<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hi Markus,<br><br>This error occurs when the two specified surfaces have no points within the specified distance range. This is a bug -- it should just report the contact area as zero in that case. I've fixed that in tonight’s daily build.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/ticket/12966">http://plato.cgl.ucsf.edu/trac/chimera/ticket/12966</a><br><br>But there is a second problem, since your commands work on Mac with 64-bit Chimera 1.8.1. The trouble is almost surely that the surface calculation for one of the two sets of atoms failed on 64-bit Windows. Unfortunately the 3rd part surface calculation code we use (MSMS) often fails. Some ideas about how to try to get surfaces are here<br><br><span class="Apple-tab-span" style="white-space:pre"> </span>http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html<br><br>although often nothing works. The surface calculation fails especially often in 64-bit Windows Chimera. You might try 32-bit Windows Chimera. Our next generation Chimera will have surface calculation that always works, but is not expected out for at least 6 months.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><div>On Mar 28, 2014, at 11:23 AM, Markus Heller <<a href="mailto:mheller@cdrd.ca">mheller@cdrd.ca</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="WordSection1" style="page: WordSection1;"><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi Elaine,<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Thanks for your reply. I just filed a bug report on this, as per Tom’s request.<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">I should also mention that I did get some result with your version, but not what I expected: essentially a couple of surface blobs, but nothing like your figure.<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Anyhow, this seems to be a genuine bug, so I’ll just hang tight and wait for a fix.<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Markus<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div><div style="border-style: solid none none; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding: 3pt 0in 0in;"><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;"><span class="Apple-converted-space"> </span>Elaine Meng [<a href="mailto:meng@cgl.ucsf.edu" style="color: purple; text-decoration: underline;">mailto:meng@cgl.ucsf.edu</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, March 27, 2014 2:39 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Markus Heller<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;">chimera-users@cgl.ucsf.edu</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Binding pocket surface command script not working<o:p></o:p></span></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Hi Markus,<o:p></o:p></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">It is a mystery to me… I tried it in both 1.8.1 and the current pre-1.9 daily build and didn't get the error. I'd say go ahead and submit a report… we can always close it if it's not reproducible.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">However, the result I got was somewhat ugly because there were several holes in the pocket. I then tried a larger cutoff, as in the folowing:<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">open 2v5z<br>delete :.b<br>split atoms :sag<br>surface<br>measure contactArea #0.2 #0.1 4 slab -.1,0 color tan<br>measure contactArea #0.2 #0.1 3.99 slab -.11,-.01 color cornflowerblue<br>~surf #0<br>~disp; ~ribbon; disp :sag<o:p></o:p></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">sop hideDust #1,2 size 1 metric sizeRank<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">which I think got rid of as many of the holes as reasonably possible, but there were still a couple of ugly places that might be surface calculation artifacts: where the blue shows through the tan near the middle of the attached image, and the little funnel on the upper right. There is a small opening through the funnel, so I'm not sure whether it's an artifact or the actual shape of the pocket. This general process would be expected to make a better-looking figure for pockets with fewer openings.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">This pocket could alternatively be considered one large pocket containing both the SAG and FAD. For example, in a separate Chimera session I tried:<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">open castp:2v5z<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">which reports the two largest pockets as the SAG/FAD pockets of the A and B chains, respectively. If you are using the "measure contactArea" approach to get the appearance of different inside and outside pocket colors as shown in the image gallery figure, it could be done for this collective pocket with "split atoms :sag,fad" (well, assuming you didn't get that mysterious error again!). Sorry for the weirdness,<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Elaine<o:p></o:p></div></div><div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">----------<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br><span><image001.png></span><o:p></o:p></div></div><p class="MsoNormal" style="margin: 0in 0in 12pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><br>On Mar 27, 2014, at 1:05 PM, Markus Heller <<a href="mailto:mheller@cdrd.ca" style="color: purple; text-decoration: underline;">mheller@cdrd.ca</a>> wrote:<o:p></o:p></p><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Hello,<br> <br>I’m trying to reproduce the Binding Pocket Surface image from the Gallery with a different pdb file.<br> <br>I can successfully reproduce with the pdb used in the example (2zcp), but not with 2v5z. Running latest Chimera.<br> <br>Steps to reproduce:<br> <br>open 2v5z<br>delete :.b<br>split atoms :sag<br>surface<br>measure contactArea #0.2 #0.1 3 slab -.1,0 color tan<br> <br>gives an error:<br> <br>error: Array must be 2-dimensional, got 1-dimensional<br> <br> <br> File "C:\Program Files\Chimera 1.8.1\share\MeasureVolume\__init__.py", line 60, in surface_area<br> area = surface_area(varray, tarray)<br> <br>See reply log for Python traceback.<br> <br>Why, and would it be helpful to file a bug report?<br> <br>Thanks and Cheers<br>Markus<br> <br>--<br>Markus Heller, Ph.D.<br>NMR Scientist<br>CDRD - The Centre for Drug Research and Development<br>2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147<br>Direct: (604) 827-1122 | F: (604) 827-1299 | E: <a href="mailto:mheller@cdrd.ca" style="color: purple; text-decoration: underline;">mheller@cdrd.ca</a> | <a href="http://www.cdrd.ca/" style="color: purple; text-decoration: underline;">www.cdrd.ca</a><br><image007.png><br> <br> <br> <br> <br><br>Follow us: <image003.jpg> <image004.jpg> <image005.png> <image006.png><br> <br>This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.<br> <br> <br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></body></html>