[Chimera-users] Center of model/volume shifts

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 23 14:41:23 PDT 2016


Glad to hear you found a solution.  I’m still disconcerted that the solution wasn’t more straightforward.  I tried opening a volume and filtering it, then saving the result, then restarting and reopening both, but they were always aligned if I hadn’t moved anything separately.  If I had moved any model separately and they weren’t aligned, then matrixcopy or reset always worked.

However, my tests were pretty simple and (in my previous experience) sometimes an annoying problem doesn’t appear until after some complex series of operations that is difficult or tedious to reproduce.
Best,
Elaine

On Mar 23, 2016, at 2:09 PM, Preeti Gipson <gipsonpreeti at gmail.com> wrote:

> It works now after changing the filename and saving it relative to the original and then using matrixcopy command. Still curious, but works at least.
> 
> Thanks again,
> Preeti
> 
> On Wed, Mar 23, 2016 at 1:34 PM, Preeti Gipson <gipsonpreeti at gmail.com> wrote:
> Hi Elaine,
> 
> Thanks for your reply. I have already tried all these options before sending it on and none of them worked.
> 
> It's a deleterious effect considering when one has finally done the work of fitting and saved a session with multiple files.
> 
> Chimera version 1.10.2 (build 40686). (BTW if its useful info, I am an advanced chimera user).
> 
> Thanks,
> Preeti
> 
> On Wed, Mar 23, 2016 at 1:12 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Preeti,
> It might not be a bug if the models were somehow moved separately.  Similar to my previous response on chimera-users to a slightly different question, it may be possible to bring them back into register by by  (A) copying the transformation of the original map to the filtered map, e.g. command:
> 
> matrixcopy #N #M
> 
> … where N is the model number of the original map and M is the model number of the filtered map (see model numbers by showing the Model Panel from the Favorites menu).
> 
> or (B) by resetting all model positions, e.g. command:
> 
> reset
> 
> If neither of those work, it would be helpful if you would report (to the chimera-bugs email address) which version of Chimera you are using (e.g. from the “version” command) and what series of steps can be used to reproduce the problem.
> Thanks,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> Begin forwarded message:
>> 
>> From: Preeti Gipson <gipsonpreeti at gmail.com>
>> Subject: Center of model/volume shifts
>> Date: March 22, 2016 at 5:39:36 PM PDT
>> To: chimera-bugs at cgl.ucsf.edu
>> 
>> Hi,
>> I notice an error in recalling the position/center of the volume map (please see image).
>> 
>> If I apply a low pass filter/mask etc and open the volume it does not overlay the current map. I never came across this issue with the same operations. I have tried restarting session, chimera & even updating.
>> 
>> It will be great to have your suggestions to fix this issue, as you can imagine. It basically means redoing an entire session, especially if pdb structures have been fit in the model.
>> 
>> Thanks, look forward to possible solutions.
>> 
>> Thanks,
>> Preeti
>> -- 
>> -------------------------------------------------------
>> Preeti Gipson
>> Postdoctoral Associate
>> Howard Hughes Medical Institute
>> Dept. of Molecular and Cellular Physiology
>> Stanford University, CA
>> 
>>  
>> <Screen Shot 2016-03-22 at 5.32.08 PM.png>
> 
> 
> 
> 
> 
> -- 
> -------------------------------------------------------
> Preeti Gipson
> Postdoctoral Associate
> Howard Hughes Medical Institute
> Dept. of Molecular and Cellular Physiology
> Stanford University, CA
> 
>  
> 
> 
> 
> -- 
> -------------------------------------------------------
> Preeti Gipson
> Postdoctoral Associate
> Howard Hughes Medical Institute
> Dept. of Molecular and Cellular Physiology
> Stanford University, CA
> 
>  




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