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

[Francesco Pietra]

A pity, in my view. As more and more complex proteins are being examined
(thanks to faster clusters), working without segname would be practically
impossible in  the frame of today pdb files. For example, how visualizing
the trajectory of a particular ligand in a 24-chain protein assembly? I can
do that with vmd, but at the price of a less clear-cut trajectory and
poorer graphics.
But I understand that there may be different viewpoints.
Cheers
francesco

On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Realistically no.  Too many other priorities.  The gap will eventually get
> filled in in ChimeraX, but even that will be awhile.
>
> —Eric
>
> On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
>
> 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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>>
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