January 2014 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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Question about opening mrc and PDB files
by Min Woo Sung 03 Feb '14

03 Feb '14

Hi, This is Min Woo Sung from Texas A&M University. I was using Chimera to see EM structure(.mrc file) and wanted to put a PDB file to fit that in EM map. I'm wondering if I can use Chimera to analyze the volume, size or domains of these two files for the purpose of analysis. I saw one PDB file seemed much bigger that EM map when I opened it in Chimera. Do I have to normalize the size of any files? If so, how can I do that? Any suggests would greatly appreciated. Best regard, Min Woo Sung

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Creating output with IDATM naming
by Nikolay Igorovich Rodionov 03 Feb '14

03 Feb '14

Hi, Does anyone know a way to rename all of the atom names in a PDB file to their IDATM types, so that a new PDB file can be generated with the IDATM naming scheme? Best, Nikolay Rodionov

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Need help in Coulombic surface coloring
by Haresh Tukaram More 30 Jan '14

30 Jan '14

Hi, I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand. Disabled GPU programs because a graphics driver bug was encountered while compiling a vertex shader. #0, chain A: COMP #0, chain B: COMP #0, chain C: COMP #0, chain D: COMP #0, chain E: COMP C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2 22 connected surface components Total solvent excluded surface area = 10393.6 component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429 Total solvent accessible surface area = 10372 component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705 No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E Chain-final residues that are not actual C terminii: 424 hydrogen bonds Hydrogens added Charge model: AMBER ff12SB Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (TFLE+TFLE) Cannot automatically determine charges for residue TFLE+TFLE; Run AddCharge tool manually to add charges and then rerun ESP Can someone please tell me a step by step procedure to make this work. Thanks & Regards, Haresh

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Re: [Chimera-users] Coloring map by curvature
by Tom Goddard 29 Jan '14

29 Jan '14

Hi Joel, I don't think surface curvature will be helpful understand the differences between two EM maps. But I was curious what it would look like. So here's a Python script and an image on a simulated map at 15 Angstroms. You use the script by opening your map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open…). Here's a description of the method it uses from the comments at the top of the curvature.py file. # Color selected surface pieces by mean curvature. # # Gray at the average curvature value over the surface, and blue and red # at +/- 3 standard deviations of curvature values across the surface. # # The curvature is estimated from the vertices and normals of the triangulated # surface in simple way which will show artifacts from non-isotropic meshes. # For each triangle edge it computes the normal vector rotation from one vertex # to the other divided by the edge length. The vertex mean curvature is the # mean of the curvatures computed for each edge. # And the steps to make the example image open 1grl molmap #0 15 grid 2 model #1 select #1 open ~/Desktop/curvature.py Tom On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote: > Hi Darrell, > Thanks for the tip! I hadn't considered mesh lab but that link you sent looks promising. I'll also wait to see if Tom has any further suggestions. > Joel > > > On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: > Hi Joel, > > I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it describes what I think Tom was communicating about enhancing surface shading: > http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-a… > > FWIW, > 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 > > > 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. > > From: <Meyerson>, "Joel [F] (NIH/NCI)" > Date: Tuesday, January 28, 2014 9:08 PM > To: Tom Goddard > Cc: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> > > Subject: Re: [Chimera-users] Coloring map by curvature > > Hi Tom, > I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on how I interpret the conformations. If there's any other info I can provide just let me know. > Thanks! > Joel > > > On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote: > Hi Joel, > > No, Chimera does not compute surface curvature. It would not be too hard to make a Python script that computed it and used it to color a surface. The main trouble is defining numerically the curvature for a triangulated surface at each vertex. Why are you interested in this? Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter? Is the idea to try it on EM maps or molecular surfaces? > > Tom > > > On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote: > > > Hi, > > Is it possible to color a map based on surface curvature? > > Thanks, > > Joel > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > >

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Coloring map by curvature
by Joel Meyerson 29 Jan '14

29 Jan '14

Hi, Is it possible to color a map based on surface curvature? Thanks, Joel

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adding GalNac moiety on Threonine residue
by Elsa Marquez 28 Jan '14

28 Jan '14

Hi there! Do you guys know if I can add or somehow draw a carbohydrate moiety such as GalNac to a single Threonine in a protein complex? Thanks! Elsa Marquez University of Alberta

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Surface Transparency Command Issues
by Joshua Carter 28 Jan '14

28 Jan '14

Hello, I'm having trouble getting the surface transparency command to work correctly. I'm currently making a movie about the formation of a protein complex and I want the subunits to be shown as ribbons while they dock and then after they dock the electrostatic surface to appear. I have the script written and the surface generated but when I use either the surftransp or transparency command nothing happens. The command is correct, if I use it to change the transparency of a ribbon or atom it does so, but if I try to make the surface appear after docking nothing changes. In addition, if I go to the Actions menu and change the surface transparency from there it also works. If you could help me figure out why the command won't work that would be extremely helpful. Thanks,Josh

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