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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