Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3. Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran
Hello Ran, In your screenshot, the @ symbol is missing in the commands. The atom specification #1:1-2 in the screenshot means "model 1, residues 1-2", but this molecule has no residues because it is not a polymer. This is why the resulting selection is empty. I suspect the command you mention in your email wouldn’t work either, because it has both : and @ (or maybe the : selector would just be ignored since you provide no residue name or number, and since doing so results in an empty selection but no error based on your screenshot). Try this instead: sel #1@1-2 (you might have to adjust the atom numbers to select the ones you want). I hope this helps, Guillaume On 2 Apr 2024, at 16:46, 洪冉 via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3. Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran <Snipaste_2024-04-02_22-39-03.jpg> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. <Snipaste_2024-04-02_22-39-03.jpg>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hello Ran, As suggested by what is shown in your Log when you use "info sel" (which I can partially see in the screenshot) you need to use @@ to indicate an attribute, as well as the attribute name, in this case serial_number. I think you want something like this, to select serial numbers 1-3: select @@serial_number>0 & @@serial_number<4 See the help on specifying atoms by attribute value: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> You don't need to give model number because there is only one model. I believe that Guillame's suggestion is not right because using a single @ means the name of the atom, not the serial number. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 2, 2024, at 8:34 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Ran, In your screenshot, the @ symbol is missing in the commands. The atom specification #1:1-2 in the screenshot means "model 1, residues 1-2", but this molecule has no residues because it is not a polymer. This is why the resulting selection is empty.
I suspect the command you mention in your email wouldn’t work either, because it has both : and @ (or maybe the : selector would just be ignored since you provide no residue name or number, and since doing so results in an empty selection but no error based on your screenshot). Try this instead: sel #1@1-2 (you might have to adjust the atom numbers to select the ones you want). I hope this helps, Guillaume
On 2 Apr 2024, at 16:46, 洪冉 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3.
Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran
<Snipaste_2024-04-02_22-39-03.jpg>
Thank you for these precisions Elaine. I always work with proteins and nucleic acids and always select by residue number or atom name, so I didn’t know that a single @ would not work to select by atom number. Cheers, Guillaume On 2 Apr 2024, at 17:44, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hello Ran, As suggested by what is shown in your Log when you use "info sel" (which I can partially see in the screenshot) you need to use @@ to indicate an attribute, as well as the attribute name, in this case serial_number. I think you want something like this, to select serial numbers 1-3: select @@serial_number>0 & @@serial_number<4 See the help on specifying atoms by attribute value: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> You don't need to give model number because there is only one model. I believe that Guillame's suggestion is not right because using a single @ means the name of the atom, not the serial number. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 2, 2024, at 8:34 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello Ran, In your screenshot, the @ symbol is missing in the commands. The atom specification #1:1-2 in the screenshot means "model 1, residues 1-2", but this molecule has no residues because it is not a polymer. This is why the resulting selection is empty. I suspect the command you mention in your email wouldn’t work either, because it has both : and @ (or maybe the : selector would just be ignored since you provide no residue name or number, and since doing so results in an empty selection but no error based on your screenshot). Try this instead: sel #1@1-2 (you might have to adjust the atom numbers to select the ones you want). I hope this helps, Guillaume On 2 Apr 2024, at 16:46, 洪冉 via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3. Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran <Snipaste_2024-04-02_22-39-03.jpg> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
participants (3)
-
Elaine Meng -
Guillaume Gaullier -
洪冉