<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Bala!<br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: 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; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""></div></div></div><div><blockquote type="cite" class=""><div class="">On Apr 19, 2018, at 6:09 AM, Bala subramanian <<a href="mailto:bala.biophysics@gmail.com" class="">bala.biophysics@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">
<span class=""></span><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">Dear
chimera lovers,</font></p><font size="2" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class="">
<br class="webkit-block-placeholder"></div><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">Good
day. I wrote a small script (pasted below) to monitor the dipole
vector of water molecules during MD. The script was adopted based available example.</font></p><div style="margin-bottom: 0in; line-height: 100%;" class="">
<br class="webkit-block-placeholder"></div><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">rc('close
#1-500')</font></p><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">m =
chimera.openModels.list()[0]</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">wat
= m.residues[2449]</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">com
= Point([a.coord() for a in wat.atoms], [a.element.mass for a in
wat.atoms])</font></p><font size="1" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class="">
<br class="webkit-block-placeholder"></div><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">#
dipl = Vector() No working, Use numpy instead</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">dipl
= np.array( [0.0,0.0,0.0] )</font></p><font size="1" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class="">
<br class="webkit-block-placeholder"></div><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">for
atm in wat.atoms: <br class=""></font></p><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class=""> #dipl
+= atm.charge * atm.coord()</font></p><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class=""> dipl
+= atm.charge * np.array( atm.coord().data() )</font></p><font size="1" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class=""><font size="1" class=""></font>
<br class="webkit-block-placeholder"></div><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">vend
= np.array(com) + 5 * dipl</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">of =
open('current.bild','w')</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">of.write('.color
green\n')</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">of.write('.cone
%f %f %f %f %f %f 0.5 \n' %
(com.x,com.y,com.z,vend[0],vend[1],vend[2]))</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">of.close()</font></p><font size="1" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="1" class="">rc('open
current.bild')</font></p><div style="margin-bottom: 0in; line-height: 100%;" class="">
<br class="webkit-block-placeholder"></div><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">Query
1)</font></p><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">The
following syntax given in a example doesnt work. What is the chimera point object indeed, an array or list ?. How
to do math operations on point object.</font></p><font size="2" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class=""><font size="2" class=""></font>
<br class="webkit-block-placeholder"></div><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">
dipl += atm.charge * a.coord()
</font></p><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">Error:</font></p><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">TypeError:
unsupported operand type(s) for *: 'float' and '_chimera.Point'</font></p><div class=""><br class=""></div></div></div></div></div></blockquote><div><br class=""></div>Well, Chimera has Point and Vector classes and is kind of pedantic about the allowed operations on them. So you can multiply a Vector but not a Point. You can add a Point and a Vector, but not a Point and a Point. Therefore, for the above to work you would need to convert the Point (what .coord() returns) to a Vector, e.g.:</div><div><br class=""></div><div>dial += atm.charge * a.coord().toVector()</div><div><br class=""><blockquote type="cite" class=""><div dir="ltr" class=""><div class=""><div class=""><font size="2" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class=""><span style="font-size: small;" class="">Query
2) In my example, I choose a specific water molecule by residue index. I am looking for some way to select the
water (or get list of water residues) that satisfy a selection on the fly, lets
say that water within 3 A from a prot. residue.</span><font size="2" class=""></font></div><font size="2" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class=""><font size="2" class=""></font>
<br class="webkit-block-placeholder"></div><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">In
short, how to handle selections inside python script in chimera
framework. I tried to play with chimera.selections but I didnt
succeed. Any example could be of help.</font></p><div class=""><br class=""></div></div></div></div></blockquote><div><br class=""></div>If you select the atoms (by whatever code/commands desired), then you can get a list of them from chimera.selection.currentAtoms()</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div dir="ltr" class=""><div class=""><div class=""><font size="2" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class=""><span style="font-size: small;" class="">Query
3) Invoke data calculated out of chimera inside a perframe script.</span><font size="2" class=""></font></div><font size="2" class="">
</font><div style="margin-bottom: 0in; line-height: 100%;" class=""><font size="2" class=""></font>
<br class="webkit-block-placeholder"></div><font size="2" class="">
</font><p style="margin-bottom:0in;line-height:100%" align="justify" class=""><font size="2" class="">If I have say 100 frames. I can do the dipole vector
calculation outside chimera and write separate “.bild” files,
1.bild, 2.bild, …..n.bild. Then inside the perframe script, I can
invoke a particular .bild fine corresponding to the frame no. Please
help me with an syntax example if this is possible.</font></p></div></div></div></blockquote><br class=""></div><div>We’re talking about MD Movie’s per-frame scripting dialog, right? In that dialog, make sure “Interpret script as” is set to “Chimera commands”, then your script could be:</div><div><br class=""></div><div>close #25</div><div>open 25 folder_your_bild_files_are_in/<FRAME>.bild</div><div><br class=""></div><div>Literally the string “<FRAME>”. Chimera will substitute in the actual frame number there. If you don’t have the frame number to have leading zeroes (e.g. 001 vs. 1) then uncheck the “Use leading zeroes…” box near the top of the dialog. The above first closes any model #25 that is open, then opens your BILD file as model #25.</div><div><br class=""></div><div>—Eric</div><br class=""><div class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></div></div></body></html>