[PyMOL] combining multiple objects into one multistate object
I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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
Re: [PyMOL] combining multiple objects into one multistate object
Jed, You are correct in that you should be using the create command: # creates new_obj from old_obj1 by copying old_obj1 # in state 1 to new_obj in state 1 create new_obj, old_obj1, 1, 1 # creates new_obj from old_obj2 by copying old_obj2 # in state 1 to new_obj in state 2 create new_obj, old_obj2, 1, 2 # creates new_obj from old_obj3 by copying old_obj3 # in state 1 to new_obj in state 3 create new_obj, old_obj3, 1, 3 If you have any empty session, this will automate the process: python for x in cmd.get_names(): cmd.create(combined_models, x, 1, -1) python end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu wrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] combining multiple objects into one multistate object
Hi Jed, On Thu, 2014-01-16 10:28 EST, Jed Goldstone jgoldst...@whoi.edu wrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). You probably have a reason for loading the models into separate objects, but my first suggestion would be to just load all of the models into a single object in the first place. You can align them using the intra_fit command. I normally load my modeller models into one object with my load_models.py script or my load_best.py script if I want them sorted by modeller's objective function value (both scripts are also on my web site). I like being able to see the models individually or all at once (with set all_states, 1). Cheers, Rob I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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
Re: [PyMOL] combining multiple objects into one multistate object
Thanks! That works. I kept trying to avoid writing a script, figuring that it should just be an option in 'create'. That is, if the selection old_obj has a wild card, then create new_obj, old_obj*,1,-1 should work. Clearly not; could this be a future feature? Jed On 1/16/2014 10:56 AM, Jason Vertrees wrote: Jed, You are correct in that you should be using the create command: # creates new_obj from old_obj1 by copying old_obj1 # in state 1 to new_obj in state 1 create new_obj, old_obj1, 1, 1 # creates new_obj from old_obj2 by copying old_obj2 # in state 1 to new_obj in state 2 create new_obj, old_obj2, 1, 2 # creates new_obj from old_obj3 by copying old_obj3 # in state 1 to new_obj in state 3 create new_obj, old_obj3, 1, 3 If you have any empty session, this will automate the process: python for x in cmd.get_names(): cmd.create(combined_models, x, 1, -1) python end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu mailto:jgoldst...@whoi.edu wrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 tel:508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net mailto: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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com mailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] combining multiple objects into one multistate object
Jed, Yes, the create command should more intelligently handle the wildcard. In fact, I started out trying the same thing you did. I'll add this as a feature request. Cheers, -- Jason On Thu, Jan 16, 2014 at 10:06 AM, Jed Goldstone jgoldst...@whoi.edu wrote: Thanks! That works. I kept trying to avoid writing a script, figuring that it should just be an option in 'create'. That is, if the selection old_obj has a wild card, then create new_obj, old_obj*,1,-1 should work. Clearly not; could this be a future feature? Jed On 1/16/2014 10:56 AM, Jason Vertrees wrote: Jed, You are correct in that you should be using the create command: # creates new_obj from old_obj1 by copying old_obj1 # in state 1 to new_obj in state 1 create new_obj, old_obj1, 1, 1 # creates new_obj from old_obj2 by copying old_obj2 # in state 1 to new_obj in state 2 create new_obj, old_obj2, 1, 2 # creates new_obj from old_obj3 by copying old_obj3 # in state 1 to new_obj in state 3 create new_obj, old_obj3, 1, 3 If you have any empty session, this will automate the process: python for x in cmd.get_names(): cmd.create(combined_models, x, 1, -1) python end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.eduwrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] combining multiple objects into one multistate object
there is a join_states command in PSICO. http://pymolwiki.org/index.php/psico Cheers, Thomas On 16 Jan 2014, at 11:15, Jason Vertrees jason.vertr...@schrodinger.com wrote: Jed, Yes, the create command should more intelligently handle the wildcard. In fact, I started out trying the same thing you did. I'll add this as a feature request. Cheers, -- Jason On Thu, Jan 16, 2014 at 10:06 AM, Jed Goldstone jgoldst...@whoi.edu wrote: Thanks! That works. I kept trying to avoid writing a script, figuring that it should just be an option in 'create'. That is, if the selection old_obj has a wild card, then create new_obj, old_obj*,1,-1 should work. Clearly not; could this be a future feature? Jed On 1/16/2014 10:56 AM, Jason Vertrees wrote: Jed, You are correct in that you should be using the create command: # creates new_obj from old_obj1 by copying old_obj1 # in state 1 to new_obj in state 1 create new_obj, old_obj1, 1, 1 # creates new_obj from old_obj2 by copying old_obj2 # in state 1 to new_obj in state 2 create new_obj, old_obj2, 1, 2 # creates new_obj from old_obj3 by copying old_obj3 # in state 1 to new_obj in state 3 create new_obj, old_obj3, 1, 3 If you have any empty session, this will automate the process: python for x in cmd.get_names(): cmd.create(combined_models, x, 1, -1) python end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu wrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Thomas Holder PyMOL Developer -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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
