February 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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exported as PDB, but structure is not the same upon reopening
by Stern, Alexander Thomas 03 Mar '14

03 Mar '14

Hello, I am attempting to attach a covalent (cysteine modifying) ligand to my protein, and I will later be optimizing/minimizing in another program. I opened my structure in Chimera, loaded the ligands, moved them roughly into place, and merged the models. I then added the bonds and exported the file as a pdb. Upon reopening that very same pdb in Chimera, the bonds I made are gone (however, the ligands are in the position I placed them in). Curious to understand what I am doing incorrectly here. Alex 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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Expanding EMdatabank map to full map
by Jason C Porta 03 Mar '14

03 Mar '14

Greetings, I am searching for a way to take a map from the EMdatabank which is just a cut-out of an icosahedral asymmetric and generate the full map via the sym operators. I see there are similar options for generating sym-related models, but is there a way to do this for a section of a map in Chimera? Many thanks, Jason P

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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 25 Feb '14

25 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 12 Feb '14

12 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 04 Feb '14

04 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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