Selecting residues in chains defined by segname
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 .
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 ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 15, 2017, at 10:40 AM, Francesco Pietra <chiendarret@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
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@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 ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 15, 2017, at 10:40 AM, Francesco Pietra <chiendarret@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
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
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
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
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mail man/listinfo/chimera-users
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 <mailto: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 <mailto: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 <mailto: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#comb... <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations>>
I hope this helps, Elaine
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@gmail.com <mailto:chiendarret@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@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:chiendarret@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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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/at om_spec.html#combinations>
I hope this helps, Elaine
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mail man/listinfo/chimera-users
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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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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#comb... <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations>>
I hope this helps, Elaine
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@gmail.com <mailto:chiendarret@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@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:chiendarret@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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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/at om_spec.html#combinations>
I hope this helps, Elaine
On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@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@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@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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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
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
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
Though segname is not preserved, Chimera automatically assigns chain IDs to the polymers in the trajectory, using A-Z, a-z, and 1-9,0 in that order. The assignments are in the reply log. Therefore you should be able to specify polymeric segments by chain ID, and ligands near a particular chain with the “zone” operator, e.g.: ":O2 & :.C zr<7" for a ligand named O2 near chain C. —Eric
On Oct 20, 2017, at 2:49 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
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Francesco Pietra