[Chimera-users] Center of model/volume shifts

Preeti Gipson gipsonpreeti at gmail.com
Wed Mar 23 14:09:46 PDT 2016


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
>>
>>
>>
>>
>>
>>
>
>
> --
>
> -------------------------------------------------------
>
> 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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