Re: [Chimera-users] making composite map using vop maximum command
Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users@cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time. Here is the ChimeraX "volume maximum" help link: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#maximum> For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command: vol max #2,3 ... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them. 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 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks
Dear Elaine Thanks for the information. I was able to use Vop max in ChimeraX and vop maximum in Chimera. As stated, the goal is to make a composite map by combining two locally refined maps. However, when I used Vop max, only one map was dominating such that the composite map is the same as the one of the maps. I think I probably have to scale the maps. Would you be able to tell me how exactly I need to scale two maps and combine? Thanks for your help Best Yuro Yuichiro H. Takagi, Ph.D. Associate Professor Scientific advisor for cryo-EM Department of Biochemistry and Molecular Biology Indiana University School of Medicine https://twitter.com/LabTakagi
On Aug 7, 2023, at 5:33 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users@cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time.
Here is the ChimeraX "volume maximum" help link: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command:
vol max #2,3
... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them.
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 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks
Dear Yuro, Please see the ChimeraX "volume maximum" help link below. There is a "scaleFactors" option for scaling the maps included in that command. However, I cannot tell you what value(s) are needed for your specific data. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#maximum> 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 10, 2023, at 10:30 AM, Takagi, Yuichiro via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine Thanks for the information. I was able to use Vop max in ChimeraX and vop maximum in Chimera. As stated, the goal is to make a composite map by combining two locally refined maps. However, when I used Vop max, only one map was dominating such that the composite map is the same as the one of the maps. I think I probably have to scale the maps. Would you be able to tell me how exactly I need to scale two maps and combine? Thanks for your help Best Yuro
Yuichiro H. Takagi, Ph.D. Associate Professor Scientific advisor for cryo-EM Department of Biochemistry and Molecular Biology Indiana University School of Medicine https://twitter.com/LabTakagi
On Aug 7, 2023, at 5:33 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.
Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users@cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time.
Here is the ChimeraX "volume maximum" help link: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command:
vol max #2,3
... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them.
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 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks
Dear Elaine I don’t understand the instruction - it’s a bit too abstract for me to write a syntax - That is why I am positing this site. It would be nice if syntax comes with some kind of actual examples in chimera instructions. Now let’s say, I have two maps A and B by which I want to make a composite map. Scale factor of map A is 1 and that of B is 2. What would be the syntax for this using vop maximum ? Thanks for your help Best Yuro
Dear Yuro, Please see the ChimeraX "volume maximum" help link below. There is a "scaleFactors" option for scaling the maps included in that command. However, I cannot tell you what value(s) are needed for your specific data.
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
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 10, 2023, at 10:30 AM, Takagi, Yuichiro via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine Thanks for the information. I was able to use Vop max in ChimeraX and vop maximum in Chimera. As stated, the goal is to make a composite map by combining two locally refined maps. However, when I used Vop max, only one map was dominating such that the composite map is the same as the one of the maps. I think I probably have to scale the maps. Would you be able to tell me how exactly I need to scale two maps and combine? Thanks for your help Best Yuro
Yuichiro H. Takagi, Ph.D. Associate Professor Scientific advisor for cryo-EM Department of Biochemistry and Molecular Biology Indiana University School of Medicine https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.co...
On Aug 7, 2023, at 5:33 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.
Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users@cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time.
Here is the ChimeraX "volume maximum" help link: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command:
vol max #2,3
... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them.
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 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks
Dear Yuro, Once you get more familiar with how to read the help it is not that complicated. Example ChimeraX command for maps #1 and #2 you want to scale x1 and x2: vol max #1,2 scaleFactors 1,2 The syntax is shown in the "volume max" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#maximum> volume maximum volume-spec [ scaleFactors f1,f2,... | fromlevels ] [ onGrid gridmap ] [ spacing S | Sx,Sy,Sz ] [ boundingGrid true | false ] [ gridStep N | Nx,Ny,Nz ] [ gridSubregion i1,j1,k1,i2,j2,k2 | all ] [ valueType value-type ] [ hideMaps true | false ] new-map-options You should read the help page because there are many options and you might want to use some of them. However, they are just options, i.e. you don't need to include them if you just want the default behaviors. The reason we have help pages is that we don't have time/resources to fully describe everything in every possible command each user needs in separate replies on this mailing list. And there is even a help page on how to read these usage lines, which explains the meaning of "[ ]" (= an option), " | " (= separator between possible values of the option), etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html> 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 10, 2023, at 11:39 AM, Takagi, Yuichiro via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine I don’t understand the instruction - it’s a bit too abstract for me to write a syntax - That is why I am positing this site. It would be nice if syntax comes with some kind of actual examples in chimera instructions.
Now let’s say, I have two maps A and B by which I want to make a composite map. Scale factor of map A is 1 and that of B is 2. What would be the syntax for this using vop maximum ?
Thanks for your help Best Yuro
Dear Yuro, Please see the ChimeraX "volume maximum" help link below. There is a "scaleFactors" option for scaling the maps included in that command. However, I cannot tell you what value(s) are needed for your specific data.
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
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 10, 2023, at 10:30 AM, Takagi, Yuichiro via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine Thanks for the information. I was able to use Vop max in ChimeraX and vop maximum in Chimera. As stated, the goal is to make a composite map by combining two locally refined maps. However, when I used Vop max, only one map was dominating such that the composite map is the same as the one of the maps. I think I probably have to scale the maps. Would you be able to tell me how exactly I need to scale two maps and combine? Thanks for your help Best Yuro
Yuichiro H. Takagi, Ph.D. Associate Professor Scientific advisor for cryo-EM Department of Biochemistry and Molecular Biology Indiana University School of Medicine https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.co...
On Aug 7, 2023, at 5:33 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.
Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users@cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time.
Here is the ChimeraX "volume maximum" help link: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command:
vol max #2,3
... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them.
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 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks
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Dear Elaine Thanks for showing syntax sample. It worked - a composite may was generated from two locally refined maps. Now, scale factor was calculated based on threshold values of both maps. Best Yuro
On Aug 10, 2023, at 3:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Dear Yuro, Once you get more familiar with how to read the help it is not that complicated. Example ChimeraX command for maps #1 and #2 you want to scale x1 and x2:
vol max #1,2 scaleFactors 1,2
The syntax is shown in the "volume max" help <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
volume maximum volume-spec [ scaleFactors f1,f2,... | fromlevels ] [ onGrid gridmap ] [ spacing S | Sx,Sy,Sz ] [ boundingGrid true | false ] [ gridStep N | Nx,Ny,Nz ] [ gridSubregion i1,j1,k1,i2,j2,k2 | all ] [ valueType value-type ] [ hideMaps true | false ] new-map-options
You should read the help page because there are many options and you might want to use some of them. However, they are just options, i.e. you don't need to include them if you just want the default behaviors.
The reason we have help pages is that we don't have time/resources to fully describe everything in every possible command each user needs in separate replies on this mailing list.
And there is even a help page on how to read these usage lines, which explains the meaning of "[ ]" (= an option), " | " (= separator between possible values of the option), etc. <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
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 10, 2023, at 11:39 AM, Takagi, Yuichiro via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine I don’t understand the instruction - it’s a bit too abstract for me to write a syntax - That is why I am positing this site. It would be nice if syntax comes with some kind of actual examples in chimera instructions.
Now let’s say, I have two maps A and B by which I want to make a composite map. Scale factor of map A is 1 and that of B is 2. What would be the syntax for this using vop maximum ?
Thanks for your help Best Yuro
participants (2)
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Elaine Meng -
Takagi, Yuichiro