[chimera-dev] Save PDB and Map before fitting

Tue May 2 02:19:47 PDT 2017

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>*
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