Hi Tom (and Eric), Thanks for the quick responses! I'm actually trying to do this demonstration for a class I'll be teaching soon. Because I'll only be demonstrating instead of doing production work, I turned the settings for the minimization down: Steepest Descent Steps: 10 Steepest Descent Step size (A): 0.02 Conjugate Gradient Steps: 0 Conjugate Gradient Step size (A): 0.02 Update interval: 1 Fixed atoms: unselected What I've figured out is that I'm getting trouble by using the "Update interval" at "1". In my cleverness, I wanted to recalculate the clash (using the "after relative motions (until dialog closed)") after every step of minimization to show the clashes going away after just a few steps of minimization. Everything works as expected when I put the "Update interval" at "5" and "10". Intervals of "1", "2", "3", and "4" don't work (RMSD = 0.000000 at each report). I haven't tried other interval settings. So it looks like I'll just use a higher interval setting for my class. BTW, thanks for the updates to the minimization engine. I really appreciate the prep options that check for alternate positions, uncomplexed ions, etc. And for the options to easily set the hydrogenation state of various residues and the charges of hetero atoms. Chimera is great! (BTW, this is Chimera 1.6.1 (build 35849) for 64-bit Mac OS X.) Cheers, Darrell On Apr 2, 2012, at 9:49 PM, Tom Goddard wrote: Hi Darrell, I've often seen Chimera's MMTK energy minimization go nowhere as you observe. I think basically it is taking miniscule steps, essentially zero, because there is a bad clash or extremely long bond. In fact whatever is causing the energy to be astronomical is what is probably what is causing the minimizer not to take any step bigger than 0. I don't know a good way to see where the high energy is coming from. Maybe you could try minimizing some very small set of the atoms with the rest fixed. By trying minimizing different movable sets of atoms you could see where the high energy is coming from. I'm not sure this will work, because it could be that the step size is forced to be tiny even if the high energy is caused by fixed atoms. You'd have to experiment to figure that out. I'll be interested to hear what you figure out. Another idea that could help you figure this out -- the Chimera "minimize" command has a new "fragment true|false" option that allows you to minimize just part of a molecule. It is different from holding atoms fixed. With fixed atoms as you have tried, the fixed atoms still contribute to the force field. With "fragment true" and the minimize command only the specified atoms contribute to the force field, the others being completely ignored. This fragment option is not available in the minimize dialog. It was added in Chimera 1.6. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html I see it would be nice to have Chimera be able to color your atoms and bonds in a way that reflects the energy terms for involving each atom and bond. Not sure if that info is available in the dynamics library Chimera uses, MMTK. That would allow you to quickly spot the problem. Tom Hi there, I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to<5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms. Am I in a local minima? Is that why nothing moves? The energy is very high (from the Reply Log): Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps Any ideas? I do have some hetero atoms... Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

Hi Tom, Great! I'm not crazy. ;) Thanks for submitting the bug report and your incredible turnaround. Cheers, Darrell On Apr 2, 2012, at 11:06 PM, Tom Goddard wrote: Hi Darrell, This is certainly a bug since the update interval is only supposed to effect how often the display is updated during the minimization. I tried your settings on PDB 1a0m with chain A selected and observed the same problem that with update interval 1 steps are all 0 with no change in energy or gradient, while update interval 10 gives a significant change in energy and a small step. The Chimera daily build has the same bug. I file a report and put your name on it so you get notified when it is fixed. Tom Hi Tom (and Eric), Thanks for the quick responses! I'm actually trying to do this demonstration for a class I'll be teaching soon. Because I'll only be demonstrating instead of doing production work, I turned the settings for the minimization down: Steepest Descent Steps: 10 Steepest Descent Step size (A): 0.02 Conjugate Gradient Steps: 0 Conjugate Gradient Step size (A): 0.02 Update interval: 1 Fixed atoms: unselected What I've figured out is that I'm getting trouble by using the "Update interval" at "1". In my cleverness, I wanted to recalculate the clash (using the "after relative motions (until dialog closed)") after every step of minimization to show the clashes going away after just a few steps of minimization. Everything works as expected when I put the "Update interval" at "5" and "10". Intervals of "1", "2", "3", and "4" don't work (RMSD = 0.000000 at each report). I haven't tried other interval settings. So it looks like I'll just use a higher interval setting for my class. BTW, thanks for the updates to the minimization engine. I really appreciate the prep options that check for alternate positions, uncomplexed ions, etc. And for the options to easily set the hydrogenation state of various residues and the charges of hetero atoms. Chimera is great! (BTW, this is Chimera 1.6.1 (build 35849) for 64-bit Mac OS X.) Cheers, Darrell On Apr 2, 2012, at 9:49 PM, Tom Goddard wrote: Hi Darrell, I've often seen Chimera's MMTK energy minimization go nowhere as you observe. I think basically it is taking miniscule steps, essentially zero, because there is a bad clash or extremely long bond. In fact whatever is causing the energy to be astronomical is what is probably what is causing the minimizer not to take any step bigger than 0. I don't know a good way to see where the high energy is coming from. Maybe you could try minimizing some very small set of the atoms with the rest fixed. By trying minimizing different movable sets of atoms you could see where the high energy is coming from. I'm not sure this will work, because it could be that the step size is forced to be tiny even if the high energy is caused by fixed atoms. You'd have to experiment to figure that out. I'll be interested to hear what you figure out. Another idea that could help you figure this out -- the Chimera "minimize" command has a new "fragment true|false" option that allows you to minimize just part of a molecule. It is different from holding atoms fixed. With fixed atoms as you have tried, the fixed atoms still contribute to the force field. With "fragment true" and the minimize command only the specified atoms contribute to the force field, the others being completely ignored. This fragment option is not available in the minimize dialog. It was added in Chimera 1.6. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html I see it would be nice to have Chimera be able to color your atoms and bonds in a way that reflects the energy terms for involving each atom and bond. Not sure if that info is available in the dynamics library Chimera uses, MMTK. That would allow you to quickly spot the problem. Tom Hi there, I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to<5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms. Am I in a local minima? Is that why nothing moves? The energy is very high (from the Reply Log): Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps Any ideas? I do have some hetero atoms... Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.