[chimera-dev] Save PDB and Map before fitting

Sun May 14 06:22:12 PDT 2017

Thank you Eric.

I have not been able to get it yet, but I tell you something in the next
days!

Regards

2017-05-09 21:53 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> Okay, I think this will do it (it assumes that the PDB and map are not
> moved moved relative to each other by hand once the fitting is done):
>
> Apply your first solution to the PDB (i.e. multiply its current xform by
> the solution xform).  That should put it in the correct place in the map.
> To put it in the second solution position you would multiply by the inverse
> of the first solution (to get back to the previous position) and then by
> the second solution xform.  Etc.
>
> Your latter idea doesn’t really simplify anything since you will still
> have to multiply by a solution matrix to put it in a fitted position, and
> then by the inverse of the solution to then apply the next solution matrix
> because the user may move the models (in tandem) which will add translation
> and rotation components to their matrices, and you need to retain those
> changes.
>
> —Eric
>
>
> On May 7, 2017, at 10:28 AM, Pablo Solar Rodríguez <pablosolar.r at gmail.com>
> wrote:
>
> Hi Eric,
>
> Or even better, would it be possible to update the old pdb xform and
> coordinates to the new ones that Midas write command already does? I think
> that would work, wouldn't it?
>
> Regards!
>
> 2017-05-02 11:19 GMT+02:00 Pablo Solar Rodríguez <pablosolar.r at gmail.com>:
>
>> Hello Eric,
>>
>> I'm sorry fornot explaining myself correctly. I'm gonna try it again
>> with two example situations:
>>
>> 1) Simple situation: I open the PDB and the Map and apply my exhaustive
>> fitting plugin. After it is finished, I can move the molecule to the
>> different fitted coordinates solutions and even I give the chance to copy a
>> solution into a new molecule in the model panel (there is a question in
>> this forum about this I posted some weeks ago)
>>
>> Now the second example and the problem of this post:
>>
>> 2) Advanced situations: I open the PDB and the Map and, before fitting, I
>> move them unchecking de 'A' checkbox in the model panel. Let's suppose that
>> I move only the PDB. Well, with this, I need to save the moved PDB to disk
>> (temp.pdb with the python scrip save.py you told me) before fitting to have
>> the new coordinates and execute the fitting algorithm with the map and this
>> saved molecule (fitting Map and temp.pdb). When the fitting is finished, I
>> should move the original molecule to the different fitted coordinates
>> solutions but it doesnt work properly.
>>
>> Related with 2, if I save the original moved molecule to disk (temp.pdb)
>> and I open this new copy in Chimera and I fit it with the map directly, it
>> works fine. There's something wrong between the acts of opening the
>> molecule, moving it, writing it to disk, fitting, and trying to move the
>> original one with the fitted coordinates (between the copy and the map) and
>> I don't know why.
>>
>> Hope it is more clear now. If not, let me know and I try to explain it
>> better.
>>
>> Thank you in advance and regards from Spain.
>>
>>
>> 2017-05-01 23:12 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>
>>> Hi Pablo,
>>> I couldn’t quite puzzle out what you were saying below.  In particular,
>>> I didn’t understand:
>>>
>>> "Then, I get the coordinates that are result from fitting
>>> "temporal.pdb" -- "mapY.ccp4" and move "chainX.pdb" opened in Chimera to
>>> these coordinates. But does not work fine.”
>>>
>>> So instead of trying to answer directly, I’ll just try to outline the
>>> principles involved and see if that helps.  You open your map and your
>>> original PDB.  Then you fit your PDB into the map.  If you want to save the
>>> fitted PDB in the same coordinate reference frame as the map, then you need
>>> to take the transformed coordinates of the PDB, apply the *inverse* of
>>> the map’s transformation matrix, and use those coordinates.
>>> You don’t really say what API you use to save the PDB file, but you
>>> could just use the “write” command with the “relative” keyword to save the
>>> PDB file.  Also, Midas.write(pdb_model, map_model, file_name) would do it.
>>> If you then open the map and new PDB file together they will be in their
>>> fitted orientation.
>>>
>>> Hope this helps,
>>>
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>>
>>>
>>> On Apr 28, 2017, at 12:32 AM, Pablo Solar Rodríguez <
>>> pablo.solar at delogica.com> wrote:
>>>
>>>
>>> Hello again!
>>>
>>> Well, I've been testing the PDB saving in my plugin and it doesn't work
>>> as I expected. I'm gonna try to explain the best I know because maybe my
>>> theoretical concepts are wrong.
>>>
>>> The aim of saving PDB is beacuse if I move (rotate and translate) my
>>> molecule on Chimera I need to save it before executing the exhaustive
>>> fitting to have the correct coordinates on disk. But when the process is
>>> finished and I move the molecule on Chimera to the fitting coordinates, it
>>> doesn't work properly. This not happens if I open the saved PDB and I
>>> execute the exhaustive fitting; in that case, the molecule moves correctly
>>> to the fitting coordinates.
>>>
>>> I'm gonna explain it with the example.
>>>
>>> 1. Suppouse I have opened "chainX.pdb" and "mapY.ccp4" in Chimera and I
>>> move the molecule (uncheckin the 'A' in the model panel):
>>>
>>> 2. If I execute the exhaustive fitting in Chimera, the process will save
>>> "temporal.pdb" from "chainX.pdb" on disk. Then, I get the coordinates that
>>> are result from fitting "temporal.pdb" -- "mapY.ccp4" and move "chainX.pdb"
>>> opened in Chimera to these coordinates. But does not work fine.
>>>
>>> 3. However, If I open "temporal.pdb" in Chimera and I execute the
>>> process, it works fine.
>>>
>>> Could be a desynchronization between the opened "chainX.pdb" in Chimera,
>>> the "temporal.pdb" saved on disk and the "mapY.ccp4"? I cannot see what
>>> could be happening...
>>>
>>> I hope to have explained myself correctly.
>>>
>>> Thank you so much in advance
>>>
>>>
>>>
>>> *<e3596d50.png>   Pablo Solar Rodríguez   *pablo.solar at delogica.com
>>> *   Delógica - *www.delogica.com
>>>
>>> España: C/Nuñez de Balboa 31, 2ª Planta - 2, 28001 Madrid, Tel.: (34)
>>> 91 431 31 09 <914%2031%2031%2009>
>>> Colombia: Edificio Torre Zimma - Carrera 15 88-70 Bogotá, PBX (571)
>>> 3000302
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>>>
>>> El 27-04-2017 20:04, Pablo Solar Rodríguez escribió:
>>>
>>> Hello Eric,
>>>
>>> Thank you for the response. I will check it!!
>>>
>>> Kind regards!
>>>
>>> 2017-04-26 19:28 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>>
>>>> Hi Pablo,
>>>> Every model has an 'openState' attribute which in turn has a 'xform'
>>>> attribute which holds the model's transformation matrix.  A newly opened
>>>> model, if it's the only model, will have the identity matrix as it's
>>>> initial xform.  If there are other models open, then its initial xform will
>>>> be the same as that of the currently open model with the lowest ID number,
>>>> in a "best effort" attempt to keep the newly opened model in the same frame
>>>> of reference as the other models.
>>>> So to see if you need to resave it you should compare the current xform
>>>> to the one it had the last time you saved it.
>>>> There is a trigger that fires when a model's transformation matrix
>>>> changes — the 'OpenState' trigger will fire in the chimera.triggers trigger
>>>> set, with the trigger data '.reasons' attribute containing 'transformation
>>>> change'.  However, there is a convenience trigger, chimera.MOTION_STOP,
>>>> that you probably want to register for instead, that will collate all the
>>>> many OpenState trigger firings that will occur during a mouse motion.  That
>>>> trigger is also in the chimera.triggers trigger set.  If you aren't
>>>> familiar with triggers, there is a programmer example about them:
>>>>
>>>> https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGui
>>>> de/Examples/Main_AtomTrigger.html
>>>>
>>>> —Eric
>>>>
>>>>
>>>> Eric Pettersen
>>>> UCSF Computer Graphics Lab
>>>>
>>>>
>>>> On Apr 26, 2017, at 12:41 AM, Pablo Solar Rodríguez <
>>>> pablo.solar at delogica.com> wrote:
>>>>
>>>> Hello Elaine,
>>>>
>>>> Thank you for the quick response. I'll check the info to find a way to
>>>> do it. Just one more thing. Is there a manner to know when the map has been
>>>> moved? Just to not resampling it each time needlessly.
>>>>
>>>> Thank you!
>>>>
>>>>
>>>>
>>>> El 25-04-2017 18:21, Elaine Meng escribió:
>>>>
>>>> Hi Pablo,
>>>> The map format doesn't include rotation information.  You would have to
>>>> resample it on a new grid to create a new map, such as with command "vop
>>>> resample"... details here on saving maps after fitting (bottom of the page):
>>>>
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.
>>>> html#afterfitting>
>>>>
>>>> I hope this helps,
>>>> Elaine
>>>> ----------
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>>
>>>> On Apr 25, 2017, at 2:24 AM, Pablo Solar Rodríguez <
>>>> pablo.solar at delogica.com> wrote:
>>>>
>>>> Hello Tom,
>>>> Thank you for your quick response. I've checked the code in my plugin
>>>> and the PDB saving works fine as I expected, even if I move the molecule.
>>>>
>>>> My question is about saving the map. I tried to move it
>>>> (rotate&translate unchecking the 'A' in the ModelPanel) and then save it
>>>> with this code, but when I open the saved map, it is similar to the
>>>> original one and does not keep the new coordinates. This could be a problem
>>>> in my plugin, because I need to save them case of moving to get correct
>>>> results in the fitting process.
>>>>
>>>> So, how can I handle this situation? Is there any other way for saving
>>>> the new map coordinates in the same way the PDB saving does? Hope I have
>>>> explained myself correctly.
>>>> Thank you in advance and kind regards,
>>>> Pablo.
>>>>
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>>>
>>>
>>> --
>>>
>>>
>>> *Pablo Solar Rodríguez*
>>> *pablosolar.r at gmail.com* <pablosolar.r at gmail.com>
>>>
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>>
>>
>> --
>>
>> *Pablo Solar Rodríguez*
>>
>> *pablosolar.r at gmail.com <pablosolar.r at gmail.com>*
>>
>>
>>
>
>
> --
>
> *Pablo Solar Rodríguez*
>
> *pablosolar.r at gmail.com <pablosolar.r at gmail.com>*
>
>
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-- 

*Pablo Solar Rodríguez*

*pablosolar.r at gmail.com <pablosolar.r at gmail.com>*
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