I guess this is a general thing in pymol, i.e. if async is 1 your command is
going to be spawned in another thread, so you keep working while it's
executed. With async = 0 things are executed in the main thread.


On Tue, May 4, 2010 at 11:24 PM, Michael Zimmermann <micha...@iastate.edu>wrote:

> Thank you Marius, that does appear to do the job.  I guess this tip is
> sortof present on the wiki page for fetch, but I didn't understand it as
> written.
>
> Sincerely,
>
> Mike
>
>
> On Tue, May 4, 2010 at 4:13 PM, Marius Retegan <marius.s.rete...@gmail.com
> > wrote:
>
>> Just a wild guess
>> fetch 1htr, async=0
>> Marius
>>
>> On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann <micha...@iastate.edu
>> > wrote:
>>
>>> Dear PyMOL users,
>>>
>>> I was just making a script to selectively download sections of PDB files
>>> using fetch.  When I run the pml from the GUI I see that all of the commands
>>> are executed and then the structure called by fetch is loaded.  Is there any
>>> way to force the other commands to wait until fetch is finished getting the
>>> PDB file?  Interestingly, if I run the script a second time, then it behaves
>>> as I would have expected it to.  If multiple PDB files are fetched and
>>> downloaded the pattern is similar; the first time the script is run all of
>>> the commands are processed, and then all of the structures are "fetched" but
>>> the second time the script is run the structures are fetched and then the
>>> next lines of code are run.  I would like to do this for hundreds of
>>> structures based on PFam domains, so it would be nice if this would work
>>> reliably.
>>>
>>> I am executing the file with
>>> >PyMOL.exe -c -k -u myscript.pml
>>>
>>> --------------------------PML-File ------------------
>>> fetch 1htr
>>> remove not (alt ''+A)
>>> alter all, alt=''
>>> select prot, (chain P and resi 2-30)
>>> save PF_1htr.pdb, prot
>>> delete all
>>> ----------------------------------------------------------
>>>
>>> ----------------------PYMOL-output-after-first-run-----------------
>>> PyMOL>@Fetch_PF07966.pml
>>> PyMOL>cd C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation
>>>  cd: now in C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation
>>> PyMOL>fetch 1htr
>>> PyMOL>remove not (alt ''+A)
>>> PyMOL>alter all, alt=''
>>>  Alter: modified 0 atoms.
>>> PyMOL>select prot, (chain P and resi 2-30)
>>>  Selector: selection "prot" defined with 0 atoms.
>>> PyMOL>save
>>> C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb,
>>> prot
>>>  Save: wrote
>>> "C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb".
>>> PyMOL>delete all
>>> HEADER    ASPARTYL PROTEASE                       21-OCT-94   1HTR
>>> TITLE     CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT
>>> TITLE    2 1.62 ANGSTROMS RESOLUTION
>>> COMPND    MOL_ID: 1;
>>> COMPND   2 MOLECULE: PROGASTRICSIN (PRO SEGMENT);
>>> COMPND   3 CHAIN: P;
>>> COMPND   4 EC: 3.4.23.3;
>>> COMPND   5 ENGINEERED: YES;
>>> COMPND   6 MOL_ID: 2;
>>> COMPND   7 MOLECULE: GASTRICSIN;
>>> COMPND   8 CHAIN: B;
>>> COMPND   9 EC: 3.4.23.3;
>>> COMPND  10 ENGINEERED: YES
>>>  ObjectMolecule: Read secondary structure assignments.
>>>  ObjectMolecule: Read crystal symmetry information.
>>>  Symmetry: Found 8 symmetry operators.
>>>  CmdLoad: ".\1htr.pdb" loaded as "1htr".
>>> -----------------------------------------
>>>
>>> ----------------------PYMOL-output-after-second-run-----------------
>>> PyMOL>fetch 1htr
>>> PyMOL>remove not (alt ''+A)
>>> HEADER    ASPARTYL PROTEASE                       21-OCT-94   1HTR
>>> TITLE     CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT
>>> TITLE    2 1.62 ANGSTROMS RESOLUTION
>>> COMPND    MOL_ID: 1;
>>> COMPND   2 MOLECULE: PROGASTRICSIN (PRO SEGMENT);
>>> COMPND   3 CHAIN: P;
>>> COMPND   4 EC: 3.4.23.3;
>>> COMPND   5 ENGINEERED: YES;
>>> COMPND   6 MOL_ID: 2;
>>> COMPND   7 MOLECULE: GASTRICSIN;
>>> COMPND   8 CHAIN: B;
>>> COMPND   9 EC: 3.4.23.3;
>>> COMPND  10 ENGINEERED: YES
>>>  ObjectMolecule: Read secondary structure assignments.
>>>  ObjectMolecule: Read crystal symmetry information.
>>>  CmdLoad: ".\1htr.pdb" appended into object "1htr", state 2.
>>>  Remove: eliminated 16 atoms in model "1htr".
>>> PyMOL>alter all, alt=''
>>>  Alter: modified 3113 atoms.
>>> PyMOL>select prot, (chain P and resi 2-30)
>>>  Selector: selection "prot" defined with 239 atoms.
>>> PyMOL>save
>>> C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb,
>>> prot
>>>  Save: wrote
>>> "C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb".
>>> PyMOL>delete all
>>> -----------------------------------------
>>>
>>> --
>>> Michael Zimmermann
>>> Ph.D. student in Bioinformatics and Computational Biology
>>> Department of Biochemistry, Biophysics and Molecular Biology
>>> Iowa State University
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University
>
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