making composite map using vop maximum command
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
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.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23maximum&data=05%7C01%7Cytakagi%40iu.edu%7Ca3298165fbf74ae6db4208db978dfda4%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638270408325719718%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RoQ6GgEfxT%2BKOGv%2FiXZ%2F2omjXNCl%2F84vT8VMDQOTXfs%3D&reserved=0>
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.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23maximum&data=05%7C01%7Cytakagi%40iu.edu%7Ca3298165fbf74ae6db4208db978dfda4%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638270408325719718%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RoQ6GgEfxT%2BKOGv%2FiXZ%2F2omjXNCl%2F84vT8VMDQOTXfs%3D&reserved=0>
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.
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.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23maximum&data=05%7C01%7Cytakagi%40iu.edu%7C8e169d1a695f4b8827ed08db99ca9f24%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C638272867758312133%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=s8d%2BJBhU8kDkmjWZAc0sn5KzGgVzrguAPn5gHswB4p4%3D&reserved=0>
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
participants (3)
-
Elaine Meng -
Takagi, Yuichiro -
ytakagi＠iu.edu