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
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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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