<html><head></head><body><div class="ydp9f2cfdcayahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div></div>
<div dir="ltr" data-setdir="false">Dear Elaine,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thanks, and "<span>vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1" should be what I intend to do.</span></div><div dir="ltr" data-setdir="false"><span><br></span></div><div dir="ltr" data-setdir="false"><span></span>B the way, I think I still have something which I do not understand so well. For the map I got by "<span><span>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><span><span>"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 dir="ltr" data-setdir="false"><span><br></span></div><div dir="ltr" data-setdir="false"><span>Besides, I also intend to learn how to realize the above aim as by "<span><span>vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1</span></span>" with the chimera "mask" command. The <span><span> "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><span>surf-models file</span></span> at specific threshold Level of A.mrc?</span></div><div dir="ltr" data-setdir="false"><span><br></span></div><div dir="ltr" data-setdir="false"><span>I am looking forward to getting your reply.</span></div><div dir="ltr" data-setdir="false"><span><br></span></div><div dir="ltr" data-setdir="false"><span>Smith<br></span></div><div dir="ltr" data-setdir="false"><span></span><br></div><div><br></div>
</div><div id="yahoo_quoted_3828480961" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div>
On Thursday, February 11, 2021, 11:37:55 PM GMT+8, Elaine Meng <meng@cgl.ucsf.edu> wrote:
</div>
<div><br></div>
<div><br></div>
<div><div dir="ltr">HI Smith,<br 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 clear="none"><br 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 clear="none"><<a shape="rect" href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#threshold" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#threshold</a>><br clear="none"><br 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 clear="none"><br clear="none">vop threshold #0 minimum 0.17 set 0 maximum 0.18 setMaximum 1<br clear="none"><br 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 clear="none"><<a shape="rect" href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html</a>><br clear="none"><br clear="none">I hope this helps,<br clear="none">Elaine<br clear="none">-----<br clear="none">Elaine C. Meng, Ph.D. <br clear="none">UCSF Chimera(X) team<br clear="none">Department of Pharmaceutical Chemistry<br clear="none">University of California, San Francisco<br clear="none"><div class="yqt9647512709" id="yqtfd79127"><br clear="none">> On Feb 11, 2021, at 3:11 AM, Smith Lee <<a shape="rect" ymailto="mailto:smith_lee123@yahoo.com" href="mailto:smith_lee123@yahoo.com">smith_lee123@yahoo.com</a>> wrote:<br clear="none">> <br clear="none">> Dear All,<br clear="none">> <br 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 clear="none">> <br 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 clear="none">> <br 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 clear="none">> <br 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 clear="none">> <br 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 clear="none">> <br clear="none">> I am looking forward to getting your reply.<br clear="none">> <br clear="none">> Smith<br clear="none"><br clear="none"></div></div></div>
</div>
</div></body></html>