Jo5qa9M%3D&reserved=0" originalsrc="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" shash="qqPFvPTdI6jjiSZ4SD5f+v4/+8vA4NB8CuNeVPLncI+wCFanH76PdiffYYQgZpKWUY8CMd9nRkgHrPM9Iba+yAuNmirwtzaAc/Ejra30ZsYeip4bL7BpFS8smLiUwD7smUexC1iRdjfXBWxTk+7w1pb2Ak22WQOn4Wq82NuFJoc=" class="" 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div></div></div></div></blockquote></div><br class=""></div></body></html>