<div dir="ltr"><div><div><div>Hi Eric:<br><br></div>Any plan to fill this gap?<br><br></div>thanks<br><br></div>francesco<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Francseco,<div><span class="m_2359467712280289256Apple-tab-span" style="white-space:pre-wrap"> </span>Unfortunately, segment IDs are not preserved by the trajectory reader.</div><div><br></div><div>—Eric</div><div><span class="HOEnZb"><font color="#888888"><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div><span class="m_2359467712280289256Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div><span class="m_2359467712280289256Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div><br></div></div><br></div></font></span><div><div class="h5"><div><blockquote type="cite"><div>On Oct 19, 2017, at 9:53 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank">chiendarret@gmail.com</a>> wrote:</div><br class="m_2359467712280289256Apple-interchange-newline"><div><div dir="ltr"><div><div><div><div><div><div>Hi Elaine:<br></div>While, as I wrote, the commands for segname did work fine with .psf/.pdb namd files,<br></div><div>in contrast, with .psf/.dcd files (movie)<br></div><div><br></div>select @/pdbSegment=C1<br><br></div>selects all chains of the protein assembly, including ligands. The same occurs with<br><br></div>select @/pdbSegment=O2C1<br><br></div>where O2C1 is the segname of the molecule dioxygen associated with chain.<br><br></div><div>This occurs both on my desktop and on a large-memory nextscale cluster on remote visualization (the latter is the actual interest)<br><br></div><div>Do you know of any remedy?<br><br></div><div>thanks a lot<br><br></div><div>francesco<br></div><div><div><div><div><div><div><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Francesco Pietra</b> <span dir="ltr"><<a href="mailto:chiendarret@gmail.com" target="_blank">chiendarret@gmail.com</a>></span><br>Date: Mon, Oct 16, 2017 at 7:12 PM<br>Subject: Re: [Chimera-users] Selecting residues in chains defined by segname<br>To: UCSF Chimera Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><br><br><br><div dir="ltr"><div><div><div>Hi Elaine:<br><br></div>Great!<br><br></div>thank you<span class="m_2359467712280289256HOEnZb"><font color="#888888"><br></font></span></div><span class="m_2359467712280289256HOEnZb"><font color="#888888">francesco<br></font></span></div><div class="m_2359467712280289256HOEnZb"><div class="m_2359467712280289256h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Francesco,<br>
The symbol for intersection is “&” ... in other words, you could use<br>
<br>
select :17 & @/pdbSegment=A1<br>
<br>
Intersection and union symbols are explained here:<br>
<<a href="http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/home<wbr>/meng/docs/UsersGuide/midas/at<wbr>om_spec.html#combinations</a>><br>
<span><br>
I hope this helps,<br>
Elaine<br>
<br>
</span><span>> On Oct 16, 2017, at 12:29 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank">chiendarret@gmail.com</a>> wrote:<br>
><br>
> Hi Elaine:<br>
</span><span>> That works fine. However, I was unable to extend your suggestions to pick up a specific residue within a specific chain. Neither "select :17 @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands (obviously expected).<br>
><br>
> On the other hand, with such complex situations, it is Xplor, with its segname features, that helps.<br>
><br>
> Should you need a pdb fine with segname, I could attach a simple one, with a single chain.<br>
><br>
> On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
> Hi Francesco,<br>
> Although I don’t have an example file with segnames to try myself, I’m told you can specify by the atom attribute pdbSegment, e.g.<br>
><br>
> select @/pdbSegment=A1<br>
> color red @/pdbSegment=F3<br>
><br>
> I hope this helps,<br>
> Elaine<br>
><br>
</span><span>> > On Oct 15, 2017, at 10:40 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank">chiendarret@gmail.com</a>> wrote:<br>
> ><br>
> > Hi Elaine:<br>
> ><br>
> > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:<br>
> > and your answer:<br>
> ><br>
> > command: select :45.a-d > or > command: select :45.* > > Or, to select residue 45 in just chains A and D: > > command: select :45.a,45.d<br>
> ><br>
> > I have a more complex case, where chains are defined by segname,<br>
> > for example<br>
> ><br>
> > A1 A2 A3 A4 A5 etc<br>
> ><br>
> > while the standard PDB definition is "A" for all them.<br>
> ><br>
> > The same for standard "B", "C" etc.<br>
> ><br>
> > As I want to display a movie of ligand pathways, where the ligand<br>
> > moves from, say, "A1" to, say, "F3", I want in the first instance<br>
> > become able to select particular residues in particular chains,<br>
> > as defined by their segname.<br>
> ><br>
> > Could you imagine a simple way not requiring selection by atom numbers?<br>
> > Thanks<br>
> > francesco pietra<br>
><br>
><br>
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</blockquote></div><br></div>
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