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 >
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