Trouble displaying missing structure dashed lines in cartoon mode
Hello ChimeraX team, I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel. I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine. I also found this thread ( https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong? My OS is Windows 11 if that matters. Thanks in advance for the help! Jonathan -- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
Hi Jonathan, So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX team,
I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.
I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.
I also found this thread (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html>), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong?
My OS is Windows 11 if that matters. Thanks in advance for the help!
Jonathan
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Eric, I can confirm that opening 1www does display pseudobonds properly. I played around with my pdb files, and it seems if the issue can be resolved if I either: 1) delete or modify a residue in ChimeraX and then resave the pdb, or 2) if I fully delete the SEQRES header of each pdb file. In any case, I'll send you separately two test pdbs I've created. Thanks for the prompt response! Jonathan On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Jonathan, So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX team,
I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.
I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.
I also found this thread ( https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong?
My OS is Windows 11 if that matters. Thanks in advance for the help!
Jonathan
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
Just for the curious bystanders, the problem is that the SEQRES records -- which are supposed to supply the complete sequence of the polymer -- indicated that the far-apart residues were consecutive in sequence. ChimeraX therefore suppressed the display of the missing-structure pseudobond. --Eric
On Jan 11, 2023, at 12:35 PM, Jonathan Jih via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
I can confirm that opening 1www does display pseudobonds properly. I played around with my pdb files, and it seems if the issue can be resolved if I either: 1) delete or modify a residue in ChimeraX and then resave the pdb, or 2) if I fully delete the SEQRES header of each pdb file.
In any case, I'll send you separately two test pdbs I've created. Thanks for the prompt response!
Jonathan
On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Jonathan, So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello ChimeraX team,
I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.
I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.
I also found this thread (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html>), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong?
My OS is Windows 11 if that matters. Thanks in advance for the help!
Jonathan
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
That makes a lot of sense - thanks for the explanation Eric! Is there perhaps a way to disable automatic SEQRES generation when saving pdbs within ChimeraX? I noticed that when I load a pdb with no SEQRES info (thereby having missing structure pseudobonds display correctly), upon resaving that pdb, new SEQRES info is automatically generated causing the issue to rear again. I then have to go back and manually delete SEQRES for each one of the pdbs I generate. Appreciate all the help. Jonathan On Wed, Jan 11, 2023 at 2:37 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Just for the curious bystanders, the problem is that the SEQRES records -- which are supposed to supply the complete sequence of the polymer -- indicated that the far-apart residues were consecutive in sequence. ChimeraX therefore suppressed the display of the missing-structure pseudobond.
--Eric
On Jan 11, 2023, at 12:35 PM, Jonathan Jih via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
I can confirm that opening 1www does display pseudobonds properly. I played around with my pdb files, and it seems if the issue can be resolved if I either: 1) delete or modify a residue in ChimeraX and then resave the pdb, or 2) if I fully delete the SEQRES header of each pdb file.
In any case, I'll send you separately two test pdbs I've created. Thanks for the prompt response!
Jonathan
On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Jonathan, So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX team,
I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.
I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.
I also found this thread ( https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong?
My OS is Windows 11 if that matters. Thanks in advance for the help!
Jonathan
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles De Novo Modeling Solutions <http://www.denovomods.com/> projects@denovomods.com | (831) 419-7729
Hmmm, oops. :-). Tomorrow's daily build will not put out SEQRES records for chains where it doesn't know the complete sequence. --Eric
On Jan 11, 2023, at 2:41 PM, Jonathan Jih <jihmailed@gmail.com> wrote:
That makes a lot of sense - thanks for the explanation Eric!
Is there perhaps a way to disable automatic SEQRES generation when saving pdbs within ChimeraX? I noticed that when I load a pdb with no SEQRES info (thereby having missing structure pseudobonds display correctly), upon resaving that pdb, new SEQRES info is automatically generated causing the issue to rear again. I then have to go back and manually delete SEQRES for each one of the pdbs I generate.
Appreciate all the help.
Jonathan
On Wed, Jan 11, 2023 at 2:37 PM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Just for the curious bystanders, the problem is that the SEQRES records -- which are supposed to supply the complete sequence of the polymer -- indicated that the far-apart residues were consecutive in sequence. ChimeraX therefore suppressed the display of the missing-structure pseudobond.
--Eric
On Jan 11, 2023, at 12:35 PM, Jonathan Jih via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Eric,
I can confirm that opening 1www does display pseudobonds properly. I played around with my pdb files, and it seems if the issue can be resolved if I either: 1) delete or modify a residue in ChimeraX and then resave the pdb, or 2) if I fully delete the SEQRES header of each pdb file.
In any case, I'll send you separately two test pdbs I've created. Thanks for the prompt response!
Jonathan
On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Jonathan, So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello ChimeraX team,
I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.
I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.
I also found this thread (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html>), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong?
My OS is Windows 11 if that matters. Thanks in advance for the help!
Jonathan
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
De Novo Modeling Solutions <http://www.denovomods.com/> projects@denovomods.com <mailto:projects@denovomods.com> | (831) 419-7729 <tel:(831)%20419-7729>
Sounds great. Thanks!! On Wed, Jan 11, 2023 at 3:59 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hmmm, oops. :-). Tomorrow's daily build will not put out SEQRES records for chains where it doesn't know the complete sequence.
--Eric
On Jan 11, 2023, at 2:41 PM, Jonathan Jih <jihmailed@gmail.com> wrote:
That makes a lot of sense - thanks for the explanation Eric!
Is there perhaps a way to disable automatic SEQRES generation when saving pdbs within ChimeraX? I noticed that when I load a pdb with no SEQRES info (thereby having missing structure pseudobonds display correctly), upon resaving that pdb, new SEQRES info is automatically generated causing the issue to rear again. I then have to go back and manually delete SEQRES for each one of the pdbs I generate.
Appreciate all the help.
Jonathan
On Wed, Jan 11, 2023 at 2:37 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Just for the curious bystanders, the problem is that the SEQRES records -- which are supposed to supply the complete sequence of the polymer -- indicated that the far-apart residues were consecutive in sequence. ChimeraX therefore suppressed the display of the missing-structure pseudobond.
--Eric
On Jan 11, 2023, at 12:35 PM, Jonathan Jih via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
I can confirm that opening 1www does display pseudobonds properly. I played around with my pdb files, and it seems if the issue can be resolved if I either: 1) delete or modify a residue in ChimeraX and then resave the pdb, or 2) if I fully delete the SEQRES header of each pdb file.
In any case, I'll send you separately two test pdbs I've created. Thanks for the prompt response!
Jonathan
On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Jonathan, So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX team,
I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.
I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.
I also found this thread ( https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong?
My OS is Windows 11 if that matters. Thanks in advance for the help!
Jonathan
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles
De Novo Modeling Solutions <http://www.denovomods.com/> projects@denovomods.com | (831) 419-7729
-- Biochemistry, Biophysics, and Structural Biology (BBSB) Molecular Biology Institute, University of California, Los Angeles De Novo Modeling Solutions <http://www.denovomods.com/> projects@denovomods.com | (831) 419-7729
participants (2)
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Eric Pettersen -
Jonathan Jih