[ccp4bb] saving coordinates with respect to map in ChimeraX
Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] saving coordinates with respect to map in ChimeraX
Hi Faisal, This is really a question for the ChimeraX-users list (chimerax-us...@cgl.ucsf.edu). But the quick run-down: using the File/Save dialogue, you'll see a checkbox with "Save relative to model: " and then a drop-down menu. Just choose the map in the drop-down menu, and you should get the result you want. Best regards, Tristan From: CCP4 bulletin board on behalf of khaja faisal tarique Sent: 28 June 2021 09:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] saving coordinates with respect to map in ChimeraX Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] saving coordinates with respect to map in ChimeraX
Hi Tristan I have posted my question in ChimeraX mailing list as well and waiting for their reply. What you are suggesting is for Chimera. I dont see any such option in ChimeraX. That save relative to section does not appear here or may be there is a different way of saving model relative to map in ChimeraX. Please correct me if I am wrong. Faisal On Mon, 28 Jun 2021, 2:44 pm Tristan Croll, wrote: > Hi Faisal, > > This is really a question for the ChimeraX-users list ( > chimerax-us...@cgl.ucsf.edu). But the quick run-down: using the File/Save > dialogue, you'll see a checkbox with "Save relative to model: " and then a > drop-down menu. Just choose the map in the drop-down menu, and you should > get the result you want. > > Best regards, > Tristan > -- > *From:* CCP4 bulletin board on behalf of khaja > faisal tarique > *Sent:* 28 June 2021 09:43 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] saving coordinates with respect to map in ChimeraX > > Hello everyone > > While doing rigid body fit we know that after placing the coordinate to > its correct position we can save it with respect to the map. Does anyone > know if a similar feature exists in ChimeraX ? Is there a way where the > coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? > > Thank you > > -- > Faisal Tarique Khaja > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] saving coordinates with respect to map in ChimeraX
Hi Faisal, Are you using the latest version (1.2.5)? That should give you a dialog that looks something like this. Best regards, Tristan [cid:c60bb51b-6f11-4646-9800-6ce976abc3f0] From: khaja faisal tarique Sent: 28 June 2021 10:29 To: Tristan Croll Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] saving coordinates with respect to map in ChimeraX Hi Tristan I have posted my question in ChimeraX mailing list as well and waiting for their reply. What you are suggesting is for Chimera. I dont see any such option in ChimeraX. That save relative to section does not appear here or may be there is a different way of saving model relative to map in ChimeraX. Please correct me if I am wrong. Faisal On Mon, 28 Jun 2021, 2:44 pm Tristan Croll, mailto:ti...@cam.ac.uk>> wrote: Hi Faisal, This is really a question for the ChimeraX-users list (chimerax-us...@cgl.ucsf.edu<mailto:chimerax-us...@cgl.ucsf.edu>). But the quick run-down: using the File/Save dialogue, you'll see a checkbox with "Save relative to model: " and then a drop-down menu. Just choose the map in the drop-down menu, and you should get the result you want. Best regards, Tristan From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of khaja faisal tarique mailto:khajafaisaltari...@gmail.com>> Sent: 28 June 2021 09:43 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] saving coordinates with respect to map in ChimeraX Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] saving coordinates with respect to map in ChimeraX
It's not important, but I am curious what 'Save relative to model/map' actually means in that widget. Is it just a case of copying the relevant CRYST1 card? I think Faisal is asking how to save new/modified coordinates but probably I misunderstood... Cheers, Jon.C. Sent from ProtonMail mobile Original Message On 28 Jun 2021, 10:32, Tristan Croll wrote: > Hi Faisal, > > Are you using the latest version (1.2.5)? That should give you a dialog that > looks something like this. > > Best regards, > Tristan > > --- > > From: khaja faisal tarique > Sent: 28 June 2021 10:29 > To: Tristan Croll > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] saving coordinates with respect to map in ChimeraX > > Hi Tristan > > I have posted my question in ChimeraX mailing list as well and waiting for > their reply. > > What you are suggesting is for Chimera. I dont see any such option in > ChimeraX. That save relative to section does not appear here or may be there > is a different way of saving model relative to map in ChimeraX. > > Please correct me if I am wrong. > > Faisal > > On Mon, 28 Jun 2021, 2:44 pm Tristan Croll, wrote: > >> Hi Faisal, >> >> This is really a question for the ChimeraX-users list >> (chimerax-us...@cgl.ucsf.edu). But the quick run-down: using the File/Save >> dialogue, you'll see a checkbox with "Save relative to model: " and then a >> drop-down menu. Just choose the map in the drop-down menu, and you should >> get the result you want. >> >> Best regards, >> Tristan >> >> --------------------------- >> >> From: CCP4 bulletin board on behalf of khaja faisal >> tarique >> Sent: 28 June 2021 09:43 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] saving coordinates with respect to map in ChimeraX >> >> Hello everyone >> >> While doing rigid body fit we know that after placing the coordinate to its >> correct position we can save it with respect to the map. Does anyone know if >> a similar feature exists in ChimeraX ? Is there a way where the coordinates >> .pdb/cif file can be saved with respect to its map in ChimeraX ? >> >> Thank you >> >> -- >> >> Faisal Tarique Khaja >> >> --- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > --- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] saving coordinates with respect to map in ChimeraX
The way things generally work in ChimeraX is that each model/map is stored internally with its original coordinates unchanged, along with one or more transforms placing it into scene coordinates. Saving model A relative to model/map B means that the coordinates to be saved are transformed such that A overlays with the original B in the same way you see in the scene. That can get a little complex if both model and map have been moved... if you just want to save things exactly as they are shown, uncheck the checkbox entirely and everything will be written in scene coordinates. -- Tristan From: Jon Cooper Sent: 28 June 2021 13:43 To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] saving coordinates with respect to map in ChimeraX It's not important, but I am curious what 'Save relative to model/map' actually means in that widget. Is it just a case of copying the relevant CRYST1 card? I think Faisal is asking how to save new/modified coordinates but probably I misunderstood... Cheers, Jon.C. Sent from ProtonMail mobile Original Message On 28 Jun 2021, 10:32, Tristan Croll < ti...@cam.ac.uk> wrote: Hi Faisal, Are you using the latest version (1.2.5)? That should give you a dialog that looks something like this. Best regards, Tristan [cid:c60bb51b-6f11-4646-9800-6ce976abc3f0] From: khaja faisal tarique Sent: 28 June 2021 10:29 To: Tristan Croll Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] saving coordinates with respect to map in ChimeraX Hi Tristan I have posted my question in ChimeraX mailing list as well and waiting for their reply. What you are suggesting is for Chimera. I dont see any such option in ChimeraX. That save relative to section does not appear here or may be there is a different way of saving model relative to map in ChimeraX. Please correct me if I am wrong. Faisal On Mon, 28 Jun 2021, 2:44 pm Tristan Croll, mailto:ti...@cam.ac.uk>> wrote: Hi Faisal, This is really a question for the ChimeraX-users list (chimerax-us...@cgl.ucsf.edu<mailto:chimerax-us...@cgl.ucsf.edu>). But the quick run-down: using the File/Save dialogue, you'll see a checkbox with "Save relative to model: " and then a drop-down menu. Just choose the map in the drop-down menu, and you should get the result you want. Best regards, Tristan From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of khaja faisal tarique mailto:khajafaisaltari...@gmail.com>> Sent: 28 June 2021 09:43 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] saving coordinates with respect to map in ChimeraX Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
