<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 Pascal,<div class=""><br class=""></div><div class=""> If you click an edge of the crosslink network graph then it will select just the crosslinks corresponding to that edge, for example the 8 crosslinks between chains C and D in the example image below. I made that graph using command "crosslink network #2" and clicking on the CD edge only selects the #2 crosslinks, not a different set of crosslinks such as model #3. I tested this and it is working in the current ChimeraX. You will probably need to zoom your graph so you can actually see an edge -- use shift drag on the graph to zoom it, and alt drag (or some similar modifier) to translate the graph so you can see it better.</div><div class=""><br class=""></div><div class=""> Now the trouble is in your example you wanted crosslinks involving 4 chains #1/r/R and #2/r/R with both upper and lowercase R chains. When you click on an edge in the graph it selects only those crosslinks between 2 chains, all others are unselected. So it won't do what you need. Might be nice to let shift-click on an edge add to the selection, but that could get pretty tedious if you need to show connections between several chains. So a command is a better choice. Here are two commands to select the pseudobonds in crosslink model #5</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>select #1/r/R #2/r/R & #5 min 6 max 35</div><div class=""><br class=""></div><div class="">The "& #5" part means intersect with model #5. Or maybe slightly clearer using 2 commands</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>select #1/r/R #2/r/R min 6 max 35</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>select intersect #5</div><div class=""><br class=""></div><div class="">These command approaches did not work in the current ChimeraX because of two separate bugs that I just fixed, so they will work in tomorrow's ChimeraX.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><img apple-inline="yes" id="384E2984-D547-44AC-8E68-C2E3F18FD9BE" width="788" height="485" src="cid:CCC10525-2B0B-45AA-BD05-E43866A8934E@cgl.ucsf.edu" class=""><br class=""><blockquote type="cite" class=""><div class="">On Mar 15, 2019, at 3:42 AM, Pascal Albanese wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div dir="auto" class="">Hi Elaine, </div></div><div dir="auto" class=""><br class=""></div><div class="">Sorry for the late response. So I don't know if I maybe have some issue </div><div dir="auto" class="">I see the connecting edges in the network window, but I can only select chains (individual chains) and the subset of pbonds are not selected:</div><div class=""><span id="cid:ii_jt9xh8y80"><image.png></span><br class=""></div><div class="">Probably is my system which is a bit complicated... somehow the pbonds can be related to individual chains or group of them? like: sel #2.1/R #2.1/r #1.1/R #1.1/r (to select the model) pbonds #3 min 6 max 35 (to select the corresponding pbonds, in which previous chains R and r are involved). And then i can save the subselection of pbonds?</div><div class=""><br class=""></div><div class="">thanks for your help, i can share session if needed, </div><div class=""><br class=""></div><div class="">Pascal</div></div><div class=""><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno ven 8 mar 2019 alle 18:20 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> ha scritto:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Pascal,<br class="">
On the crosslinks network, clicking the edge between two chains selects the corresponding pseudobonds (those between the two chains). Is that what you mean?<br class="">
<br class="">
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#network" rel="noreferrer" target="_blank" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#network</a>><br class="">
<br class="">
Or if you meant all those between the two chains, plus the ones within each chain, then Tom’s example command selecting pseudobonds of chains A and B should work.<br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
> On Mar 8, 2019, at 6:21 AM, Pascal Albanese <<a href="mailto:pascal.albanese@polito.it" target="_blank" class="">pascal.albanese@polito.it</a>> wrote:<br class="">
> <br class="">
> Dear Tom, <br class="">
> Thank for the add, it works and is very useful. However, I don't know if I might haven't explained well: I have a complex set of pseudobonds (let's say #2) involving several Chains of #1. In the "crosslinks network" feature I'm able to subselect chains, but not subgroups of pseudobonds involving, for instance, chains A and B (can be either clicking on the network or with the command line). Would be possible to add this? <br class="">
> Thanks!<br class="">
> Pascal<br class="">
> <br class="">
> Il giorno mer 6 mar 2019 alle 21:33 Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank" class="">goddard@sonic.net</a>> ha scritto:<br class="">
> Hi Pascal,<br class="">
> <br class="">
> I added the ability to save pseudobond files (.pb suffix) in ChimeraX, will be in tonight's builds,<br class="">
> <br class="">
> select /A,B min 15 max 24<br class="">
> save somelinks.pb selectedOnly true<br class="">
> <br class="">
> This saves crosslinks between chains A and B with lengths between 15 and 24. The link colors and radii are also saved.<br class="">
> <br class="">
> Tom<br class="">
> <br class="">
>> On Mar 6, 2019, at 2:33 AM, Pascal Albanese wrote:<br class="">
>> <br class="">
>> Dear ChimearX Users and developers, <br class="">
>> I'm using ChimeraX for visualization and analysis of pseudobonds datasets from Crosslinking-MS and i found new features very useful (min max selection etc). <br class="">
>> I think it would be useful (but i don't know how much effort will be required) to be able to select subsets of distances (e.g. form 15 to 24 Angstroms, or involving chain A and B) and being able to create and export these subsets. for instance i have a Complex of A, B and C and i want to select all pseudo-bonds involving A and B and export them as pb file (to be able to load them as a separate model lateron). Or to sel min 15 max 24, and then export them as pb file (with "save" function). <br class="">
>> <br class="">
>> I think it would be really useful for both crosslinks visualization and analysis (i work with datasets of thousands of crosslinks on big complexes which make difficult to subselect them, i have to do it with pymol, then generate subsets and reformat them as .pb files). <br class="">
>> <br class="">
>> i had a look to previous threads, but i didn't found similar topics. If i'm wrong my apologize.<br class="">
>> Thank you!<br class="">
>> Pascal<br class="">
<br class="">
</blockquote></div></div>
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