[Chimera-users] Fwd: Selecting residues in chains defined by segname

[Francesco Pietra]

Hi Eric:

Any plan to fill this gap?

thanks

francesco

On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Francseco,
> Unfortunately, segment IDs are not preserved by the trajectory reader.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
>
> Hi Elaine:
> While, as I wrote, the commands for segname did work fine with .psf/.pdb
> namd files,
> in contrast, with .psf/.dcd files (movie)
>
> select @/pdbSegment=C1
>
> selects all chains of the protein assembly, including ligands. The same
> occurs with
>
> select @/pdbSegment=O2C1
>
> where O2C1 is the segname of the molecule dioxygen associated with chain.
>
> This occurs both on my desktop and on a large-memory nextscale cluster on
> remote visualization (the latter is the actual interest)
>
> Do you know of any remedy?
>
> thanks a lot
>
> francesco
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Mon, Oct 16, 2017 at 7:12 PM
> Subject: Re: [Chimera-users] Selecting residues in chains defined by
> segname
> To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
>
>
> Hi Elaine:
>
> Great!
>
> thank you
> francesco
>
> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi Francesco,
>> The symbol for intersection is “&” ... in other words, you could use
>>
>> select :17 & @/pdbSegment=A1
>>
>> Intersection and union symbols are explained here:
>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/at
>> om_spec.html#combinations>
>>
>> I hope this helps,
>> Elaine
>>
>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret at gmail.com>
>> wrote:
>> >
>> > Hi Elaine:
>> > 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).
>> >
>> > On the other hand, with such complex situations, it is Xplor, with its
>> segname features, that helps.
>> >
>> > Should you need a pdb fine with segname, I could attach a simple one,
>> with a single chain.
>> >
>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> > Hi Francesco,
>> > 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.
>> >
>> > select @/pdbSegment=A1
>> > color red @/pdbSegment=F3
>> >
>> > I hope this helps,
>> > Elaine
>> >
>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra <chiendarret at gmail.com>
>> wrote:
>> > >
>> > > Hi Elaine:
>> > >
>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:
>> > >  and your answer:
>> > >
>> > > 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
>> > >
>> > > I have a more complex case, where chains are defined by segname,
>> > > for example
>> > >
>> > > A1 A2 A3 A4 A5 etc
>> > >
>> > > while the standard PDB definition is "A" for all them.
>> > >
>> > > The same for standard "B", "C" etc.
>> > >
>> > > As I want to display a movie of ligand pathways, where the ligand
>> > > moves from, say, "A1" to, say, "F3", I want in the first instance
>> > > become able to select particular residues in particular chains,
>> > > as defined by their segname.
>> > >
>> > > Could you imagine a simple way not requiring selection by atom
>> numbers?
>> > > Thanks
>> > > francesco pietra
>> >
>> >
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