Hi Elaine, Thanks for your prompt reply. For instance, I would like to show the structure in a ribbon representation; however, with certain residues shown as atoms (one of them for instance would be residue 47 in chain P). When I have a ribbon representation and I select /P:47, the command for atom presentation of this residue is not working... Picture 1 is what I have, picture 2 is what I would like to show. Hope that makes sense... Thanks, Hana On 12/17/21, 12:23, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. Hello Hana, I can't tell what you have selected, so it is impossible to say. Remember, the "sel" in the command means the current selection. Do you have any atoms selected? Also, when I open structure 7ovr in ChimeraX, all of the atoms are shown already. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 17, 2021, at 9:18 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > To whom it may concern, > > The command “show sel atoms’ does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine. > > Would you know what could be the cause? > > Thanks, > Hana

Hi Elaine, Thanks for highlighting this; I wasn’t sure how to check if they're present. Best, Hana On 12/17/21, 12:37, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. Hi Hana, This structure is missing many (all?) side chains. The ones you are trying to show simply are not in the structure. For example if you download the PDB format from RCSB you can see a lot of atoms listed under REMARK 470 MISSING ATOM. Best, Elaine > On Dec 17, 2021, at 9:27 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi Elaine, > > Thanks for your prompt reply. For instance, I would like to show the structure in a ribbon representation; however, with certain residues shown as atoms (one of them for instance would be residue 47 in chain P). When I have a ribbon representation and I select /P:47, the command for atom presentation of this residue is not working... > > Picture 1 is what I have, picture 2 is what I would like to show. > > Hope that makes sense... > > Thanks, > Hana > > On 12/17/21, 12:23, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: > > CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. > > > Hello Hana, > I can't tell what you have selected, so it is impossible to say. Remember, the "sel" in the command means the current selection. Do you have any atoms selected? > > Also, when I open structure 7ovr in ChimeraX, all of the atoms are shown already. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Dec 17, 2021, at 9:18 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: >> >> To whom it may concern, >> >> The command “show sel atoms’ does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine. >> >> Would you know what could be the cause? >> >> Thanks, >> Hana > > > <picture 1.png><picture 2.png>_______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Hi Elaine, That works, thanks! Best, Hana On 12/17/21, 12:48, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. Besides looking at the PDB file with a text-editor, you can use the ChimeraX "sticks" preset to show all the atoms in a structure as sticks. E.g. menu: Presets... Initial Styles... sticks, or command "preset sticks" Elaine > On Dec 17, 2021, at 9:38 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi Elaine, > > Thanks for highlighting this; I wasn’t sure how to check if they're present. > > Best, > Hana > > > On 12/17/21, 12:37, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: > > CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. > > > Hi Hana, > This structure is missing many (all?) side chains. The ones you are trying to show simply are not in the structure. For example if you download the PDB format from RCSB you can see a lot of atoms listed under REMARK 470 MISSING ATOM. > Best, > Elaine > > >> On Dec 17, 2021, at 9:27 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: >> >> Hi Elaine, >> >> Thanks for your prompt reply. For instance, I would like to show the structure in a ribbon representation; however, with certain residues shown as atoms (one of them for instance would be residue 47 in chain P). When I have a ribbon representation and I select /P:47, the command for atom presentation of this residue is not working... >> >> Picture 1 is what I have, picture 2 is what I would like to show. >> >> Hope that makes sense... >> >> Thanks, >> Hana >> >> On 12/17/21, 12:23, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: >> >> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. >> >> >> Hello Hana, >> I can't tell what you have selected, so it is impossible to say. Remember, the "sel" in the command means the current selection. Do you have any atoms selected? >> >> Also, when I open structure 7ovr in ChimeraX, all of the atoms are shown already. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Dec 17, 2021, at 9:18 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: >>> >>> To whom it may concern, >>> >>> The command “show sel atoms’ does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine. >>> >>> Would you know what could be the cause? >>> >>> Thanks, >>> Hana >> >> >> <picture 1.png><picture 2.png>_______________________________________________ >> 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 >