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

[Elaine Meng]

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 at 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 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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