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

[Elaine Meng]

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 at 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 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
>>>> 
>>>> _______________________________________________
>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>>> Manage subscription: https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409369482&sdata=CovI3tPrPnKG0QSl%2BhN2g52Z2JIrwPO%2BiXpAvOfxTI0%3D&reserved=0
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> Manage subscription: https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C1c4a978faa124ab74e7708d6fa6e2afa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636971748409369482&sdata=CovI3tPrPnKG0QSl%2BhN2g52Z2JIrwPO%2BiXpAvOfxTI0%3D&reserved=0
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>