<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Oct 17, 2012, at 9:47 AM, Marek Maly wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello all,<br><br>#1<br>I am just curious if it is in Chimera implemented possibility<br>to select all the molecules which are connected via H-bonds with previously<br>selected ("primary") molecule.<br><br>If it is not implemented I would vote for putting it in the developers queue<br>as it would allow to show easily and clearly (after action command "show selected only") just<br>all the molecules from the given solution directly interacting<br>with previously selected "primary" molecule and it would be a nice and useful feature I think.<br><br>Perhaps the optimal solution would be to add into "H-bond Parameters" table an additional "clik choice" which would ensure (if marked) that together with visualizing of all H-bonds (defined in the table) will be also selected all molecules which are connected by that H-bonds.<br><br>(as the supplementary option might be eventually selection of end residues only (not whole molecules) which might be also useful in some cases)<br></div></blockquote><div><br></div>Hi Marek,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>This is sort of possible now, depending on whether your molecules are single residues or separate models. Here's the recipe:</div><div><br></div><div>1) Find the H-bonds</div><div>2) Go to Tools->General Controls and open the Pseudobond Panel</div><div>3) Select the hydrogen bonds group in the panel</div><div>4) Click the panel's Select Bonded button</div><div>5) Use the up arrow key to increase the selection to residues (if your molecules are residues, e.g. water), or use up arrow a few more times if your molecules are models.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If your molecules aren't single residues / chains / models then you are kind of stuck, since the selection increase/decrease mechanism doesn't have a "molecule" level per se. Perhaps I could make it so that if you hold the shift key down with up-arrow, the selection changes</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>atom -> residue -> connected fragment (molecule) -> model</div><div><br></div><div>instead of</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>atom -> residue -> chain (by chain ID) -> model</div><div><br></div><div>I'll think about it.</div><div><br><blockquote type="cite"><div>#2<br>Similarly would be cool to have in menu-table "Select -> Zone..." except<br><br>"Select all atoms/bonds of any residue in selection zone" also<br>possibility like:<br><br>"Select all atoms/bonds of any MOLECULE having at least one atom in selection zone".<br><br>Then again using the action "show selected only" one might have quick and nice<br>picture only of all and WHOLE molecules which are in the defined neighbourhood of the<br>initially selected "primary" molecule.<br></div></blockquote><div><br></div><div>Again, up-arrow could possibly be helpful here. Nonetheless, a useful suggestion.</div><br><blockquote type="cite"><div><br>#3<br>Perhaps is it shame :)) but until now I was not able to find the right button to clear/delete<br>previously visualized H-bonds.<br><br>So my solution (probably not so much elegant) is that I simply select one atom (which is<br>really not the candidate for H-bond ) like C atom and then I ask to visualize all H-bonds<br>which has this atom as the one end. So naturally no H-bond is found and if<br>I do not mark "Retain currently displayed H-bonds" also the previously visualized H-bonds<br>are deleted. But perhaps there is more elegant solution, if not button so at least some command ?</div></blockquote><br></div><div>The command "~hb" will remove H-bonds. Also, in the Pseudobond Panel you can close the "hydrogen bonds" group.</div><div><br></div><div>--Eric</div><br><div>
<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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