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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