Hi Team, I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Hi Pranav, We'll look into it. I made a bug-report ticket and put you on the notification list. In the meanwhile, try command: style sphere <https://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html> (or click the sphere-style icon in the Home or Molecule Display tabs) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms?
Best, Pranav
Hello, with Avogadro I built and optimized simple tri-peptide which I read as pdb into ChimeraX, see the attachments. When I wanted to display coulombic potential, I got the following error message below. Looks like Avogadro's pdb protocol does not fit for ChimeraX...although all atoms and bonds in the tripeptide example are correct. Any help, please ? The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLU 2 CG /A GLU 2 OE2 /A GLU 2 CA /A GLU 2 CD /A GLU 2 CB /A GLU 2 OE1 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /A LEU 3 HO bonded to atom that should not have hydrogens (/A LEU 3 OXT) -- doc. RNDr. Miroslav Iliaš, PhD. Katedra chémie Fakulta prírodných vied Univerzita Mateja Bela Tajovského 40 97401 Banská Bystrica tel: +421 48 446 7351 email : Miroslav.Ilias@umb.sk Miroslav Iliaš, PhD. Department of Chemistry Faculty of Natural Sciences Matej Bel University Tajovského 40 97401 Banska Bystrica Slovakia tel: +421 48 446 7351 email : Miroslav.Ilias@umb.sk
Hello, Your PDB file has problems. (1) The second residue GLU is in HETATM lines instead of ATOM lines, and it does not have the standard atom names for GLU. Instead all of its carbons are named C, all of its hydrogens are named H, and all of its oxygens are named O. You would need to change all the HETATM lines to ATOM lines and also make sure they use the standard atom names for glutamate residues: <http://ligand-expo.rcsb.org/reports/G/GLU/GLU_D3L1.gif> (2) Also Avogadro made everything neutral, instead of the negatively charged carboxylates and positively charged N-terminus. So it put extra H on each of the CO2 groups, and omitted one of the N-terminal hydrogens. ChimeraX (and Chimera) would normally work on structures without hydrogens, and infer negatively charged carboxylates and positively charged N-terminus. So if you want to do that you should probably just remove all the hydrogens. Actually I manually edited your file for you (see attached) but you would need to do it yourself in the future! You can just open it and use command "coulombic" or click the Coulombic coloring icon. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2021, at 8:50 AM, Ilias Miroslav, doc. RNDr., PhD. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
with Avogadro I built and optimized simple tri-peptide which I read as pdb into ChimeraX, see the attachments.
When I wanted to display coulombic potential, I got the following error message below.
Looks like Avogadro's pdb protocol does not fit for ChimeraX...although all atoms and bonds in the tripeptide example are correct.
Any help, please ?
The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLU 2 CG /A GLU 2 OE2 /A GLU 2 CA /A GLU 2 CD /A GLU 2 CB /A GLU 2 OE1
Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /A LEU 3 HO bonded to atom that should not have hydrogens (/A LEU 3 OXT)
-- doc. RNDr. Miroslav Iliaš, PhD.
Katedra chémie Fakulta prírodných vied Univerzita Mateja Bela Tajovského 40 97401 Banská Bystrica tel: +421 48 446 7351 email : Miroslav.Ilias@umb.sk
Miroslav Iliaš, PhD. Department of Chemistry Faculty of Natural Sciences Matej Bel University Tajovského 40 97401 Banska Bystrica Slovakia tel: +421 48 446 7351 email : Miroslav.Ilias@umb.sk
<N-Ala-Glu-Leu.pdb><N-Ala-Glu-Leu.xyz>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Pranav, The main think that makes ChimeraX sluggish when moving individual models with the mouse for doing rigid-body fitting is full or soft lighting modes that cast ambient shadows. If you switch to simple lighting using the Home toolbar icon or command "light simple" then graphics updating will be many times faster. The reason for the slow graphics with ambient shadows is that it is recomputing shadows from 64 different directions when you move one model relative to the other because the models cast shadows on each other. I am thinking of having ChimeraX issue warning when graphics becomes slow due to continuous updating of ambient shadows so it will be more obvious how you fix it. Tom
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, I was aware of this and had therefore done exactly what you suggested! :) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Mon, Aug 2, 2021 at 6:36 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
The main think that makes ChimeraX sluggish when moving individual models with the mouse for doing rigid-body fitting is full or soft lighting modes that cast ambient shadows. If you switch to simple lighting using the Home toolbar icon or command "light simple" then graphics updating will be many times faster. The reason for the slow graphics with ambient shadows is that it is recomputing shadows from 64 different directions when you move one model relative to the other because the models cast shadows on each other. I am thinking of having ChimeraX issue warning when graphics becomes slow due to continuous updating of ambient shadows so it will be more obvious how you fix it.
Tom
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
And did using simple lighting fix the slow rigid-body fitting? If not, is the slowness when you are trying to move one model with the mouse. If so, what graphics card are you using? ChimeraX should easily move a million atoms pretty smoothly with a mid-range graphics card. If you want to further discuss this probably good to use ChimeraX menu Help / Report a Bug so we get you computer system info. Tom
On Aug 2, 2021, at 10:58 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Tom, I was aware of this and had therefore done exactly what you suggested! :) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Aug 2, 2021 at 6:36 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
The main think that makes ChimeraX sluggish when moving individual models with the mouse for doing rigid-body fitting is full or soft lighting modes that cast ambient shadows. If you switch to simple lighting using the Home toolbar icon or command "light simple" then graphics updating will be many times faster. The reason for the slow graphics with ambient shadows is that it is recomputing shadows from 64 different directions when you move one model relative to the other because the models cast shadows on each other. I am thinking of having ChimeraX issue warning when graphics becomes slow due to continuous updating of ambient shadows so it will be more obvious how you fix it.
Tom
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, I have filed a bug report, with a description as well as the PDB file that I was using when I chanced upon this observation. Looking forward to hearing from you. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Mon, Aug 2, 2021 at 7:08 PM Tom Goddard <goddard@sonic.net> wrote:
And did using simple lighting fix the slow rigid-body fitting? If not, is the slowness when you are trying to move one model with the mouse. If so, what graphics card are you using? ChimeraX should easily move a million atoms pretty smoothly with a mid-range graphics card. If you want to further discuss this probably good to use ChimeraX menu Help / Report a Bug so we get you computer system info.
Tom
On Aug 2, 2021, at 10:58 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Tom, I was aware of this and had therefore done exactly what you suggested! :) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Aug 2, 2021 at 6:36 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
The main think that makes ChimeraX sluggish when moving individual models with the mouse for doing rigid-body fitting is full or soft lighting modes that cast ambient shadows. If you switch to simple lighting using the Home toolbar icon or command "light simple" then graphics updating will be many times faster. The reason for the slow graphics with ambient shadows is that it is recomputing shadows from 64 different directions when you move one model relative to the other because the models cast shadows on each other. I am thinking of having ChimeraX issue warning when graphics becomes slow due to continuous updating of ambient shadows so it will be more obvious how you fix it.
Tom
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Pranav, Got it. The 3 million atom rotavirus capsid 3kz4 rotates pretty well for me on a MacBook Pro laptop, maybe 10 frames/second with simple lighting, so I am surprised that with your much more powerful Nvidia RTX 2080 graphics it is slow. Let's discuss further via your bug report https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4997 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4997> The problem with your CA only PDB file seems to be a bug in ChimeraX that we will fix, here's the bug report https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4991 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4991> but it works correctly for me if you save in mmCIF format. Tom
On Aug 3, 2021, at 3:53 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
I have filed a bug report, with a description as well as the PDB file that I was using when I chanced upon this observation. Looking forward to hearing from you.
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Aug 2, 2021 at 7:08 PM Tom Goddard <goddard@sonic.net> wrote:
And did using simple lighting fix the slow rigid-body fitting? If not, is the slowness when you are trying to move one model with the mouse. If so, what graphics card are you using? ChimeraX should easily move a million atoms pretty smoothly with a mid-range graphics card. If you want to further discuss this probably good to use ChimeraX menu Help / Report a Bug so we get you computer system info.
Tom
On Aug 2, 2021, at 10:58 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Tom, I was aware of this and had therefore done exactly what you suggested! :) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Aug 2, 2021 at 6:36 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
The main think that makes ChimeraX sluggish when moving individual models with the mouse for doing rigid-body fitting is full or soft lighting modes that cast ambient shadows. If you switch to simple lighting using the Home toolbar icon or command "light simple" then graphics updating will be many times faster. The reason for the slow graphics with ambient shadows is that it is recomputing shadows from 64 different directions when you move one model relative to the other because the models cast shadows on each other. I am thinking of having ChimeraX issue warning when graphics becomes slow due to continuous updating of ambient shadows so it will be more obvious how you fix it.
Tom
On Aug 2, 2021, at 7:15 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
Ilias Miroslav, doc. RNDr., PhD. -
Pranav Shah -
Tom Goddard