<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="">Stephane's problem with the MRC map written by ChimeraX looking like noise in Coot was because the map origin was not correct.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Begin forwarded message:</div><br class="Apple-interchange-newline"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Stéphane ROCHE <br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">RE: [chimerax-users] Troubles when saving a map</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">June 18, 2021 at 5:37:12 AM PDT<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"Vadim Kotov" , "Tom Goddard" <br class=""></span></div><br class=""><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: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class="">Thanks to both of you for your help !<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class="">I have finally understood what was happening, the origin of my map was changed and it was a very long way from its old position given that the box was quite large. So basically, when if I was looking around for densities, I was only scrolling inside the solvent.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class="">Thanks again,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class="">Stephane Roche<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On 17.06.21 10:07, Stéphane ROCHE via ChimeraX-users wrote:<o:p class=""></o:p></div></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class="" type="cite"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Mr/Mrs,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am new to ChimeraX (v 0.7) and I have a trouble when saving a map.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class=""><span class="">-<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";" class=""> <span class="Apple-converted-space"> </span></span></span>Opening the map is fine.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class=""><span class="">-<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";" class=""> <span class="Apple-converted-space"> </span></span></span>Then I change the pixel voxelsize which is also fine.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class=""><span class="">-<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";" class=""> <span class="Apple-converted-space"> </span></span></span>I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format).<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class=""><span class="">-<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";" class=""> <span class="Apple-converted-space"> </span></span></span>However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Do you know what I could do to solve this problem ?<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Stephane Roche<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Institut de Biologie Intégrative de la Cellule<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">91198 Gif sur Yvette<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">France<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 12pt; font-family: "Times New Roman", serif;" class=""><br class=""></span></div></blockquote></div></div></blockquote></div><br class=""></div></body></html>