Hi Elaine:

Yes, I could build a stereo-pair of the trajectory (of centroids) using atomIDs, and coloring the subunits involved also trough atomIDs.

Thanks

francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret@gmail.com>
Date: Sat, Oct 21, 2017 at 8:53 AM
Subject: Re: [Chimera-users] Selecting residues in chains defined by segname
To: chimera <chimera-users@cgl.ucsf.edu>

Hi Elaine:

Same residue name and number. Different segname and atom id. You are probably correct correct that I could try to visualize the trajectories with (with centroids) with atom id number even in this complex situation. I'll try, thanks.

At any event, I maintain that segname is a powerful aid, making it easier, for example, to assign different colors to the different chains. Therefore, in my view, making chimera able to deal with segname in MD trajectories is high priority.

frsncesco

On Fri, Oct 20, 2017 at 11:49 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Francesco,
Is it not possible to specify the ligand without using the segname? You can use residue number, chain number, residue name… are you saying that there is more than one residue in the same chain with both the same name and the same number?
Elaine

> On Oct 20, 2017, at 2:37 PM, Francesco Pietra <chiendarret@gmail.com> wrote:
>
> 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@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@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@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@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@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@cgl.ucsf.edu>
>>>
>>>
>>> Hi Elaine:
>>>
>>> Great!
>>>
>>> thank you
>>> francesco
>>>
>>> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng@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/atom_spec.html#combinations>
>>>
>>> I hope this helps,
>>> Elaine