Saving .pdb file in location of .mrc file
Hi Chimera, I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1. So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1. An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
Hi Chimera, I was able to figure this out after several hours. You can disregard the below email. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file Hi Chimera, I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1. So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1. An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yes, that is explained in the link in my previous message. Elaine
On Jun 26, 2019, at 9:23 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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I am still having some trouble. It was working last night but this morning my script started having trouble again. 'open ' + paths['input'] + '\n' 'open ' + paths['test'] + '\n' move cofr mod #1\n' 'write relative #0 #1 ' + paths['centered_test'] + '\n' 'open ' + paths['centered_test'] + '\n The objective is to have ‘test’ in line with ‘input’, but when I check the save file it never got moved and is still offset. What is strange is last night it was working fine. Best, Ryan Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 12:40:37 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file Yes, that is explained in the link in my previous message. Elaine
On Jun 26, 2019, at 9:23 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
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Hi Ryan, Your “move” command just generates an error. Move requires an axis (direction of movement). <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> Elaine
On Jun 27, 2019, at 9:56 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
I am still having some trouble. It was working last night but this morning my script started having trouble again.
'open ' + paths['input'] + '\n' 'open ' + paths['test'] + '\n' move cofr mod #1\n' 'write relative #0 #1 ' + paths['centered_test'] + '\n' 'open ' + paths['centered_test'] + '\n
The objective is to have ‘test’ in line with ‘input’, but when I check the save file it never got moved and is still offset. What is strange is last night it was working fine.
Best, Ryan
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 12:40:37 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
Yes, that is explained in the link in my previous message.
Elaine
On Jun 26, 2019, at 9:23 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
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Oh sorry, I have been answering many chimerax and chimera questions simultaneously and got confused and gave a chimeraX answer for your chimera question. Ignore previous answer… For Chimera <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> I would say to try this with a different move command where the movement may be more obvious. Maybe your model seemed to stay in the same position because it was already at or close to the center of rotation? Maybe it would be more obvious with something like a 10-Angstrom translation. move y 10 mod #1 Then when you reopen you can also open a copy of the original and see that they are 10 A apart. Elaine
On Jun 27, 2019, at 2:08 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ryan, Your “move” command just generates an error. Move requires an axis (direction of movement). <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html>
Elaine
On Jun 27, 2019, at 9:56 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
I am still having some trouble. It was working last night but this morning my script started having trouble again.
'open ' + paths['input'] + '\n' 'open ' + paths['test'] + '\n' move cofr mod #1\n' 'write relative #0 #1 ' + paths['centered_test'] + '\n' 'open ' + paths['centered_test'] + '\n
The objective is to have ‘test’ in line with ‘input’, but when I check the save file it never got moved and is still offset. What is strange is last night it was working fine.
Best, Ryan
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 12:40:37 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
Yes, that is explained in the link in my previous message.
Elaine
On Jun 26, 2019, at 9:23 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
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Are you using ‘open’ or ’source’ to process the command file? Those should work AFAIK. If you use ‘read’ though, it will not wait for the ‘move cofr’ to finish before going on to the ‘write’ command, so nothing will have moved. Seems unlikely you’re using ‘read’ though… —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 27, 2019, at 9:56 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
I am still having some trouble. It was working last night but this morning my script started having trouble again.
'open ' + paths['input'] + '\n' 'open ' + paths['test'] + '\n' move cofr mod #1\n' 'write relative #0 #1 ' + paths['centered_test'] + '\n' 'open ' + paths['centered_test'] + '\n
The objective is to have ‘test’ in line with ‘input’, but when I check the save file it never got moved and is still offset. What is strange is last night it was working fine.
Best, Ryan
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Wednesday, June 26, 2019 12:40:37 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
Yes, that is explained in the link in my previous message.
Elaine
On Jun 26, 2019, at 9:23 AM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):
<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html%23afterfitting&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409359477&sdata=FnFgKvNsF1uTW3hV5nIkwJdGLKzzFsHlrZm0U3Ra90c%3D&reserved=0 <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html%23afterfitting&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409359477&sdata=FnFgKvNsF1uTW3hV5nIkwJdGLKzzFsHlrZm0U3Ra90c%3D&reserved=0>>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
Sent from Mail for Windows 10
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Put “cofr fixed” between your two open commands. —Eric
On Jun 27, 2019, at 2:32 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Are you using ‘open’ or ’source’ to process the command file? Those should work AFAIK. If you use ‘read’ though, it will not wait for the ‘move cofr’ to finish before going on to the ‘write’ command, so nothing will have moved. Seems unlikely you’re using ‘read’ though…
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 27, 2019, at 9:56 AM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
I am still having some trouble. It was working last night but this morning my script started having trouble again.
'open ' + paths['input'] + '\n' 'open ' + paths['test'] + '\n' move cofr mod #1\n' 'write relative #0 #1 ' + paths['centered_test'] + '\n' 'open ' + paths['centered_test'] + '\n
The objective is to have ‘test’ in line with ‘input’, but when I check the save file it never got moved and is still offset. What is strange is last night it was working fine.
Best, Ryan
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From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Wednesday, June 26, 2019 12:40:37 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
Yes, that is explained in the link in my previous message.
Elaine
On Jun 26, 2019, at 9:23 AM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
If you move and save a volume and reopen it, it does not appear in new place but rather original place. If you move and save a .ent/.pdb and reopen it, it appears in new place.
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From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Wednesday, June 26, 2019 9:20:21 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Saving .pdb file in location of .mrc file
For the others on the list, although I’m not sure what solution you hit upon, the issue is discussed here, in “Saving Maps after Fitting” (bottom of page):
<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html%23afterfitting&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409359477&sdata=FnFgKvNsF1uTW3hV5nIkwJdGLKzzFsHlrZm0U3Ra90c%3D&reserved=0 <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html%23afterfitting&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409359477&sdata=FnFgKvNsF1uTW3hV5nIkwJdGLKzzFsHlrZm0U3Ra90c%3D&reserved=0>>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2019, at 6:49 PM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
Hi Chimera,
I was able to figure this out after several hours. You can disregard the below email.
Best, Ryan Harlich
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From: Ryan Harlich Sent: Tuesday, June 25, 2019 4:46:11 PM To: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Saving .pdb file in location of .mrc file
Hi Chimera,
I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1.
So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1.
An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there.
Best, Ryan Harlich
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Ryan Harlich