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Re: [Chimera-users] [Open Babel] UCSF Dock mol2 files
by Scott Brozell 06 Apr '12

06 Apr '12

Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ? thanks, scott On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 > http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek(a)wojcikowski.pl > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff(a)geoffhutchison.net> napisał: > > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff

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Selecting submodels when they are density maps
by Javier Velazquez 05 Apr '12

05 Apr '12

Hi, I am interested in generating a map from a PDB with 2 chains, and color each chain differently. I can do it very easily using the graphical interface, but I couldn't figure out how to do it from the command line. Here are my commands: molmap #0:.A 7 molmap #0:.B 7 And now adding color is simple: volume #0 color red But this adds color to both maps. Is there a way to specify a submap, so I can add color separately. I am looking for something like this: volume #0:.A color red which I tried and didn't work. Thank you for your help. Javier

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Merge the protein sequences of two different chains
by Hsih-Te Yang 05 Apr '12

05 Apr '12

Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te

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Solvate models
by Nikolay Igorovich Rodionov 05 Apr '12

05 Apr '12

Hi all, I was wondering if some could explain to me the differences between the water models available under the solvate option. * POL3BOX - POL3 water model * SPCBOX - SPC/E water model * SPCFWBOX - SPC/Fw water model * QSPCFWBOX - qSPC/Fw water model * TIP3PBOX - TIP3P water model * TIP3PFBOX - TIP3P/F water model * TIP4PBOX - TIP4P water model * TIP4PEWBOX - TIP4P/Ew water model Thank you all in advance, Nikolay Rodionov

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Coloring distance labels
by George Tzotzos 05 Apr '12

05 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

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Coloring distance labels
by George Tzotzos 05 Apr '12

05 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

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color by RMSD
by Thomas Evangelidis 04 Apr '12

04 Apr '12

Dear UCSF Chimera users and developers, Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them? thanks in advance, Thomas

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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] 03 Apr '12

03 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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