- Chimera-users - RBVI Mailing Lists

pocket cavity file produced by rdock
by Fabian Glaser 02 Mar '14

02 Mar '14

Hi all, I am trying to upload and examine the cavity file produced by the rbcavity program from rdock, an open source docking program. There are both a binary form and a regular file "RBT FFT GRID" but I am not able to upload or visualize them. Can you please help me to do it? Files are attached. Thanks a lot, Fabian

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Using sym command to generate icosahedral cage
by Yen-Ting Lai 26 Feb '14

26 Feb '14

Hi, I noticed that the sym command can be used to generate icosahedral symmetry, but it requires that the molecule to be oriented in specific ways (222, 2n5, n25, ...), which requires aligning the symmetry axes to the X, Y or Z axes. I am wondering if there is a way to specify the symmetries axes by vectors (instead of aligning them to the three principal axes) and then use sym command to generate the whole icosahedral cage? Yen

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Chimera hardware resources
by Derrick Smith 18 Feb '14

18 Feb '14

Hi Chimera users, I've been working with what are probably some pretty big files (400 MB - 3 GB) for ultramicrotomed sections of holograms. I've trimmed the volume down as well as I can while keeping it large enough to see what we ultimately were aiming for. However, I am running into some hardware resource issues. None of our computers in the lab can handle it, so I've been using my gaming rig at home to do it. I run a server off it also, so have some decent hardware to work with, but I cannot figure out how to reallocate the resources that Chimera seems to default to. I have 64 GB of system RAM available, and after recording 1-2 movies of rotations or a flythrough of clippings etc. Chimera has never used more than 1.5 GB. My graphics card has 4 GB. After filtering and post-processing, before any rotation or video capturing, the vid card has used around 2 GB already. During video capture, depending on if I'm rotating or clipping (clipping uses up a lot more faster), the vid card memory slowly gets eaten up, eventually crashing Chimera altogether. I can usually only get about 800-1000 frames before this happens on a smaller file (400 MB), and usually can't get through a whole 10s, or 250 framed, video on one of the larger files. I have pretty limited experience with this program, so I'm hoping it's a simple settings or otherwise fix I've overlooked. Any suggestions on this? Best, Derrick -- Derrick Smith Drexel University Soft Materials Group Philadelphia PA 19104 dms348(a)drexel.edu http://www.mse.drexel.edu/srg/

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Receptor-Ligand bonding at the LBP
by Graziella Portelli 13 Feb '14

13 Feb '14

To whom it may concern I would like to ask if there is a function where the bonds with which the ligand binds inside the LBP of the receptor would be visualised, or whether one has to search the amino acids involved in binding with the ligand one by one? I thank you in advance for your time Graziella Portelli

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Symmetry-aware segmentation?
by Joel Meyerson 13 Feb '14

13 Feb '14

Is it possible for Chimera to segment with an awareness of symmetry, such that the collection of segments in the asymmetric units are identical? For example, a molecule with C2 symmetry would have two copies of each segment. Also, is it possible to select a segment and then have Chimera further sub-divide that segment into additional segments? Thanks, Joel

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when will NoResidueRotamersError be raised?
by Xiao-Bo Li 13 Feb '14

13 Feb '14

I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original. I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY. If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error. XBL

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Problem in using BondRot
by amin＠imtech.res.in 13 Feb '14

13 Feb '14

Dear Chimera users, I am trying to write a script to change the phi and psi angle of a peptide. I am trying to adapt the code from http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-September/000456.html . I am trying to invert the angles so I am multiplying the angles by -1. My code is import chimera from chimera import selection, UserError, BondRot, replyobj opened = chimera.openModels.open('fun.pdb') mol = opened[0] RES_LIST = mol.residues for res in mol.residues: b = str(res.phi) if b != 'None': c = -1*float(b) atomsMap = res.atomsMap N = atomsMap['N'][0] CA = atomsMap['CA'][0] C = atomsMap['C'][0] CAmap = CA.bondsMap phiBond = CAmap[N] psiBond = CAmap[C] phiAnchor = N psiAnchor = CA phi = BondRot(phiBond) phi.setAngle(c, phiAnchor) When I run this script i get the error phi.setAngle(c, phiAnchor) AttributeError: '_molecule.BondRot' object has no attribute 'setAngle' Can someone please help me with this? Warm regards. Amin.

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un-subscribe
by Ted Holman 13 Feb '14

13 Feb '14

hi there i made a mistake and signed up for the email questions on chimera to be copied to me. i tried to un-subscribe but it did not work. can you tell me how to do this? thanks ted ___ Ted Holman, Ph.D. Professor Chemistry and Biochemistry Department 250 PSB, Thimann Receiving University of California, Santa Cruz Santa Cruz, CA 95064 Phone: 831-459-5884 Email: holman(a)ucsc.edu

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vrml lighting
by Dougherty, Matthew T 12 Feb '14

12 Feb '14

I have a multiple vrml models that vary by scale. 1, 10 & 100 I notice the lighting significantly drops off as the scale increases. When I have another model, say PDB, that is in approximate relation (ie, viewable in regards to the volume size similar to the vrml files volumes); the PDB file looks good regardless of size (eg, tRNA or ribosome). I can increase the brightness to compensate (10-20) but it washes out the PDB models when brightness goes beyond 2. is the lighting handled differently between these different types of models? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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superimposing two structures based on a specific selection
by David Martin 10 Feb '14

10 Feb '14

Chimera 1.8 on Windows I have been trying to align (superimpose) models based on a specific conserved region. Unfortunately Chimera doesn't seem to do what the documentation claims it does. I run (example): match #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA and get an RMSD calculation (more on this below), but no movement of the model occurs. I specify 'move true show true' as options. Still no movement but I have a transformation matrix. Unfortunately this is not in a form that can be understood by Transform Coordinates. How do I persuade my structures to superimpose on the specific atoms? The RMSD calculation appears to be broken. If I take the command rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA then I will get a number If I then run rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,21-31@CA I get exactly the same number. In fact, if I specify atom sets of different sizes (as long as it is not the first block) then I continue to get exactly the same number rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-35@CA This should fail but doesn't Have I completely misunderstood what Chimera should be doing here? ..d The University of Dundee is a registered Scottish Charity, No: SC015096

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Query on introducing an external protein
by Aditya Padhi 06 Feb '14

06 Feb '14

Dear All, I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different. Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions. Thanking you, Regards Aditya.

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Query on introducing a protein
by Aditya Padhi 05 Feb '14

05 Feb '14

Dear All, I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different. Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions. Thanking you, Regards Aditya.

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Question about "Color Zone" and "Render by Attribute"
by Helge Paternoga 04 Feb '14

04 Feb '14

Hello, I have a question regarding the colouring of surfaces and their caps. I am trying to recreate the colouring by hydrophobicity on capped surfaces as shown in (on the right side): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.… So first I've opened the "Render by Attribute" dialog and assigned "kdHydrophobicity". This only coloured the surface and not the surface cap though. I am assuming this is done by "Color Zone"? Indeed this colours the surface cap but I have one problem: The colouring of the surface is different between "Render by Attribute" and "Color Zone" and I don't know why. The differences are small but I would like to know which one is more accurate (intuitively I would say the one from "Render by Attribute"). I've played around with the radius of "Color Zone" but this doesn't achieve the same colouring as "Render by Attribute". So my question is: How can I achieve the same surface colouring by "Color Zone" as in "Render by Attribute"? Does it have something to to with "bondzone" or the hierachy in which the atoms apply their respective colour in "Color Zone"? Thanks for reading! Helge

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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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Zoom problem?
by Damien Larivière 03 Feb '14

03 Feb '14

Dear all, I try to zoom in the scene, to get very close to my model shown here below. I cannot be closer than in the image below, the zooming function is at its maximum. When zooming, I get the error message : /refocus to continue scaling/ I do not know whether it is a bug or something I'm doing wrong. Thanks for your help, Damien

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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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Re: [Chimera-users] Overlay structures in Chimera (UNCLASSIFIED)
by Elaine Meng 28 Jan '14

28 Jan '14

On Jan 28, 2014, at 9:45 AM, "Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US)" <sarah.l.keasey.ctr(a)mail.mil> wrote: > Elaine, > > I have a new question regarding overlaying structures using Chimera. > > I have opened two structures in Chimera. I am trying to move them so that they are overlaid. It appears as though I should be able to inactivate one of the structures in order to freely move the other, but this doesn't work for me and I'm not sure where I am going wrong. When I inactivate one structure, I can freely rotate the other, but not move it from one place to another. I have watched the youtube video here: http://www.youtube.com/watch?v=6VGYo1pRRZ8 which deals with merging two structures, and also watched the "Sequential Fitting" video on the "Videos" page of the UCSF Chimera site. > > Any suggestions for what I am doing wrong? I apologize for such elementary questions, I am a new Chimera user. > > Thanks in advance, > Sarah Keasey Hi Sarah, (we generally ask everyone to send questions to chimera-users(a)cgl.ucsf.edu, CC'd here, so that everybody can benefit, unless the data are private) Those videos aren't that relevant to your situation. More relevant is the manual page discussing the various ways to superimpose structures. The Chimera User's Guide can be searched or browsed from the Help menu, or you can see the same thing on our website, e.g.: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> If using the mouse to move one structure, what you did is exactly correct: inactivate the other structure. The mouse should continue to work exactly the same for the movable structure as when everything was movable (both rotation and translation). The default control for XY-translation is middle mouse button, if you have one. For touchpad or mouse with fewer buttons, see here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> However, more often one doesn't use the tedious approach of trying to do it by hand, and instead uses one of the other superposition methods. The easiest is usually MatchMaker (in the menu under Tools… Structure Comparison), so I would try that first. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> To help you become more familiar with Chimera, there are several tutorials in the User's Guide (again also available from Help menu), ranging from "getting started" to more advanced. <http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> 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

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Multialign Viewer Header Definition File (UNCLASSIFIED)
by Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US) 24 Jan '14

24 Jan '14

Classification: UNCLASSIFIED Caveats: NONE Hello, I would like to generate a Header Definition File to load in to Multialign Viewer. I am unclear on the format of the file though, I keep getting errors when I try to load the file in and I think it has something to do with the way I am formatting the file. Would you be able to provide an example Header Definition file? Thank you in advance, Sarah Keasey Graduate Student University of Maryland, Baltimore County ORISE participant, USAMRIID, Fort Detrick MD Classification: UNCLASSIFIED Caveats: NONE

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Segger : command line
by agnel-praveen.joseph＠stfc.ac.uk 24 Jan '14

24 Jan '14

Hi, I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs? Many Thanks. -- Scanned by iCritical.

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Chimera Issues
by Roy Assis 22 Jan '14

22 Jan '14

Hello ! For some time i've been using chimera, but for some reason a week ago, when I try to lunch chimera, I get an error message (attached). Please help Roy Assis

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movie recode
by Wenda Wang 21 Jan '14

21 Jan '14

Dear List, I am trying to use UCSF chimera to make a movie after TEM reconstruction using IMOD. But an error message always pops out, even I use the script in the examples. Belows shows the error messages in the Reply Log. Can anyone take a look and give me some clue where the problem is? Thank you. ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -vf crop=(in_w/2)*2:(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -vb 200.0k C:\Users\Public\Desktop\rock.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libvpx -f webm -vb 200.0k C:\Users\Public\Desktop\rock.webm An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libtheora -f ogg -vb 200.0k C:\Users\Public\Desktop\rock.ogv An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: Thank you very much, Wenda Wenda Wang, PhD candidate Department of Materials Sciences and Engineering, Drexel University, Philadelphia, PA 215-6883348

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Morphing
by James Naismith 20 Jan '14

20 Jan '14

I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work. I am using a MAC OSX latest version. I have created my morph which is running nicely. What I would like to do is analyse the morph for VDW clashes. (That is in going from structure 1 to structure 2, what residues would have to move). First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations When I click OK or apply I get a new box residue interaction contact parameters This always generates an error “No atoms designated for clash detection’ I seem only to have four options themselves all others atoms (default) other atoms in same model second set of designated atoms Any help gratefully received (Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version) best Jim Jim Naismith The University of St Andrews is a charity registered in Scotland : No SC013532

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Re: [Chimera-users] [Chimera] #12778: failure assigning charges to FAD (was: Chimera bug report submission)
by Eric Pettersen 17 Jan '14

17 Jan '14

Hi Will, The underlying program that Chimera uses to compute charges, antechamber/sqm from AmberTools, frequently fails for molecules with regions of concentrated negative charge, such as the central phosphate connector of FAD. It not really something I can do much about. Nonetheless, the failure not only depends on the charge density but also on the specific atomic geometry. So for instance, I can compute the charges for the FAD in 4kpu, though it does take a long time (about 10 minutes). This means that there is kind of a work around. Compute the charges in a structure that works and then transfer them to your structure. You do this by bringing up the Render by Attribute tool after successfully computing charges and using it's File->Save Attributes menu entry to save the charges to a file. You should select the FAD and then restrict the save to selected atoms. Edit the resulting file and change the residue name and chain ID (in this case 401.A) to FAD so that it can be applied to all FADs in your structure. Then in the Chimera with your structure open, read in the charge-attribute file with the Define Attributes tool. To save you a lot of the effort here, I've attached the edited charge-attribute file I saved from 4kpu. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to display coordinate axes
by Michael H Peters 17 Jan '14

17 Jan '14

Hi: I have a simple question - How do I display the lab or fixed frame coordinate axes? I am using the windows 32 bit UCSF Chimera on my desktop. In rasmol the command is "axes on". I cannot find anything similar in Chimera. Thanks for your help. An axes display is critical if you need to know the spatial orientation wrt the lab frame. Best wishes, Michael Dr. Michael H. Peters mpeters(a)vcu.edu 804-828-7790 www.engineering.vcu.edu/proteinengineering

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pyroglutamate distorted in 3PFJ
by Craig Dana 17 Jan '14

17 Jan '14

I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is clearly distorted, but when I open the same PDB file in VMD, the pyroglutamate is not distorted.

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Failed to start chimera
by jupiter 17 Jan '14

17 Jan '14

Hi, I installed Chimera 1.7 on CentOS 6.4. I can run any opengl applications, but failed to run chimera , it got following error message. Appreciate any tips to fix this issue. X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 72 (X_PutImage) Serial number of failed request: 34 Current serial number in output stream: 37

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Re: [Chimera-users] rna and set shadows commands
by Elaine Meng 16 Jan '14

16 Jan '14

On Jan 9, 2014, at 12:07 PM, "pythonchemia Gazeta.pl" <pythonchemia(a)gazeta.pl> wrote: > > Hello Elaine C. Meng > > Thank you very much for your reply and sorry that I answer only now. > When it comes to command rna path and rna model your tips helped me. :) > Although I do not know how to define the path for the command operations rna duplex. : ( > > Unfortunately for me the system WinXP / Chimera 1.8 - 32bit shadows set command does not work. : ( > Chimera returns this message: > > - Unable to turn on shadows (shadows not supported) > > After opening the Chimera Reply log returns this message: > > Disabled programs because the GPU and graphics driver bug > you encountered while compiling a vertex shader. > -------------------------------------------------- ----------- > > Maybe my graphics card is inappropriate? > > The User's Guide about the Build Structure writes that the helical DNA / RNA (not yet Implemented ) > and this option is disabled. > > Sincerely, Janusz Grabowski Hi Janusz, The message suggests your computer can't do the shadows. It might help to update your graphics driver, but I don't know for certain. However, other "set" options should work, for example: set bgColor white As mentioned in the "rna duplex" description, the path file is created using the command "rna path": <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#duplex> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#path> Also, as mentioned in an earlier message you have to get a daily build (version 1.9), also available from our download page, to use the "helical DNA/RNA" option in Build Structure. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009497.html> It is recommended to send chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly. Thanks, Elaine

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Re: [Chimera-users] batch writing of attributes
by Eric Pettersen 14 Jan '14

14 Jan '14

Hi Jay, We thought as much really. Well, you are going to have to use a Python script. The good news is that it's a really simple Python script. Put the following in a file whose name ends in ".py": from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): from OpenSave import osOpen f = osOpen("~/surfData/%s.data" % m.name, "w") for a in m.atoms: print>>f, a, getattr(a, "areaSES", 0.0) f.close() The indentation matters, so make sure to preserve it. Then once you open your model and surface it, you can run the above script simply by opening it with the "open" command. It will create a file with a list of atoms and corresponding surface areas. The file will be named <model name>.data and it will be in the "surfData" folder in your home directory, so make sure that folder exists beforehand or modify the script to have it go to another location. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 14, 2014, at 5:56 AM, "Eifler, Jay Q. (UMKC-Student)" wrote: > Actually I'm doing ab-initio quantum mechanical calculations and need > to analyze on a atom and residue basis. I've already been able to > save the atom and residue results but can't figure out how to automate > it since you have got to click buttons in the render/select attribute. The > Chimera notes seem to imply it should be possible to save attributes to > file. However, areaSAS is supposed to be an attribute but doesn't seem > to belong to the model attributes. > From: Eric Pettersen > Sent: Monday, January 13, 2014 4:05 PM > To: Eifler, Jay Q. (UMKC-Student) > Cc: <Chimera-users(a)cgl.ucsf.edu> List > Subject: Re: [Chimera-users] batch writing of attributes > > On Jan 11, 2014, at 1:58 PM, Jay Eifler wrote: > >> >> I'm trying to automate saving the areaSAS for a bunch >> of models. I've got no problem loading the models, etc. >> The problem is simply how do I use command line >> arguments to save the areaSAS. I've tried writesel. This >> works all fine in Render/Select by attribute simply >> because it has a feature to save the areaSAS to a file. >> Thanks. > > Hi Jay, > Do you really need the values on a per-atom basis? If you just need the grand total, it's reported in the reply log so you could just open and surface your structures one by one via a script (one by one to avoid possibly running out of memory) and then afterward save the reply log contents to a file manually (there's a "Save" button on the reply log). > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu

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Problem with HEADER keyword in PDBs
by Thomas Hrabe 14 Jan '14

14 Jan '14

Hi everyone, I believe I found a problem with the >HEADER< keyword in PDB files. Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below. PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain. Thanks, Thomas

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MD trajectory play by commandline
by inhee park 14 Jan '14

14 Jan '14

Dear Chimera developers and users: I am using Chimera (production version 1.8 (build 38824) 2013-06-07 21:09:20 UTC). I wanted to process MD trajectories to extract their detailed H-bond information. To do so, I would like to process by script with Hbond.py file. $ chimera --script Hbond.py #---[Hbond.py] from chimera import runCommand # pr trajectory movie with open("metafile", 'w') as m: meta_input = """amber mypdb.prmtop pr_dry_netcdf.crd """ print >> m, meta_input # runCommand("open movie:metafile") runCommand("alias ^myhb hbond relax true savefile hbond.$1") runCommand("perframe myhb") runCommand("coordset #0 1,1000,10; wait 100") #----------------------- As I have many MD trajectories to be processed, I was looking for a commandline in lieu of actually clicking buttons in MD movie GUI to play. I thought that "coordset #0 1,10000,10; wait 100" may operate like automatically starting the MD movie to load frame 1 to 1000 at every 100 interval. But resulting saved H-bond files contain same information all about the first frame (because graphically displayed was the first frame without any update unless clicking the button in MD movie GUI). Is there a way to achieve an automatic play via commandline? Thank you, inhee park

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RMSD per residue NMR structure
by cantini＠cerm.unifi.it 14 Jan '14

14 Jan '14

Dear users Does anyone knows how to calculate through CHIMERA the backbone rmsd per residue of a NMR ensembles of protein structures ? thank a lot Francesca Cantini ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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batch writing of attributes
by Jay Eifler 13 Jan '14

13 Jan '14

I'm trying to automate saving the areaSAS for a bunch of models. I've got no problem loading the models, etc. The problem is simply how do I use command line arguments to save the areaSAS. I've tried writesel. This works all fine in Render/Select by attribute simply because it has a feature to save the areaSAS to a file. Thanks.

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Computing solvent accessible area without internal cavities
by Tom Goddard 13 Jan '14

13 Jan '14

Hi Numan, Chimera uses the MSMS program to compute solvent accessible surface area, and MSMS has an option to only compute for the outside surface component without internal cavities. So I think this is just what you want. Although you could script it in Chimera you might find it easier to write a script that uses the standalone program directly from Michel Sanner http://mgl.scripps.edu/people/sanner/html/msms_home.html The one trouble you may run into is the calculation failing on some molecules due to numerical instabilities. The older version of the MSMS library we use in Chimera often fails to compute the surfaces and areas for molecules larger than 10,000 atoms, and sometimes fails for much smaller molecules. The standalone program from Michel failed much less often in tests I did a few years ago, probably because it used some newer more reliable code. Tom On Jan 13, 2014, at 11:13 AM, "Oezguen, Numan" wrote: > Dear Tom, > > I am facing a problem that you have most probably already have solved and hoping you could help me out. I need to identify atoms that are solvent accessible. For this I used the program Getarea from Werner Braun’s group in Galveston Texas. It works fine, however it lists also internal cavity surface atoms as solvent exposed. Technically it is correct… but I am interested only in those surface areas that are not internal i.e. surface areas that are accessible to molecules approaching it from outside. > > Do you know of any commercial or free (preferably) program that can do this. Ideally it should be possible to call it from scripts (shell or Perl). > > Thank you very much for you time and help, > Numan > > > Numan Oezguen, Dr. rer. nat. > Instructor of Pathology & Immunology > Texas Children’s Microbiome Center > Feigin Center, Suite 830 > 1102 Bates Avenue > Houston, TX 77030

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Registration ?
by Jean-Paul Boissel 13 Jan '14

13 Jan '14

Just downloaded the new dally build. At opening got the message: Registration file "/Users/JPB/.chimera/registration" has expired. Do we have to register again for 2014 Thanks > > Dr. Jean-Paul Boissel, Team Leader > Solute Transport Through Biological Membranes/ Ellen I. Closs' group > Department of Pharmacology > University Medical Center of the Johannes Gutenberg-University > Obere Zahlbacher Strasse 67, D-55101 Mainz > Tel.: +49 6131-17 9189 > FAX: +49 6131-17 9329 > e-mail: boissel(a)uni-mainz.de > http://www.unimedizin-mainz.de/pharmakologie/research/solute-transport-thro… > -biological-membranes.html?L=1 > This e-mail contains confidential information and may also be legally > privileged. If you are not the intended recipient or received this mail by > mistake, please inform the sender immediately and delete the mail. Any > un-authorized use, copying, disclosure or forwarding of this mail and of > information contained therein is prohibited.

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displaying electrostatic field
by Bala subramanian 10 Jan '14

10 Jan '14

Friends, Kindly see the following link (Fig 22, left panel). http://www.bioscience.org/2009/v14/af/3398/fulltext.php?bframe=figures.htm Has anyone tried making the display of electric field in Chimera. Is there any way i can make the same in chimera. Thanks, Bala -- C. Balasubramanian

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running wild with Chimera :-)
by Eric Pettersen 09 Jan '14

09 Jan '14

New Year Cards in 3D

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BioPython in a Chimera Python script; PDBio?
by Hurt, Darrell (NIH/NIAID) [E] 08 Jan '14

08 Jan '14

Hi Chimera friends, I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63: http://biopython.org/wiki/Download#Installation_Instructions The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck. I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython). Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix? Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information. Finally, is there an analogous "EMDBio" for EMDB records? 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 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> 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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Updating coordinates without having to regenerate the depiction of an atomic model
by Mike Lawrence 07 Jan '14

07 Jan '14

Hi, Within Chimera is there any way in which the underlying coordinates of an atomic model can be updated in order to yield the same depiction but based on the new coordinates, or (equivalently) can the attributes of one model be transferred to another, assuming of course that they have the same underlying protein sequence, etc. thanks Mike Lawrence Walter + Eliza Hall Institute of Medical Research Parkville Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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the old Mac OX 10.4 can not run Chimera
by Zhang, Yinghui 06 Jan '14

06 Jan '14

Dear Sir/Madam, This is Yinghui Zhang from Massachusetts General Hospital. I am a postdoc here and my project requires me to use the Chimera often. However, the desktop I used is some old and I can not update and use Chimera right now. The Chimera installed is 1.2 version but cannot be started. The specifics of computer is as follows: Apple PowerMac G5 chip, duo core and 3G memory. The OS is Mac OX 10.4.11. The operating system very probably cannot be updated because of chip version problem. Could you please give us some information if there is some alternative we can install executable Chimera on this computer? Thank you very much! Yinghui Zhang EDR 514, Dept. of Anesthesia MGH Boston, MA 02148 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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General question about Chimera
by Lili Peng 06 Jan '14

06 Jan '14

Hi, When I load a structure of a protein into Chimera, the structure is automatically rendered in ribbon mode, with select atoms being rendered in stick mode. I am curious as to why certain atoms are rendered as sticks, and other are not. What is the selection criteria? Thank you, Lili

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How to measure the radius of density map
by Jian Guan 03 Jan '14

03 Jan '14

Hi all, I have density map of virus (mrc format) and want to measure the radius of it. I tried measure command, High-order structure-->Icosahedron surface. Both of them need me to measure it manually by eye. Are there any tools to measure the radius by chimera, so we can get more accurate result? Or does anybody know how to measure it accurately? Thank you so much. Sincerely yours, Happy New Year. Jian -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request(a)cgl.ucsf.edu Sent: 2014年1月2日 15:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 129, Issue 1 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. rate of a reaction (Haider Abbas) 2. Error in generating sqm for FAD (Isha) 3. Re: rate of a reaction (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jan 2014 10:51:05 +0530 From: Haider Abbas <haiderabbasphy(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] rate of a reaction Message-ID: <CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas

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Error in generating sqm for FAD
by Isha 02 Jan '14

02 Jan '14

Dear Sir/Mam I used antechamber in chimera to add charges to ligand "FAD" using am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was Tools > structure editing > add H and then add charge. The error shown is : Charge model: AMBER ff03.r1 Assigning partial charges to residue FAD (net charge +1) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/binantechamber -ek qm_theory='AM1', -i c:usersamehtaappdatalocaltemptmpjjpoaqante.in.mol2 -fi mol2 -o c:usersamehtaappdatalocaltemptmpjjpoaqante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 412; net charge: 1 (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out (FAD) Error: cannot run ""C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue FAD Please help as it is very urgent. Hope for your reply. I have also attached the ligand. Please find the attachment. With Regards, Isha C/O Dr. Raman Parkesh Protein Science & Engg. Institute of Microbial Technology Sector 39A, Chandigarh 160036 Ext: 0172-6665489

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rate of a reaction
by Haider Abbas 02 Jan '14

02 Jan '14

Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas

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Set and rna commands
by pythonchemia Gazeta.pl 31 Dec '13

31 Dec '13

Hello ! I have winXP and Chimera version 1.8. I wanted to use the commands rna and set. Unfortunately, they do not work. Why? What is it? I tried to repeat the example of the User's Guide for rna command and failed. Please help me or give me examples on the set command and rna Sincerely, Janusz Grabowski

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Find pseudo 2-fold axes relating heavy and light chain
by Jian Guan 30 Dec '13

30 Dec '13

Dear all, I am trying to find pseudo 2-fold axes relating heavy and light chains in the constant domain and variable domain respectively in Fab. I tried Define Axes, it failed. And I made artificial double heavy chain, it failed again. I can only get axis which is horizontal passing through both light chain and heavy chain. It is not what I want. Can anyone help to give some clues? Thanks Jian

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