Generate a volume from a shape
Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. Thank you in advance, Guillaume 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
Hi Guillaume - could it be a simple typo? `volume onesmask` works for me with that syntax Cheers Oli
On Sep 18, 2025, at 10:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with:
shape sphere radius 30 center cofr
I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this:
volume onemask #2 ongrid #1
At which point I get this error: Expected a density maps specifier or a keyword
The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem.
Thank you in advance,
Guillaume
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/
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Hey Guillaume! I think its because the sphere isn’t a density volume until you do the following, then resample on grid. volume onesmask #2 fullMap true valueType float32 volume resample [newspheredesity] ongrid #1 But I might be answering the wrong question 😊 Kako From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, 18 September 2025 at 15:10 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Generate a volume from a shape Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. Thank you in advance, Guillaume 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
Hi Oli and Kako, Both your suggestions fixed it, thank you! What you suggest Kako is functionally equivalent, but can be done in a single step with adequate options to 'volume onesmask' (and with 'ones' plural in this command's name, as Oli points out!). I indeed had this typo all along, which means enough ChimeraX for me for today... Cheers, Guillaume ________________________________ From: Kako Stapleton <Kako.Stapleton@glasgow.ac.uk> Sent: Thursday, September 18, 2025 4:34:58 PM To: Guillaume Gaullier; ChimeraX Users Help Subject: Re: Generate a volume from a shape Hey Guillaume! I think its because the sphere isn’t a density volume until you do the following, then resample on grid. volume onesmask #2 fullMap true valueType float32 volume resample [newspheredesity] ongrid #1 But I might be answering the wrong question 😊 Kako From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, 18 September 2025 at 15:10 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Generate a volume from a shape Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. Thank you in advance, Guillaume 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 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.
participants (3)
-
Guillaume Gaullier -
Kako Stapleton -
Oliver Clarke