April 2012 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [Chimera] #10638: heme not included in morph trajectory
by Elaine Meng 04 Apr '12

04 Apr '12

Hi Francesco, There is some progress... in the newest daily build (Apr 4) I can run the commands below to successfully show a morph of 1hho and 2hhb that includes heme and iron. 1hho only has two chains, so it is necessary to delete C,D from 2hhb before morphing. To include heme and iron, it is necessary to delete all the other het residues that may be different between the structures. I hope this helps, Elaine Here between "----" are contents of Chimera command file, which you could save as plain text file named something.cmd and open in Chimera to execute the commands. Lines starting with # are just comments/explanation and don't do anything. ------------- open 2hhb open 1hho # # delete 2hhb chains C,D # delete #0:.c-d # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose the structures; I used "mm" with defaults but it could be # done with options, or MatchMaker GUI, or "match" command, # or manually with mouse # mm #0 #1 # # create morph trajectory which will be model #2 # morph start #0 frames 25 morph interpolate #1 frames 25 morph movie ~modeldisp #0,1 --------------------- Then I tried to get fancy and make a tetramer of 1hho so that the morph could be from tetramer to tetramer. However, then only the heme/iron from A and B were included, not from C and D. I don't know why, because they are all in the input structures!! Here is that script in case it might be useful: --------------------- open 2hhb open 1hho # # make 1hho tetramer; #1 is original, #2 additional copy # sym #1 # # combine #1,2 dimers into tetramer model #3, close #1,2 # combine #1,2 name 1hho-tetra newchainids true close true # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose #0 and #3 # mm #0 #3 # # create morph trajectory which will be model #1 # morph start #0 frames 25 morph interpolate #3 frames 25 morph movie ~modeldisp #0,3 ---------------------

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occupancy field
by Darjan Andrejc 03 Apr '12

03 Apr '12

Hey, Is it possible to change occupancy field to 1.0 in Chimera? I need a pdb file of my protein for docking and the file needs to have an occupancy field 1.0. Thanks for the help Darjan Andrejc, Mpharm PhD student, Department of Biotechnology National institute of Chemistry, Ljubljana, Slovenia

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Minimize with fixed atoms
by Hurt, Darrell (NIH/NIAID) [E] 02 Apr '12

02 Apr '12

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.

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Chimera-users April 2012