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
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