[Chimera-users] Saving .pdb file in location of .mrc file

[Ryan Harlich]

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 at cgl.ucsf.edu>
Sent: Wednesday, June 26, 2019 12:40:37 PM
To: Ryan Harlich
Cc: chimera-users at 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 at 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 at cgl.ucsf.edu>
> Sent: Wednesday, June 26, 2019 9:20:21 AM
> To: Ryan Harlich
> Cc: chimera-users at 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>
>
> 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 at 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 at 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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