<span style="font-family: sans-serif;">Hi sir, </span><div id="yiv8860182797yMail_cursorElementTracker_1572826482834" style="overflow-wrap: break-word; font-family: sans-serif;">I downloaded chimera 1.13.1 at a website for free. Also, I am able to use the software without any licence needed. I carried out some research work using the software. Presently I am about to submit a paper for publication using your references. In this case, Will it be proper for me to submit a paper for publication using your references. </div><div id="yiv8860182797yMail_cursorElementTracker_1572827375801" style="overflow-wrap: break-word; font-family: sans-serif;">Best wishes </div><div id="yiv8860182797yMail_cursorElementTracker_1572827394996" style="overflow-wrap: break-word; font-family: sans-serif;">Billy. </div><br><div id="ymail_android_signature"><a id="ymail_android_signature_link" href="https://go.onelink.me/107872968?pid=InProduct&c=Global_Internal_YGrowth_AndroidEmailSig__AndroidUsers&af_wl=ym&af_sub1=Internal&af_sub2=Global_YGrowth&af_sub3=EmailSignature">Sent from Yahoo Mail on Android</a></div> <br> <blockquote style="margin: 0 0 20px 0;"> <div style="font-family:Roboto, sans-serif; color:#6D00F6;"> <div>On Wed, 9 Oct 2019 at 8:18 PM, Elaine Meng</div><div><meng@cgl.ucsf.edu> wrote:</div> </div> <div style="padding: 10px 0 0 20px; margin: 10px 0 0 0; border-left: 1px solid #6D00F6;"> Hi Clara,<br clear="none">Maybe you want the “vop cover” command with “atomBox” option.  Also, this makes a new volume, so you would measure that new volume (not #0).<br clear="none"><br clear="none">For example, commands:<br clear="none"><br clear="none">open edsID:1a0m<br clear="none">open 1a0m<br clear="none"><br clear="none">… now the map is #0 and the atomic model is #1 …<br clear="none"><br clear="none">~ribbon<br clear="none">display<br clear="none">volume #0 level 0.7<br clear="none">sel :6.a<br clear="none">vop cover #0 atomBox sel<br clear="none"><br clear="none">… this makes new map #2 …  there is also a “pad" option, see <br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover</a>><br clear="none"><br clear="none">volume #0 hide<br clear="none">measure volume #2<br clear="none"><br clear="none">However, is that really what you want to measure, the volume inside the isosurface within a rectangular box?  See also the Volume Viewer “Zone” feature and/or command “vop zone.”<br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#zone" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#zone</a>><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone</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="yqt6010242217 yQTDBase" id="yqtfd82603"><br clear="none">> On Oct 8, 2019, at 8:32 AM, MARIA CLARA BLANES MIRA <<a shape="rect" ymailto="mailto:c.blanes@goumh.umh.es" href="mailto:c.blanes@goumh.umh.es">c.blanes@goumh.umh.es</a>> wrote:<br clear="none">> <br clear="none">> Dear Chimera experts,<br clear="none">> I have been measuring surface volumes by using the atom box option in order to obtain a surface slice volume and then the volume measure.  But how could I use the atom box in the command line?<br clear="none">> Thank you!<br clear="none">> clara<br clear="none">> <br clear="none">> import chimera<br clear="none">> import os<br clear="none">> from chimera import runCommand<br clear="none">> runCommand(’sel :2.A,19.A,25.A, 5.B, 23.B, 26.B’)  # to define the box<br clear="none">> runCommand(‘atomBox ????’)<br clear="none">> runCommand('measure volume #0')<br clear="none">> runCommand('close all')<br clear="none"><br clear="none"><br clear="none">_______________________________________________<br clear="none">Chimera-users mailing list: <a shape="rect" ymailto="mailto:Chimera-users@cgl.ucsf.edu" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br clear="none">Manage subscription: <a shape="rect" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br clear="none"></div> </div> </blockquote>