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Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?
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From: Marko H. <mh...@ca...> - 2019-09-12 07:58:37
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<tt>Hi Yeping, <br>
<br>
Click on the bar object "Action" > "Levels" for a few preset
levels/scales.<br>
<br>
hth, Marko </tt><br>
<br>
<div class="moz-cite-prefix">On 12/09/2019 08:03, sunyeping via
PyMOL-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:506...@al...">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div class="__aliyun_email_body_block">
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Dear
all,</span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><br>
</span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">I
am trying to compare the vacuum electrostatics of three
related proteins. I loaded them in pymol and use
"Action>generate>vacuum electrostatics menu to
generate the <span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;">vacuum </span><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;">electrostatics
of the three proteins. I find that the lower and upper
limit of the gradient bars generated with the <span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"> </span><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">vacuum </span><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">electrostatics
of the three proteins are different. They are
-64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. </span></span></span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><br>
</span></span></span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">I
wonder whether I could define the lower and upper limit
of the gradients to the same values so that the <span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">vacuum </span><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">electrostatics
of the three proteins can be better compared?</span></span></span></span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><br>
</span></span></span></span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">Best
regards.</span></span></span></span></div>
<div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">Yeping</span></span></span></span></div>
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<pre class="moz-signature" cols="72">--
Marko Hyvonen
Department of Biochemistry, University of Cambridge
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