Hi Sean, > To clarify, B.dcd matches the number of atoms in B.pdb and A.dcd also > matches the number of atoms in A.pdb. In the previous example, if I perform > steps 3 and 4 first then it works in loading B.dcd into object "B". Then, > if I try to open up A.pdb into a separate PyMOL window, loading of A.dcd > into object "A" fails with the same error (obviously, with the atom numbers > reversed). Thus, somehow, the second PyMOL window is retaining/obtaining > information from the first PyMOL window.
Is this the open-source build or Incentive MacPyMOL? Also, what command do you issue to start MacPyMOL from the command line? > Okay, I've managed to make a little bit more progress on identifying this > problem. After navigating to the directory for A.pdb (/path/to/A/), I open > A.pdb and load in A.dcd (the window is kept open). No problem. Then, on > the command line (not in PyMOL), I navigate to the directory for B.pdb > (/path/to/B/) and open B.pdb in a new PyMOL window (i.e. "pymol B.pdb"). In > this (B) window, if I do a "pwd" in the PyMOL GUI, instead of saying > "/path/to/B" it returns "/path/to/A"! For some reason, it doesn't recognize > that I've changed directories. This explains why it was throwing the "atoms > in object did not equal number of atoms" error because it was indeed trying > to load A.dcd into object "B" (which have different atom numbers). I > assumed that navigating to "/path/to/B" on the command line (outside of > PyMOL) and then calling PyMOL from there was enough for PyMOL to know where > it was. However, it appears that having one instance of PyMOL already open > will somehow affect the path of the second window. Perhaps there's a > workaround for this? I've never encountered this behaviour on Linux before. Interesting. I could see how this could get confusing, especially since in reality your files are named the same thing. > For now, to get around this, in the second window, I have to re-navigate to > the right directory within MacPyMOL as the command line is not enough. Glad you found a workaround for now. Please let me know about the above. Cheers, -- Jason >> From: jason.vertr...@schrodinger.com >> Date: Wed, 1 Feb 2012 09:40:20 -0500 >> Subject: Re: [PyMOL] MacPyMOL Knowledge of Opened Structures >> To: magic...@hotmail.com >> CC: pymol-users@lists.sourceforge.net > >> >> Hi Sean, >> >> Sorry to hear you're having problems. >> >> > 1) Load A.pdb into MacPyMOL via "pymol A.pdb" >> > 2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, >> > A" >> > >> > 3) Load a completely different structure (must have different number of >> > atoms than A.pdb), B.pdb, into a separate/new instance/window of >> > MacPyMOL >> > via "pymol B.pdb" >> > 4) Load a CHARMM simulation trajectory into object "B" via "load B.dcd, >> > B" >> > >> > Loading of this second trajectory complains with the following error: >> > >> > ObjectMolecule: plugin 'dcd' cannot open file because the number of >> > atoms in >> > the object (4551) did not equal the number of atoms in the 'dcd' (5889) >> > file. >> >> I wrote this error message. PyMOL counts the atoms in the object and >> makes sure each frame of the trajectory has an equivalent number. This >> stops PyMOLers from accidentally working with incorrectly paired data >> -- which happened quite a bit. >> >> > I should mention that in the real example, "A.pdb" and "B.pdb" actually >> > have >> > the same name but are located in different directories (in case it >> > matters). >> >> Seeing this makes me think of two possibilities. First, you possibly >> made a simple mistake on disk and B.pdb and B.dcd don't actually >> match. Do these _exact_ files using the exact same commands work the >> same in Linux? (Can you md5sum the files to check?) Second, if PyMOL >> is sharing data then, because they have the same file name, you'll >> have to rename one to something else, like "A2". >> >> Let us know. >> >> Cheers, >> >> -- Jason >> >> >> >> > >> > In this error, the number "5889" corresponds to the number of atoms in >> > A.pdb >> > while "4551" corresponds to the number of atoms in B.pdb. Again, these >> > are >> > two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb >> > into >> > the same window). Somehow, the first instance of PyMOL sees what is >> > happening in the other. >> > >> > I should mention that in the real example, "A.pdb" and "B.pdb" actually >> > have >> > the same name but are located in different directories (in case it >> > matters). >> > >> > On a non-Mac machine, these commands are fine. As an "experienced" >> > PyMOL >> > user, it was quite embarrassing when a set of commands/steps that worked >> > on >> > a Linux workstation does not work on a Mac (especially when I was trying >> > to >> > show the simulations to a VMD user). I'm fairly new to Macs so maybe >> > there's something that I need to do? >> > >> > Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't >> > seem >> > to run "hide all" and "show cartoon" from my .pymolrc. >> > >> > Any help/suggestions would be greatly appreciated! >> > >> > Sean >> > >> > >> > ------------------------------------------------------------------------------ >> > Keep Your Developer Skills Current with LearnDevNow! >> > The most comprehensive online learning library for Microsoft developers >> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> > Metro Style Apps, more. Free future releases when you subscribe now! >> > http://p.sf.net/sfu/learndevnow-d2d >> > _______________________________________________ >> > 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 >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. 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