Trouble Morphing 2 Proteins
Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew
Hi Andrew, These two protein structures have the same backbone conformation as each other, or at least so similar that I can't see any difference. Morphing shows changes in backbone conformation, as well as in sidechains that are the same type in the two proteins. These might have some different sidechains but morphing will not show the "mutation" of the sidechain atoms, it will only keep the atoms that are the same between the two proteins. So anyway, morphing works fine for me, but essentially the whole morphing trajectory is just motionless because the conformation is the same between the two endpoints -- in other words, it doesn't make sense to morph them. Maybe I am misunderstanding the situation, but that's what it looks like to me. I don't know which tutorial you were using, so I couldn't understand what you meant by "tutorial proteins" either. If you want to see a morph that actually changes conformation, try commands: open 2gbp open 2fw0 mm #2 to #1 morph #1,2 If that doesn't work, there is also some other problem. If so, instead of sending email we recommend using menu: Help... Report a Bug to report it, including some description of what you did and what happened, and your email address if you would like a reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 1:27 PM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew<NBD2 test.1.pdb><N1303KH++.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello, To whom it may see this message. I see, there is a mutation between the 2 structures at the location of 1303 and I am trying to see how it effects the protein wild type. Do you have any recommendations to be able to see the effects of this mutation better? Best, Andrew Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, February 20, 2025 5:00:48 PM To: Andrew Mejia Garnica <amejiagarnica1@catamount.wcu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trouble Morphing 2 Proteins [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi Andrew, These two protein structures have the same backbone conformation as each other, or at least so similar that I can't see any difference. Morphing shows changes in backbone conformation, as well as in sidechains that are the same type in the two proteins. These might have some different sidechains but morphing will not show the "mutation" of the sidechain atoms, it will only keep the atoms that are the same between the two proteins. So anyway, morphing works fine for me, but essentially the whole morphing trajectory is just motionless because the conformation is the same between the two endpoints -- in other words, it doesn't make sense to morph them. Maybe I am misunderstanding the situation, but that's what it looks like to me. I don't know which tutorial you were using, so I couldn't understand what you meant by "tutorial proteins" either. If you want to see a morph that actually changes conformation, try commands: open 2gbp open 2fw0 mm #2 to #1 morph #1,2 If that doesn't work, there is also some other problem. If so, instead of sending email we recommend using menu: Help... Report a Bug to report it, including some description of what you did and what happened, and your email address if you would like a reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 1:27 PM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew<NBD2 test.1.pdb><N1303KH++.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Camejiagarnica1%40catamount.wcu.edu%7Cf03e715080314aa8dcd908dd51fa13df%7Cc5b35b5a16d544148ee17bde70543f1b%7C0%7C0%7C638756856943762929%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=3Xv25jUi7tl1kVy5Q5tE60T%2FByUjleXaIR6OyoO84Kg%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
Hi Andrew, Just changing the side chain does not predict how the whole protein structure may change, it may only provide some hints depending on whether you gain/lose interactions. You could either show the two structures superimposed in two different colors or make a side-by-side close up of the same orientation (one protein on the left, on on the right). Or you could try to use some other software that predicts larger changes, not just changing the side chain atoms. I don't have a specific recommendation for that, sorry. Best, Elaine
On Feb 21, 2025, at 6:51 AM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, To whom it may see this message. I see, there is a mutation between the 2 structures at the location of 1303 and I am trying to see how it effects the protein wild type. Do you have any recommendations to be able to see the effects of this mutation better? Best, Andrew
Get Outlook for iOS From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, February 20, 2025 5:00:48 PM To: Andrew Mejia Garnica <amejiagarnica1@catamount.wcu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trouble Morphing 2 Proteins [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Hi Andrew, These two protein structures have the same backbone conformation as each other, or at least so similar that I can't see any difference. Morphing shows changes in backbone conformation, as well as in sidechains that are the same type in the two proteins. These might have some different sidechains but morphing will not show the "mutation" of the sidechain atoms, it will only keep the atoms that are the same between the two proteins. So anyway, morphing works fine for me, but essentially the whole morphing trajectory is just motionless because the conformation is the same between the two endpoints -- in other words, it doesn't make sense to morph them.
Maybe I am misunderstanding the situation, but that's what it looks like to me.
I don't know which tutorial you were using, so I couldn't understand what you meant by "tutorial proteins" either.
If you want to see a morph that actually changes conformation, try commands:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2
If that doesn't work, there is also some other problem. If so, instead of sending email we recommend using menu: Help... Report a Bug to report it, including some description of what you did and what happened, and your email address if you would like a reply.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 1:27 PM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew<NBD2 test.1.pdb><N1303KH++.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.u...
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Elaine, Would it be possible to get a video recording of the morphing for recording keeping? Best, Andrew ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, February 21, 2025 12:22 PM To: Andrew Mejia Garnica <amejiagarnica1@catamount.wcu.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trouble Morphing 2 Proteins [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi Andrew, Just changing the side chain does not predict how the whole protein structure may change, it may only provide some hints depending on whether you gain/lose interactions. You could either show the two structures superimposed in two different colors or make a side-by-side close up of the same orientation (one protein on the left, on on the right). Or you could try to use some other software that predicts larger changes, not just changing the side chain atoms. I don't have a specific recommendation for that, sorry. Best, Elaine
On Feb 21, 2025, at 6:51 AM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, To whom it may see this message. I see, there is a mutation between the 2 structures at the location of 1303 and I am trying to see how it effects the protein wild type. Do you have any recommendations to be able to see the effects of this mutation better? Best, Andrew
Get Outlook for iOS From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, February 20, 2025 5:00:48 PM To: Andrew Mejia Garnica <amejiagarnica1@catamount.wcu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trouble Morphing 2 Proteins [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Hi Andrew, These two protein structures have the same backbone conformation as each other, or at least so similar that I can't see any difference. Morphing shows changes in backbone conformation, as well as in sidechains that are the same type in the two proteins. These might have some different sidechains but morphing will not show the "mutation" of the sidechain atoms, it will only keep the atoms that are the same between the two proteins. So anyway, morphing works fine for me, but essentially the whole morphing trajectory is just motionless because the conformation is the same between the two endpoints -- in other words, it doesn't make sense to morph them.
Maybe I am misunderstanding the situation, but that's what it looks like to me.
I don't know which tutorial you were using, so I couldn't understand what you meant by "tutorial proteins" either.
If you want to see a morph that actually changes conformation, try commands:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2
If that doesn't work, there is also some other problem. If so, instead of sending email we recommend using menu: Help... Report a Bug to report it, including some description of what you did and what happened, and your email address if you would like a reply.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 1:27 PM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew<NBD2 test.1.pdb><N1303KH++.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Camejiagarnica1%40catamount.wcu.edu%7C843d88ee60b24f6d0fa908dd529c5bba%7Cc5b35b5a16d544148ee17bde70543f1b%7C0%7C0%7C638757553741456924%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=WYd9uVur5bWsSl%2FZh2LRDuUD6MWDm0mM3EP9wt3xbPc%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Camejiagarnica1%40catamount.wcu.edu%7C843d88ee60b24f6d0fa908dd529c5bba%7Cc5b35b5a16d544148ee17bde70543f1b%7C0%7C0%7C638757553741472023%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=7SRbb3%2BTEI1CtWyLFo%2BNdoGxMTjObAf%2B%2BBxFrtiwElA%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
As I tried to explain before, there is nothing to show for your two proteins, the backbone conformation does not change. Even if you make a morph and play it, it will be the same as staring at the ribbon of either protein by itself without moving it. If you actually have created a morph trajectory that moves, you can click the red record button on the slider to save a movie, or use commands to record it, as explained in the help. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> Elaine
On Feb 24, 2025, at 1:08 PM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Would it be possible to get a video recording of the morphing for recording keeping? Best, AndrewFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, February 21, 2025 12:22 PM To: Andrew Mejia Garnica <amejiagarnica1@catamount.wcu.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trouble Morphing 2 Proteins [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important athttps://aka.ms/LearnAboutSenderIdentification ]
Hi Andrew, Just changing the side chain does not predict how the whole protein structure may change, it may only provide some hints depending on whether you gain/lose interactions. You could either show the two structures superimposed in two different colors or make a side-by-side close up of the same orientation (one protein on the left, on on the right). Or you could try to use some other software that predicts larger changes, not just changing the side chain atoms. I don't have a specific recommendation for that, sorry. Best, Elaine
On Feb 21, 2025, at 6:51 AM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, To whom it may see this message. I see, there is a mutation between the 2 structures at the location of 1303 and I am trying to see how it effects the protein wild type. Do you have any recommendations to be able to see the effects of this mutation better? Best, Andrew
Get Outlook for iOS From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, February 20, 2025 5:00:48 PM To: Andrew Mejia Garnica <amejiagarnica1@catamount.wcu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trouble Morphing 2 Proteins [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Hi Andrew, These two protein structures have the same backbone conformation as each other, or at least so similar that I can't see any difference. Morphing shows changes in backbone conformation, as well as in sidechains that are the same type in the two proteins. These might have some different sidechains but morphing will not show the "mutation" of the sidechain atoms, it will only keep the atoms that are the same between the two proteins. So anyway, morphing works fine for me, but essentially the whole morphing trajectory is just motionless because the conformation is the same between the two endpoints -- in other words, it doesn't make sense to morph them.
Maybe I am misunderstanding the situation, but that's what it looks like to me.
I don't know which tutorial you were using, so I couldn't understand what you meant by "tutorial proteins" either.
If you want to see a morph that actually changes conformation, try commands:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2
If that doesn't work, there is also some other problem. If so, instead of sending email we recommend using menu: Help... Report a Bug to report it, including some description of what you did and what happened, and your email address if you would like a reply.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 1:27 PM, Andrew Mejia Garnica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew<NBD2 test.1.pdb><N1303KH++.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.u...
participants (2)
-
Andrew Mejia Garnica -
Elaine Meng