<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Realistically no. Too many other priorities. The gap will eventually get filled in in ChimeraX, but even that will be awhile.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 19, 2017, at 1:24 PM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" class="">chiendarret@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Hi Eric:<br class=""><br class=""></div>Any plan to fill this gap?<br class=""><br class=""></div>thanks<br class=""><br class=""></div>francesco<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <span dir="ltr" class=""><<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Francseco,<div class=""><span class="m_2359467712280289256Apple-tab-span" style="white-space:pre-wrap"> </span>Unfortunately, segment IDs are not preserved by the trajectory reader.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><span class="HOEnZb"><font color="#888888" class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;" class=""><div class=""><span class="m_2359467712280289256Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div class=""><span class="m_2359467712280289256Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class=""></div></font></span><div class=""><div class="h5"><div class=""><blockquote type="cite" class=""><div class="">On Oct 19, 2017, at 9:53 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank" class="">chiendarret@gmail.com</a>> wrote:</div><br class="m_2359467712280289256Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi Elaine:<br class=""></div>While, as I wrote, the commands for segname did work fine with .psf/.pdb namd files,<br class=""></div><div class="">in contrast, with .psf/.dcd files (movie)<br class=""></div><div class=""><br class=""></div>select @/pdbSegment=C1<br class=""><br class=""></div>selects all chains of the protein assembly, including ligands. The same occurs with<br class=""><br class=""></div>select @/pdbSegment=O2C1<br class=""><br class=""></div>where O2C1 is the segname of the molecule dioxygen associated with chain.<br class=""><br class=""></div><div class="">This occurs both on my desktop and on a large-memory nextscale cluster on remote visualization (the latter is the actual interest)<br class=""><br class=""></div><div class="">Do you know of any remedy?<br class=""><br class=""></div><div class="">thanks a lot<br class=""><br class=""></div><div class="">francesco<br class=""></div><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="gmail_quote">---------- Forwarded message ----------<br class="">From: <b class="gmail_sendername">Francesco Pietra</b> <span dir="ltr" class=""><<a href="mailto:chiendarret@gmail.com" target="_blank" class="">chiendarret@gmail.com</a>></span><br class="">Date: Mon, Oct 16, 2017 at 7:12 PM<br class="">Subject: Re: [Chimera-users] Selecting residues in chains defined by segname<br class="">To: UCSF Chimera Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><br class=""><br class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Hi Elaine:<br class=""><br class=""></div>Great!<br class=""><br class=""></div>thank you<span class="m_2359467712280289256HOEnZb"><font color="#888888" class=""><br class=""></font></span></div><span class="m_2359467712280289256HOEnZb"><font color="#888888" class="">francesco<br class=""></font></span></div><div class="m_2359467712280289256HOEnZb"><div class="m_2359467712280289256h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <span dir="ltr" class=""><<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Francesco,<br class="">
The symbol for intersection is “&” ... in other words, you could use<br class="">
<br class="">
select :17 & @/pdbSegment=A1<br class="">
<br class="">
Intersection and union symbols are explained here:<br class="">
<<a href="http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/home<wbr class="">/meng/docs/UsersGuide/midas/at<wbr class="">om_spec.html#combinations</a>><br class="">
<span class=""><br class="">
I hope this helps,<br class="">
Elaine<br class="">
<br class="">
</span><span class="">> On Oct 16, 2017, at 12:29 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank" class="">chiendarret@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi Elaine:<br class="">
</span><span class="">> 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 class="">
><br class="">
> On the other hand, with such complex situations, it is Xplor, with its segname features, that helps.<br class="">
><br class="">
> Should you need a pdb fine with segname, I could attach a simple one, with a single chain.<br class="">
><br class="">
> On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
> Hi Francesco,<br class="">
> 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 class="">
><br class="">
> select @/pdbSegment=A1<br class="">
> color red @/pdbSegment=F3<br class="">
><br class="">
> I hope this helps,<br class="">
> Elaine<br class="">
><br class="">
</span><span class="">> > On Oct 15, 2017, at 10:40 AM, Francesco Pietra <<a href="mailto:chiendarret@gmail.com" target="_blank" class="">chiendarret@gmail.com</a>> wrote:<br class="">
> ><br class="">
> > Hi Elaine:<br class="">
> ><br class="">
> > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:<br class="">
> > and your answer:<br class="">
> ><br class="">
> > 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 class="">
> ><br class="">
> > I have a more complex case, where chains are defined by segname,<br class="">
> > for example<br class="">
> ><br class="">
> > A1 A2 A3 A4 A5 etc<br class="">
> ><br class="">
> > while the standard PDB definition is "A" for all them.<br class="">
> ><br class="">
> > The same for standard "B", "C" etc.<br class="">
> ><br class="">
> > As I want to display a movie of ligand pathways, where the ligand<br class="">
> > moves from, say, "A1" to, say, "F3", I want in the first instance<br class="">
> > become able to select particular residues in particular chains,<br class="">
> > as defined by their segname.<br class="">
> ><br class="">
> > Could you imagine a simple way not requiring selection by atom numbers?<br class="">
> > Thanks<br class="">
> > francesco pietra<br class="">
><br class="">
><br class="">
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