<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 5, 2014, at 7:38 AM, sapeptides <<a href="mailto:sapeptides@gmail.com">sapeptides@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div class="gmail_extra">Hi Erik,</div><div class="gmail_extra"><br></div><div class="gmail_extra">I'm writing because I have noticed that in the new versions of chimera when I create a surface and then try to "cut" it (with the side view tool) to see inside the model I obtain this weird picture (attached), whereas in the old versions (how old I do not remember but I created a stunning images of various active sites) it was possible to check all the cavities inside the molecular structures.</div>
<div class="gmail_extra">I was wondering if you could suggest how to visualize pockets and clefts when the vdw or solvent accessible surface is present.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Thanks a lot!</div>
<div class="gmail_extra">Susanna</div></div></blockquote><br></div><div><br></div><img id="9dceca60-9bd1-4669-abf7-fb0d489d8f63" height="704" width="1097" apple-width="yes" apple-height="yes" src="cid:5FD0E5FB-C6E7-4531-9FFD-03CBAA5B0D0E@cgl.ucsf.edu"><div><br></div><div>Hi Susanna,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>It's best to send questions like this to the chimera-users list rather than me directly so that others can benefit from the answer and since I may not actually be the best person to answer the question. For instance, I have no good ideas about showing cavities effectively with VDW or solvent-accessible surfaces and hope someone else can chime in there.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>As for the lack of cavities in your image, did Chimera issue a warning when it computed the surface saying that "[c]alculation of some surface components failed" and that "[a] single component of the surface was calculated"? If so, that means that calculation of interior cavities failed and Chimera is showing the exterior surface only (which the error message does say if you read it in its entirety). That would produce the lack of interior cavities you observed. If you didn't get such a message, can you supply the PDB ID for this structure (or PDB file) so I can investigate? Thanks!</div><div><br></div><div>--Eric</div><div><br></div><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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