<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Smith,<div class=""><br class=""></div><div class=""> The map file is exactly that -- the list of all the values at each grid point -- usually millions of points, and you'd have to understand the binary format to make use of it. For a contour surface, every point on the surface has the same value, the value you set for the threshold.</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><br class=""><blockquote type="cite" class=""><div class="">On Feb 12, 2021, at 5:47 PM, Smith Lee <<a href="mailto:smith_lee123@yahoo.com" class="">smith_lee123@yahoo.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div class="ydp7e9d58ffyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div class=""></div>
<div dir="ltr" data-setdir="false" class="">Dear Tom,</div><div dir="ltr" data-setdir="false" class=""><br class=""></div><div dir="ltr" data-setdir="false" class="">Thanks.</div><div dir="ltr" data-setdir="false" class=""><br class=""></div><div dir="ltr" data-setdir="false" class="">By the way, is any method to show the value of the density map (mrc file for example) for each point? I guess the value should be density, like what we have taked either 0 or 1, or between a range, for example from -0.10 to 1.6.</div><div dir="ltr" data-setdir="false" class=""><br class=""></div><div dir="ltr" data-setdir="false" class="">Best wishes,</div><div dir="ltr" data-setdir="false" class=""><br class=""></div><div dir="ltr" data-setdir="false" class="">Smith<br class=""></div><div class=""><br class=""></div>
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On Saturday, February 13, 2021, 4:02:38 AM GMT+8, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:
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<div class=""><div id="yiv8060422056" class=""><div class="">Hi Smith,<div class="yiv8060422056"><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056"> If a map has only the two values 0 and 1 then the surface will still change at thresholds between 0 and 1. The reason is that the 0 and 1 values are at the grid points of the maps. Between the grid points the values are interpolated. So if you set a threshold 0.5 then the surface will pass half way between a grid point that has value 0 and and a neighbor grid point that has value 1. If the threshold is 0 the surface will pass right through the grid point with value 0, and if the threshold is 1 it will pass right through the grid point with value 1. So the surface does appear different for every threshold value between 0 and 1.</div><div class="yiv8060422056"><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056"> Your command</div><div class="yiv8060422056"><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056"><span class="yiv8060422056Apple-tab-span" style="white-space:pre;"> </span>vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1</div><div class="yiv8060422056"><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056">makes a new map where all values of the original map below 0.17 become 0 and all values above 0.18 become 1. So the new map will have values 0, 1, and 0.17 - 0.18 (where the value was unchanged from the original map). Do get a map that is all 0 and 1 you could try</div><div class="yiv8060422056"><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056"><span class="yiv8060422056Apple-tab-span" style="white-space:pre;"> </span>vop threshold #0 minimum 0.17 set 0 maximum 0.17 setMaximum 1<br class="yiv8060422056" clear="none"><div class=""><br class="yiv8060422056" clear="none"></div><div class="">which makes all values below 0.17 equal to 0 and all above 0.17 equal to 1. But if there are any values exactly equal to 0.17 then the remain 0.17. If you want make all values 0 or 1 you would have to use something like</div><div class=""><br class="yiv8060422056" clear="none"></div><div class=""><span class="yiv8060422056Apple-tab-span" style="white-space:pre;"> </span>vop threshold #0 minimum 0.17 set 0 maximum 0.1699 setMaximum 1</div><div class=""><br class="yiv8060422056" clear="none"></div><div class="">This sets all values below 0.17 to 0 and then sets all remaining values above 0.1699 to 1. First it does the minimum and then it does the maximum. So the result is that all below 0.17 are 0 and all greater than or equal to 0.17 become 1.</div><div class=""><br class="yiv8060422056" clear="none"></div><div class=""><span class="yiv8060422056Apple-tab-span" style="white-space:pre;"> </span>Tom</div><div class=""><br class="yiv8060422056" clear="none"></div><div class=""><br class="yiv8060422056" clear="none"><blockquote class="yiv8060422056" type="cite"><div class="yiv8060422056yqt3895732125" id="yiv8060422056yqt20173"><div class="yiv8060422056">On Feb 12, 2021, at 12:01 AM, Smith Lee <<a rel="nofollow noopener noreferrer" shape="rect" class="yiv8060422056" ymailto="mailto:smith_lee123@yahoo.com" target="_blank" href="mailto:smith_lee123@yahoo.com">smith_lee123@yahoo.com</a>> wrote:</div><br class="yiv8060422056Apple-interchange-newline" clear="none"><div class="yiv8060422056"><div class="yiv8060422056"><div class="yiv8060422056ydp9f2cfdcayahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div class="yiv8060422056"></div>
<div class="yiv8060422056" dir="ltr">Dear Elaine,</div><div class="yiv8060422056" dir="ltr"><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056" dir="ltr">Thanks, and "<span class="yiv8060422056">vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1" should be what I intend to do.</span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056"><br class="yiv8060422056" clear="none"></span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056"></span>B the way, I think I still have something which I do not understand so well. For the map I got by "<span class="yiv8060422056"><span class="yiv8060422056">vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1</span></span>", as for all values above 0.18 will be set to 1 and all values lower than 0.17 will be set to 0, will you please explain to me, why the got map by <span class="yiv8060422056"><span class="yiv8060422056"><span class="yiv8060422056">"vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1</span></span>", which was displayed in the chimera window, changes its appearance gradually when I modulate the "Level" in the whole Range from 0 to 1, rather than displayed in only 2 appearances, one fixed appearance with all Level values lower than 0.17, and another fixed appearance with all Level values higher than 0.18?</span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056"><br class="yiv8060422056" clear="none"></span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056">Besides, I also intend to learn how to realize the above aim as by "<span class="yiv8060422056"><span class="yiv8060422056">vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1</span></span>" with the chimera "mask" command. The <span class="yiv8060422056"><span class="yiv8060422056"> "mask" command</span></span> needs a surf-models file. For a specific A.mrc which I intend to get its mask.mrc, will you please explain to me step by step how to get the "mask" command requested <span class="yiv8060422056"><span class="yiv8060422056">surf-models file</span></span> at specific threshold Level of A.mrc?</span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056"><br class="yiv8060422056" clear="none"></span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056">I am looking forward to getting your reply.</span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056"><br class="yiv8060422056" clear="none"></span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056">Smith<br class="yiv8060422056" clear="none"></span></div><div class="yiv8060422056" dir="ltr"><span class="yiv8060422056"></span><br class="yiv8060422056" clear="none"></div><div class="yiv8060422056"><br class="yiv8060422056" clear="none"></div>
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On Thursday, February 11, 2021, 11:37:55 PM GMT+8, Elaine Meng <<a rel="nofollow noopener noreferrer" shape="rect" class="yiv8060422056" ymailto="mailto:meng@cgl.ucsf.edu" target="_blank" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:
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<div class="yiv8060422056"><div class="yiv8060422056" dir="ltr">HI Smith,<br class="yiv8060422056" clear="none">Your process makes no sense to me. It is not possible to do both of these things (1) make values below 0.18 = 0 and (2) make values above 0.17 = 1, because values in the range 0.17-0.18 cannot equal both 0 and 1 at the same time.<br class="yiv8060422056" clear="none"><br class="yiv8060422056" clear="none">Also, your second command didn't work as expected because you need the "setMaximum" keyword to set a new maximum. As shown in the help, the "set" keyword just sets a a new minimum.<br class="yiv8060422056" clear="none"><<a rel="nofollow noopener noreferrer" shape="rect" class="yiv8060422056" target="_blank" href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#threshold">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#threshold</a>><br class="yiv8060422056" clear="none"><br class="yiv8060422056" clear="none">Did you instead mean (1) make values below 0.17 = 0 and (2) make values above 0.18 =1 ? If so, instead try:<br class="yiv8060422056" clear="none"><br class="yiv8060422056" clear="none">vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1<br class="yiv8060422056" clear="none"><br class="yiv8060422056" clear="none">However, it is unclear why you even want to do that. If you just want to make a new map with values inside the current map isosurface as 1 and values outside the isosurface as 0 (or vice versa) just use the "mask" command instead.<br class="yiv8060422056" clear="none"><<a rel="nofollow noopener noreferrer" shape="rect" class="yiv8060422056" target="_blank" href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html</a>><br class="yiv8060422056" clear="none"><br class="yiv8060422056" clear="none">I hope this helps,<br class="yiv8060422056" clear="none">Elaine<br class="yiv8060422056" clear="none">-----<br class="yiv8060422056" clear="none">Elaine C. Meng, Ph.D. <br class="yiv8060422056" clear="none">UCSF Chimera(X) team<br class="yiv8060422056" clear="none">Department of Pharmaceutical Chemistry<br class="yiv8060422056" clear="none">University of California, San Francisco<br class="yiv8060422056" clear="none"><div class="yiv8060422056yqt9647512709" id="yiv8060422056yqtfd79127"><br class="yiv8060422056" clear="none">> On Feb 11, 2021, at 3:11 AM, Smith Lee <<a rel="nofollow noopener noreferrer" shape="rect" class="yiv8060422056" ymailto="mailto:smith_lee123@yahoo.com" target="_blank" href="mailto:smith_lee123@yahoo.com">smith_lee123@yahoo.com</a>> wrote:<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> Dear All,<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> I have a map (A.mrc). When I open it in chimera (the map should be #0), the Volume Viewer shows the Range is -0.618 to 1.63, the default Level is 0.175.<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> With command "vop threshold #0 minimum 0.18 set 0" I got another map (let us call it B.mrc, should be #1), the Volume Viewer shows the Range is 0 to 1.63 (understandable, the maximum value is still 1.63 as in A.mrc, the minimum value is 0 as for all values not higher than 0.18 has been set to 0), the default Level is still 0.175.<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> Immediately I run the command "vop threshold #1 maximum 0.17 set 1". Before I running the command, I guess all the density value should be either "0" or "1", because all the value lower than 0.18 has been set to "0", and all value higher than 0.17 has been set to "1".<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> However after I run the command "vop threshold #1 maximum 0.17 set 1", I got another map (let us call it C.mrc, should be #2),the Volume Viewer shows the Range is 0 to 0.17 rather than 0 to 1, and wen I change the Level, the image of #2 changes correspondingly with the Level from 0 to 0.17.<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> Here I would ask, why the command "vop threshold #1 maximum 0.17 set 1" did not lead to a map with all values greater than 0,17 as 1? How to get a map based on A.mrc so that all values less than 0.18 as 0 and all values greater than 0.17 as 1 (please tell me the specific method)? Is any significance for the obtained C.mrc with range from 0 to 0.17? <br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> I am looking forward to getting your reply.<br class="yiv8060422056" clear="none">> <br class="yiv8060422056" clear="none">> Smith<br class="yiv8060422056" clear="none"><br class="yiv8060422056" clear="none"></div></div></div>
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