Does getcrd return coordinates in pixels or in angstroms?
Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide<https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/local...>). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/getcrd.html>). KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.
Hi Sam, XYZ coordinates such as from "getcrd" are in the physical distance units of your dataset, most likely angstroms (not pixels or grid indices). Also (looking in that cryosparc guide) if you were also using "measure center," note that the ChimeraX implementation of "measure center" reports the center location in both grid indices and xyz coordinates. Example Log contents from ChimeraX: measure center #2 Center of mass grid index for 2gbp map 4 = (10.83, 9.99, 11.02) Center of mass xyz scene coordinates for 2gbp map 4 = (37.37, 30.58, 49.61) 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 24, 2023, at 3:33 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)). KR, Sam
Hi Elaine, Thanks for the information. Would it be possible to update the documentation for these commands to specify that this is how the units are returned? KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 24 August 2023 21:09 To: Samuel Haysom <Samuel.Haysom@SoseiHeptares.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Does getcrd return coordinates in pixels or in angstroms? Hi Sam, XYZ coordinates such as from "getcrd" are in the physical distance units of your dataset, most likely angstroms (not pixels or grid indices). Also (looking in that cryosparc guide) if you were also using "measure center," note that the ChimeraX implementation of "measure center" reports the center location in both grid indices and xyz coordinates. Example Log contents from ChimeraX: measure center #2 Center of mass grid index for 2gbp map 4 = (10.83, 9.99, 11.02) Center of mass xyz scene coordinates for 2gbp map 4 = (37.37, 30.58, 49.61) 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 24, 2023, at 3:33 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)). KR, Sam
Hi Sam, It depends on whatever distance units your data are in. So if your data are in nanometers it will be in nanometers. Getcrd is for getting the coordinates of atoms which are normally in Angstroms, but it is not inherent to the functionality. Getcrd has nothing to do with maps, so there is no reason somebody would expect it to refer to the grid indices of a map. In the cryosparc page you mentioned earlier, it was used to get the coordinates of a marker, which is essentially a fake atom without any data from the map, even if you defined that marker originally from a map. Elaine
On Aug 25, 2023, at 5:28 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks for the information. Would it be possible to update the documentation for these commands to specify that this is how the units are returned?
KR, Sam
Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 24 August 2023 21:09 To: Samuel Haysom <Samuel.Haysom@SoseiHeptares.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Does getcrd return coordinates in pixels or in angstroms?
Hi Sam, XYZ coordinates such as from "getcrd" are in the physical distance units of your dataset, most likely angstroms (not pixels or grid indices).
Also (looking in that cryosparc guide) if you were also using "measure center," note that the ChimeraX implementation of "measure center" reports the center location in both grid indices and xyz coordinates. Example Log contents from ChimeraX:
measure center #2
Center of mass grid index for 2gbp map 4 = (10.83, 9.99, 11.02) Center of mass xyz scene coordinates for 2gbp map 4 = (37.37, 30.58, 49.61)
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 24, 2023, at 3:33 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)). KR, Sam
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I see what you mean. Maybe just a sentence to say that the coordinate are given in distance units determined by the underlying data but I understand if you think this is so vague its not worth adding. -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 25 August 2023 16:01 To: Samuel Haysom <Samuel.Haysom@SoseiHeptares.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Does getcrd return coordinates in pixels or in angstroms? Hi Sam, It depends on whatever distance units your data are in. So if your data are in nanometers it will be in nanometers. Getcrd is for getting the coordinates of atoms which are normally in Angstroms, but it is not inherent to the functionality. Getcrd has nothing to do with maps, so there is no reason somebody would expect it to refer to the grid indices of a map. In the cryosparc page you mentioned earlier, it was used to get the coordinates of a marker, which is essentially a fake atom without any data from the map, even if you defined that marker originally from a map. Elaine
On Aug 25, 2023, at 5:28 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks for the information. Would it be possible to update the documentation for these commands to specify that this is how the units are returned?
KR, Sam
Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 24 August 2023 21:09 To: Samuel Haysom <Samuel.Haysom@SoseiHeptares.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Does getcrd return coordinates in pixels or in angstroms?
Hi Sam, XYZ coordinates such as from "getcrd" are in the physical distance units of your dataset, most likely angstroms (not pixels or grid indices).
Also (looking in that cryosparc guide) if you were also using "measure center," note that the ChimeraX implementation of "measure center" reports the center location in both grid indices and xyz coordinates. Example Log contents from ChimeraX:
measure center #2
Center of mass grid index for 2gbp map 4 = (10.83, 9.99, 11.02) Center of mass xyz scene coordinates for 2gbp map 4 = (37.37, 30.58, 49.61)
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 24, 2023, at 3:33 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)). KR, Sam
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participants (2)
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Elaine Meng -
Samuel Haysom