saving several pdb files in one
Dear Elaine and all, I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so? Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates! I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess.... Is there an easy way of doing so? Thanks, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail:dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Hi Dieter, I don't have any great ideas other than using zone like you said. The program wasn't designed for this situation! My only other ideas: (A) make a molmap (see "molmap" command) from all of those atoms, then adjust the molmap display threshold to where you want it, and then use the molmap surface to mask the original density map of interest. However, that would no longer be a precise distance from all of the atom centers, because making a molmap "smears" them out and there will be additive effects from clumps of atoms. Also I don't know if creating the molmap from all those atoms would be slow or not. Molmap command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> (B) change the combined PDB file of atoms into a giant Chimera marker file instead to avoid chemical perception when it is read. However, that would be a lot of work and I can't think of a way to make Chimera do the format conversion for you. Marker files: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
If you include at least one valid HELIX or SHEET record in your combined PDB file, then Chimera will think that secondary structure has been assigned and will not try to compute it itself. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 9:08 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dieter, I don't have any great ideas other than using zone like you said. The program wasn't designed for this situation! My only other ideas:
(A) make a molmap (see "molmap" command) from all of those atoms, then adjust the molmap display threshold to where you want it, and then use the molmap surface to mask the original density map of interest. However, that would no longer be a precise distance from all of the atom centers, because making a molmap "smears" them out and there will be additive effects from clumps of atoms. Also I don't know if creating the molmap from all those atoms would be slow or not. Molmap command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
(B) change the combined PDB file of atoms into a giant Chimera marker file instead to avoid chemical perception when it is read. However, that would be a lot of work and I can't think of a way to make Chimera do the format conversion for you. Marker files: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
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Hi Elaine and Eric, thanks a lot! Will Eric's suggestion handle thus many atoms? BTW: I could load all pdbs but moving them together is somewhat slow and tedious. Is there a way of handling them as one? I might then even use fit-in-map! best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 18.02.2021 18:15, Eric Pettersen wrote:
If you include at least one valid HELIX or SHEET record in your combined PDB file, then Chimera will think that secondary structure has been assigned and will not try to compute it itself.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 9:08 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dieter, I don't have any great ideas other than using zone like you said. The program wasn't designed for this situation! My only other ideas:
(A) make a molmap (see "molmap" command) from all of those atoms, then adjust the molmap display threshold to where you want it, and then use the molmap surface to mask the original density map of interest. However, that would no longer be a precise distance from all of the atom centers, because making a molmap "smears" them out and there will be additive effects from clumps of atoms. Also I don't know if creating the molmap from all those atoms would be slow or not. Molmap command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
(B) change the combined PDB file of atoms into a giant Chimera marker file instead to avoid chemical perception when it is read. However, that would be a lot of work and I can't think of a way to make Chimera do the format conversion for you. Marker files: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Dieter, What is difficult with 100 coordinate files? Don't you just inactivate the map and the 100 models as a group and then use the vop zone command? Tom
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail:dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
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Hi Tom, this is surely possible but very slow to move them all together. Furthermore, I am wondering how I might be able to finally fit the entire ensemble into the map! bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 18.02.2021 19:03, Tom Goddard wrote:
Hi Dieter,
What is difficult with 100 coordinate files? Don't you just inactivate the map and the 100 models as a group and then use the vop zone command?
Tom
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail:dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
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Hi Dieter, Ok, I am surprised it is slow, 100 atomic models of 1000 atoms each is only 100,000 atoms and that is not a lot -- single structures like ribosomes are larger and move just fine. Maybe Chimera is somehow inefficient moving so many models. If you have something selected Chimera can be slow because drawing the selection outline is slow. To fit them all as a rigid group in the map just select them all and use the Fit in Map tool with the Fit "selected atoms". ChimeraX our newer program is better at handling large models. Tom
On Feb 18, 2021, at 10:06 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Tom,
this is surely possible but very slow to move them all together. Furthermore, I am wondering how I might be able to finally fit the entire ensemble into the map!
bw Dieter
------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
On 18.02.2021 19:03, Tom Goddard wrote:
Hi Dieter,
What is difficult with 100 coordinate files? Don't you just inactivate the map and the 100 models as a group and then use the vop zone command?
Tom
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail:dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, I'll try! Thank you very much, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 18.02.2021 19:12, Tom Goddard wrote:
Hi Dieter,
Ok, I am surprised it is slow, 100 atomic models of 1000 atoms each is only 100,000 atoms and that is not a lot -- single structures like ribosomes are larger and move just fine. Maybe Chimera is somehow inefficient moving so many models. If you have something selected Chimera can be slow because drawing the selection outline is slow.
To fit them all as a rigid group in the map just select them all and use the Fit in Map tool with the Fit "selected atoms".
ChimeraX our newer program is better at handling large models.
Tom
On Feb 18, 2021, at 10:06 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Tom,
this is surely possible but very slow to move them all together. Furthermore, I am wondering how I might be able to finally fit the entire ensemble into the map!
bw Dieter
------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
On 18.02.2021 19:03, Tom Goddard wrote:
Hi Dieter,
What is difficult with 100 coordinate files? Don't you just inactivate the map and the 100 models as a group and then use the vop zone command?
Tom
On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine and all,
I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
Is there an easy way of doing so?
Thanks, best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail:dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Dieter Blaas -
Elaine Meng -
Eric Pettersen -
Tom Goddard