Dear Expert,
at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help.
Kind regards,
Maciek
Hi Maciek, Glad you like ChimeraX!
I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms. If you show the atoms, then all of the H-bonds will be shown.
You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:
nuc atoms
If you only want to show all atoms for part of the molecule you can select that part before clicking the icon. You can also make the command apply to selection, for example:
nuc sel atoms
See "nucleotides" command (I was using "nuc" above for short): https://rbvi.ucsf.edu/chimerax/docs/user/commands/nucleotides.html
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 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek
Hi Elaine,
thank you for your response! Unfortunately, this is a thing I have already tried. And atoms are even selected and highlighted after hbonds calculation. I wonder if hydrogen atoms need to be added? Or the problem lies in the fact that user-defined assembly is loaded and only intra-submodel hbonds are displayed?
Once again, thank you for your time!
Best,
Maciek ________________________________ Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: czwartek, 7 października 2021 18:24 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, Glad you like ChimeraX!
I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms. If you show the atoms, then all of the H-bonds will be shown.
You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:
nuc atoms
If you only want to show all atoms for part of the molecule you can select that part before clicking the icon. You can also make the command apply to selection, for example:
nuc sel atoms
See "nucleotides" command (I was using "nuc" above for short): https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fnucleotides.html&data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C851e235d140043e077ba08d989aefa22%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637692207413181946%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=02yyckn52a%2Fe0tRdK29QYpHOf5yAOI9TX9to7FmoUqU%3D&reserved=0
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 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek
Hi Maciek, If you show all atoms, it will show all the H-bonds that it reports, even if you don't have hydrogens. However, there is one more issue. Frequently there are two H-bond lines exactly in the same place because both donor -> acceptor and acceptor -> donor are both possible between the same two heavy (nonhydrogen) atoms. You can see this if you write details to the Log or a file. If you really really want to see a separate line for each possible predicted H-bond, however, you could add hydrogens first. Then even though the same two heavy atoms could be each both donor and acceptor, the lines will be drawn to the specific hydrogens instead of to the heavy atoms. However, you have may fewer total H-bonds predicted when explicit hydrogens are present, because then only their positions are used, instead of all the possible positions of inferred hydrogens. 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 8, 2021, at 1:16 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine,
thank you for your response! Unfortunately, this is a thing I have already tried. And atoms are even selected and highlighted after hbonds calculation. I wonder if hydrogen atoms need to be added? Or the problem lies in the fact that user-defined assembly is loaded and only intra-submodel hbonds are displayed?
Once again, thank you for your time!
Best,
Maciek Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: czwartek, 7 października 2021 18:24 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, Glad you like ChimeraX!
I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms. If you show the atoms, then all of the H-bonds will be shown.
You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:
nuc atoms
If you only want to show all atoms for part of the molecule you can select that part before clicking the icon. You can also make the command apply to selection, for example:
nuc sel atoms
See "nucleotides" command (I was using "nuc" above for short): https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fnucleotides.html&data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C851e235d140043e077ba08d989aefa22%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637692207413181946%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=02yyckn52a%2Fe0tRdK29QYpHOf5yAOI9TX9to7FmoUqU%3D&reserved=0
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 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine,
thank you, but I am afraid it does not solve my issue - having 87 calculated hbonds and done the steps you mentioned, only one is visualised. Moreover, the one is located on the same RNA strand, while in ChimeraX I can clearly see that there are base pairs between two strands. I am using stable version 1.2.5. May I send you some screenshots with models and options just before hbonds calculation? I would be grateful for your permission.
Kind regards,
Maciek ________________________________ Od: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu w imieniu użytkownika Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Wysłane: piątek, 8 października 2021 18:01 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, If you show all atoms, it will show all the H-bonds that it reports, even if you don't have hydrogens. However, there is one more issue. Frequently there are two H-bond lines exactly in the same place because both donor -> acceptor and acceptor -> donor are both possible between the same two heavy (nonhydrogen) atoms. You can see this if you write details to the Log or a file. If you really really want to see a separate line for each possible predicted H-bond, however, you could add hydrogens first. Then even though the same two heavy atoms could be each both donor and acceptor, the lines will be drawn to the specific hydrogens instead of to the heavy atoms. However, you have may fewer total H-bonds predicted when explicit hydrogens are present, because then only their positions are used, instead of all the possible positions of inferred hydrogens. 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 8, 2021, at 1:16 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine,
thank you for your response! Unfortunately, this is a thing I have already tried. And atoms are even selected and highlighted after hbonds calculation. I wonder if hydrogen atoms need to be added? Or the problem lies in the fact that user-defined assembly is loaded and only intra-submodel hbonds are displayed?
Once again, thank you for your time!
Best,
Maciek Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: czwartek, 7 października 2021 18:24 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, Glad you like ChimeraX!
I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms. If you show the atoms, then all of the H-bonds will be shown.
You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:
nuc atoms
If you only want to show all atoms for part of the molecule you can select that part before clicking the icon. You can also make the command apply to selection, for example:
nuc sel atoms
See "nucleotides" command (I was using "nuc" above for short): https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fnucleotides.html&data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C6a5d2c4050654a24174408d98a752b33%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637693058656581461%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=J%2FYOs1WQCenLDXbc2jW1UBcMXaiQY18QQpKcvN4sR78%3D&reserved=0
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 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
Hi Maciek, In general when you believe there is a bug, please use ChimeraX menu: Help... Report a Bug and attach either a session file or just the PDB file if that is enough to reproduce the problem. In the bug report form please also include a short a description of what you did and what the problem is, and your e-mail address if you want feedback from that. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2021, at 10:24 AM, Maciej Basczok mmaciej.basczok@amu.edu.pl wrote:
Hi Elaine,
thank you, but I am afraid it does not solve my issue - having 87 calculated hbonds and done the steps you mentioned, only one is visualised. Moreover, the one is located on the same RNA strand, while in ChimeraX I can clearly see that there are base pairs between two strands. I am using stable version 1.2.5. May I send you some screenshots with models and options just before hbonds calculation? I would be grateful for your permission.
Kind regards,
Maciek Od: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu w imieniu użytkownika Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Wysłane: piątek, 8 października 2021 18:01 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, If you show all atoms, it will show all the H-bonds that it reports, even if you don't have hydrogens. However, there is one more issue. Frequently there are two H-bond lines exactly in the same place because both donor -> acceptor and acceptor -> donor are both possible between the same two heavy (nonhydrogen) atoms. You can see this if you write details to the Log or a file. If you really really want to see a separate line for each possible predicted H-bond, however, you could add hydrogens first. Then even though the same two heavy atoms could be each both donor and acceptor, the lines will be drawn to the specific hydrogens instead of to the heavy atoms. However, you have may fewer total H-bonds predicted when explicit hydrogens are present, because then only their positions are used, instead of all the possible positions of inferred hydrogens. 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 8, 2021, at 1:16 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine,
thank you for your response! Unfortunately, this is a thing I have already tried. And atoms are even selected and highlighted after hbonds calculation. I wonder if hydrogen atoms need to be added? Or the problem lies in the fact that user-defined assembly is loaded and only intra-submodel hbonds are displayed?
Once again, thank you for your time!
Best,
Maciek Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: czwartek, 7 października 2021 18:24 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, Glad you like ChimeraX!
I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms. If you show the atoms, then all of the H-bonds will be shown.
You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:
nuc atoms
If you only want to show all atoms for part of the molecule you can select that part before clicking the icon. You can also make the command apply to selection, for example:
nuc sel atoms
See "nucleotides" command (I was using "nuc" above for short): https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fnucleotides.html&data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C6a5d2c4050654a24174408d98a752b33%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637693058656581461%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=J%2FYOs1WQCenLDXbc2jW1UBcMXaiQY18QQpKcvN4sR78%3D&reserved=0
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 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
All right, I will surely do it, thank you!
Best,
Maciek ________________________________ Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: piątek, 8 października 2021 20:03 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, In general when you believe there is a bug, please use ChimeraX menu: Help... Report a Bug and attach either a session file or just the PDB file if that is enough to reproduce the problem. In the bug report form please also include a short a description of what you did and what the problem is, and your e-mail address if you want feedback from that. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2021, at 10:24 AM, Maciej Basczok mmaciej.basczok@amu.edu.pl wrote:
Hi Elaine,
thank you, but I am afraid it does not solve my issue - having 87 calculated hbonds and done the steps you mentioned, only one is visualised. Moreover, the one is located on the same RNA strand, while in ChimeraX I can clearly see that there are base pairs between two strands. I am using stable version 1.2.5. May I send you some screenshots with models and options just before hbonds calculation? I would be grateful for your permission.
Kind regards,
Maciek Od: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu w imieniu użytkownika Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Wysłane: piątek, 8 października 2021 18:01 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, If you show all atoms, it will show all the H-bonds that it reports, even if you don't have hydrogens. However, there is one more issue. Frequently there are two H-bond lines exactly in the same place because both donor -> acceptor and acceptor -> donor are both possible between the same two heavy (nonhydrogen) atoms. You can see this if you write details to the Log or a file. If you really really want to see a separate line for each possible predicted H-bond, however, you could add hydrogens first. Then even though the same two heavy atoms could be each both donor and acceptor, the lines will be drawn to the specific hydrogens instead of to the heavy atoms. However, you have may fewer total H-bonds predicted when explicit hydrogens are present, because then only their positions are used, instead of all the possible positions of inferred hydrogens. 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 8, 2021, at 1:16 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine,
thank you for your response! Unfortunately, this is a thing I have already tried. And atoms are even selected and highlighted after hbonds calculation. I wonder if hydrogen atoms need to be added? Or the problem lies in the fact that user-defined assembly is loaded and only intra-submodel hbonds are displayed?
Once again, thank you for your time!
Best,
Maciek Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: czwartek, 7 października 2021 18:24 Do: Maciej Basczok mmaciej.basczok@amu.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] hbonds display problem
Hi Maciek, Glad you like ChimeraX!
I'm guessing that you are displaying the RNA as simplified objects like tubes and slabs instead of atoms. If you show the atoms, then all of the H-bonds will be shown.
You can do this by clicking the all-atom icon in the Nucleotides tab of the toolbar across the top, or command:
nuc atoms
If you only want to show all atoms for part of the molecule you can select that part before clicking the icon. You can also make the command apply to selection, for example:
nuc sel atoms
See "nucleotides" command (I was using "nuc" above for short): https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fnucleotides.html&data=04%7C01%7Cmmaciej.basczok%40amu.edu.pl%7C7b2602ae86aa41cf2e5e08d98a85ecbf%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637693130503082387%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=v2EMwdP61wd5nETFFMtKeFGoCK6l66o2FRdcaiEx1%2FA%3D&reserved=0
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 7, 2021, at 1:13 AM, Maciej Basczok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl....
participants (2)
-
Elaine Meng -
Maciej Basczok