- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] vop cover
by Elaine Meng 18 Sep '13

18 Sep '13

Hi Pradeep, That message is saying you must specify the density map. I.e. if the atomic structure is model #0 and the density map is model #1, the command could be something like vop cover #1 atom #0 Command usage and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. it is recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly - thanks! On Sep 18, 2013, at 2:02 PM, Pradeep Pallan wrote: > Hi Elaine, > > I was looking at using vop cover. I have a case where part of the molecule > is not within electron density box. The map cuts off at the unit cell dimensions, > and my space group is P1. Where I need edensity is approximately at y= -10. > When I try the command > 'vop cover "atom"', it gives the message "file.pdb is not a volume". > > Is this the right way of getting the molecule covered in e density or do I need > to use a different option. > > Thank you, > PP

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Problem Using Transparency Command in Chimera
by Joshua Carter 18 Sep '13

18 Sep '13

Hi, My name is Josh Carter and I am an undergraduate researcher working at Montana State University. I am using chimera to make a movie a a protein complex interaction and I'm having trouble with the transparency command. When I type in just the command into chimera it doesn't even recognize it as a command. surftransp works but transp or transparency aren't recognized. Is there a bug fix I can run for this? Thanks,Josh

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How to determine the distance from SG of Cys to the centroid of a nearby Trp ring
by Pande, Ajay K 17 Sep '13

17 Sep '13

I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.

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colour by attributes is only colouring one chain of the dimer, how to make the colouring apply to both chains of homodimer
by Anne-Frances Miller 17 Sep '13

17 Sep '13

Dear team Chimers 1- Thank you for GREAT software ! 2- How to make the colouring apply to both chains of homodimer ? I have a homodimer in which features of the active site derive from both monomers so the degree of active site conservation will only show up if I can apply colour by attributes to both monomers (attribute will be conservation) Right now, colour by attributes is only colouring one chain of the dimer, chain A. Anne-Frances Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055

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Chimera Questions
by Serina Doolittle 16 Sep '13

16 Sep '13

Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view. If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do. Serina Doolittle serinadoolittle(a)me.com 912-665-3259 Armstrong Atlantic State University Student

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How to move a domain in mouse mode /move selection
by Juergen Joachim Mueller 12 Sep '13

12 Sep '13

Hallo, how can I move a domain consisting of 3 chains using mouse mode/ move selection? I will use chain A: 6-121, chainB: 7-103, Chain C: 6-103. The selection by command line takes always the longest number 121 for all three chains - A:6-121, B:7-121, C:6-121. Greetings, Jürgen (Chimera production version 1.8 (build 38824) Windows8)

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How to modify a structure to put some atoms in a plane....
by Sergio Garay 12 Sep '13

12 Sep '13

Hi all I'm trying to put a Nitrogen atoms of a Nitro group in the same plane that a imidazol ring, but until now with no success. I've tried using modify structure and changing the bond and geometry of the carbon to which the Nitrogen is joined, but it did not work. I attached an image with the problem. I've also tried to minimize the structure using AMBER ff (despite I know that this ff is not appropriate for small organic molecules) but it can fix the problem. May be I'm not clear enough so, I summarize: I want to put the Nitro group in the same plane of a imidazol ring (look at the picture, please). Any advice will be appreciated. [image: Inline image 1] Sergio -- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Solvent Channel Dimensions
by Thompson, Matthew K 12 Sep '13

12 Sep '13

How can I measure the dimensions of a solvent channel in a protein? The channel is clearly visible after the surface in generated. In addition, the cavity can be created with Surfnet. Something like "Measure and Color Blobs" does not give the dimensions I need. I am interested in the width of the channel at its most narrow point. Thanks Matt

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Re: [Chimera-users] automatically calculated labels for quantitative tomography data
by Tom Goddard 11 Sep '13

11 Sep '13

Hi Martin, Thanks for the detailed explanation. I think a generalization of your idea might be useful to more people. Basically you could create a text label including an automatically updated numeric value, but that number could be calculated from a density map contour level, or a molecular dynamics trajectory energy value, or a distance between a residue and ligand during a conformational change -- in other words the numerical value could measure many things. The case of just density map threshold levels has some utility, but since the same value can be seen in the volume dialog where you actually change the value, it seems more for presentation than analysis. The general tool would take significant work, because Chimera doesn't have a framework for providing measurement updates. We are working on the next generation of Chimera and this graphical label idea is interesting because we are looking at having fewer dialogs -- even a Chimera in a web browser. Maybe instead of using a separate volume dialog you could just display the threshold levels like you have done, and simply use the mouse to directly change those values in the graphics window. You've mentioned movie making. The labeling in your figure can be included in Chimera movies now, and the values can change, and labels fade in and out. Most Chimera movies are made with command scripts and these label operations would use the 2dlabels command. Granted with your proposed tool it might be easier to make the movie, but I'd say only slightly easier, because the overall movie making is not simple and the labels are just one small aspect. I have worked with Carolyn Larabell's group looking at their x-ray tomography data using Chimera some years back. They concluded Amira better suited their needs for doing segmentation. Here is a demo I gave showing what Chimera could do with their Pombe cell tomography. http://www.cgl.ucsf.edu/chimera/data/ncxt-feb2008/xraytomography.html Tom On Sep 11, 2013, at 5:05 PM, Martin de Jonge wrote: > Hi Tom, > > Thanks for the reply. I guess you raise a few questions, so I'll try and pick them individually. > > 1. the concept > >>> Or maybe it doesn't need a separate window -- you might just be able to say display colored labels in the graphics (e.g. "Zn 11" "Cu 47" "Ca 1500") for several density maps that list both an element name and the current contour level. You could control those levels using the Volume Viewer dialog and the labels would automatically update. > > Yes, I think that's what I was thinking. In the image I linked you to earlier, the threshold levels were manually entered into the color key. Every time the threshold changed these entries had to be updated also. In the new implementation one might enter into the color key dialog: "Ca {#3 * 1000}", where "#3" represents the threshold level for model number 3, the " * 1000" indicates multiplication by 1000, and the curly brackets indicate the presence of a substitutional expression. (Of course you would want to make this syntax consistent with Chimera!) > > The thinking about the simple mathematical operations is that sometimes the reconstructed data is only relatively scaled, and needs a final conversion factor to become a 'real' unit. Alternately, one might have data in ng/µm^3 and wish to convert to ug/cm^3, in which case multiplication by some power of 10 would be nice. In other cases the mathematical function could enable a change from units of mass/volume to molarity. Don't worry too much about this idea - it is probably not worth the effort, and can probably be performed by other means. > > 2. the user base > > I agree that at present there is not much call for this feature, however I note that two forms of x-ray tomography have recently entered the quantitative domain: x-ray fluorescence tomography (now performed by 10+ groups around the world) and soft-x-ray absorption tomography, performed most notably by the group of Larabell and LeGros at the UCSF (see eg http://www.ncbi.nlm.nih.gov/pubmed/21360734) (have you made contact with that group? I /think/ they render with Amira, but they are putting heaps of computing effort into automated segmentation of their LAC data, and I imagine this could be a good team to collaborate / share resources with). But I appreciate that the tomography user base would not rise to 1000 within 5 years, and therefore that this extension may not be practicable. > > I think this feature would be useful for the other main Chimera user base, which I gather is the protein crystallography (PX) / molecular modelling / imaging people. I guess my thinking here is that one of the great features of Chimera is the ability to explore the dataset dynamically, by adjusting thresholds, rotating, etc. This applies also for molecular / PX data. For all cases it is useful to adjust the threshold (being now generalised to either linear absorption coefficient (LAC), elemental concentration, or electron density) to see different features. This is usually done with the slider, or from the cmd line, but can also be scripted in movies etc. My suggestion (that I think you have understood in general, but repeat for clarity) is that there could be a mechanism to display the present threshold in a key on the display window. As such it could be one (electron density, LAC) or several (elemental concentration) numbers that are transferred into the key. > > Why am I saying this? Just in case you think there might be some other call for this feature from the other user base! I leave it to you to decide, and fully accept your knowledge of the Chimera user base! > > Thanks for the response, and for developing a great piece of software. Let me know if there is anything I can do in return (besides acknowledgement / citation!). > > [PS - I took the chimera-users off the response just in case you think the Larabell comments are politically sensitive. I don't mind if they go out - I stand by my words - I'll leave it to you to decide, and to forward the mail to the development team as you see fit.] > > Yours, > > Martin de Jonge > > > > > > -----Original Message----- > From: Tom Goddard [mailto:goddard@sonic.net] > Sent: Thursday, 12 September 2013 8:16 AM > To: Martin de Jonge > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] automatically calculated labels for quantitative tomography data > > Hi Martin, > > Your elemental abundance tomography is interesting. I'm not sure I understand your Chimera suggestion. Do you mean there would be a separate window that lists the threshold levels for Zn, Cu, Fe, Mn density maps in type-in fields and adjusting the values would both change the contour level (as is done by the Volume Viewer tool) and update the labels displayed in the graphics window (as with the 2D Label tool)? Or maybe it doesn't need a separate window -- you might just be able to say display colored labels in the graphics (e.g. "Zn 11" "Cu 47" "Ca 1500") for several density maps that list both an element name and the current contour level. You could control those levels using the Volume Viewer dialog and the labels would automatically update. (By the way, did you know you can display 6 or 10 histograms in the Volume Viewer dialog instead of the normal limit of 3? Use volume dialog menu Features / Data Display Options and change "Maximum number of Histograms.", and use Features / Save Default Dialog Settings if you want that to be the default for future Chimera uses.) I don't understand what you mean by "include simple mathematical operations". > > If I understand your basic idea, I think it is specialized enough that only a few Chimera users would use it. I'm not sure I've ever seen a figure like yours with values that correspond directly to density map levels, because usually the density map values have some meaningless normalization. Most often presentation figure keys need to be created in an entirely custom way appropriate to the content of the figure. Still I think the feature you suggest would be cool, but given the hundreds of improvements people have requested we try to work on ones that lots of Chimera users (500 or 1000) will benefit from, or requests that allow you to do something that isn't otherwise possible. > > Tom > > > On Sep 10, 2013, at 7:56 PM, Martin de Jonge wrote: > >> Hi all, >> >> this might sound like a strange feature, but I use Chimera to render quantitative tomography data. I typically render somewhere between 2 and 6 separate elements (i.e., Zn, Cu, Fe, Mn, etc) and present these with a colour key, along with a numerical value to indicate the threshold concentration (typically in mmol or similar unit). There is an example of such data in: http://www.pnas.org/content/107/36/15676/F1.expansion.html >> >> When exploring such data it is very useful to adjust the display threshold, as various anatomical features appear at very different concentration levels. My suggestion / request is to have a numerical field in the colour key that can be linked to (eg) the per-model thresholds to indicate the concentration threshold at that moment. This would be particularly useful for making movies for presentations and articles. >> >> Some thoughts on useful properties of this numerical field: >> >> - it should inherit the colour of the colour-key label that it is associated with (or be able to select to be inheritable) >> - it could include simple mathematical operations, for when there is a simple relationship between the data and the reportable concentration eg, *, /, +, - >> - one should be able to specify the format of the number (using the usual formatting codes). >> >> thanks >> >> Martin de Jonge >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

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automatically calculated labels for quantitative tomography data
by Martin de Jonge 11 Sep '13

11 Sep '13

Hi all, this might sound like a strange feature, but I use Chimera to render quantitative tomography data. I typically render somewhere between 2 and 6 separate elements (i.e., Zn, Cu, Fe, Mn, etc) and present these with a colour key, along with a numerical value to indicate the threshold concentration (typically in mmol or similar unit). There is an example of such data in: http://www.pnas.org/content/107/36/15676/F1.expansion.html When exploring such data it is very useful to adjust the display threshold, as various anatomical features appear at very different concentration levels. My suggestion / request is to have a numerical field in the colour key that can be linked to (eg) the per-model thresholds to indicate the concentration threshold at that moment. This would be particularly useful for making movies for presentations and articles. Some thoughts on useful properties of this numerical field: - it should inherit the colour of the colour-key label that it is associated with (or be able to select to be inheritable) - it could include simple mathematical operations, for when there is a simple relationship between the data and the reportable concentration eg, *, /, +, - - one should be able to specify the format of the number (using the usual formatting codes). thanks Martin de Jonge

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Re: [Chimera-users] accuracy of fitting atomic structure in density map at different resolution
by Tom Goddard 11 Sep '13

11 Sep '13

Hi Andy, Do you mean how much fits vary depending on EM map resolution? I suppose you could apply Gaussian filtering to the EM map to produce a lower resolution EM map, then fit your atomic model, then see how much motion and rotation there is of a fit at one resolution from a fit at another resolution. All that is easy in Chimera. To compare different fits I would open multiple copies of the same atomic model and fit one to each different map then use the "measure rotation" command (e.g. "measure rotation #2 #3") to see how much motion there is between fits. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation With any other fitting software you could do the same test by exporting the Gaussian smoothed maps from Chimera, fitting with other software, writing out fit PDBs with the other software and then loading those PDBs in Chimera and comparing their orientation. In that case you'd want to use the Chimera "match" command to measure the motion between models (e.g. match #2 #3 showMatrix true, the look in Reply Log for results). The "measure rotation" only reports coordinate frame motions done within Chimera, whereas "match" aligns two atomic models. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Tom On Sep 11, 2013, at 7:13 AM, Anindito Sen <emailanindito(a)yahoo.co.in> wrote: > Hi Tom, > > Is there any method by which, we can figure out the accuracy of docking of an atomic structure into its EM density map generated at different resolutions and by different software packages? > > Thanks > > Andy > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo >> Tel & fax: +81-3-5841-3339 >

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Minimization units
by Elisabeth Ortega 09 Sep '13

09 Sep '13

Dear Chimera dev. team, I have a very simple question regarding Energy Minimization. The energy units are kcal/mol or kJ/mol? In this function, chimera uses the MMTK function to calculate the energy, and, as far as I know, MMTK energy units are kJ/mol (in share/MMMD/MMTKinter.py the units of the length are corrected to angstroms, but the energies don't). I took a look in the previous e-mails of the chimera-users list. I saw some texts that refers to the energy in kcal/mol and I am a bit confused. Thank you for your time. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: eortega(a)qf.uab.cat

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Querie: Ligand superimposition
by Graziella Portelli 09 Sep '13

09 Sep '13

Dear Chimera Team Hope this email finds you in good health. I am using UCSF Chimeria for my de Novo drug design disseration. I am still learning the basic functions that this software offers, however have not been able to figure out the following. Basically I need to put into one picture/frame the original ligand or my receptor and the possible ligands (generated by Ligbuilder). They have the same general structure with some changes and I need to superimpose them, but show them at separate levels. Is this possible to do this for only the ligands and not the receptor protein? I eagerly await your reply, Graziella Portelli B.Pharm

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Color Isosurface in Chimera
by Gregor Weiss 05 Sep '13

05 Sep '13

Hello, I tried to color different parts of an isosurface obtained by an electron cryotomogram to point out structures more clearly. Unfortunately, I didn't figure out how I can select different areas and color them differently. Which tool fits here the best? I can determine an area and subsequent color all structures in this area with the tool "Color Zone", but I was not able to select another area and choose a different color. Thank you very much for your help! With best regards, Gregor Weiss -- Gregor Weiss, B.Sc. Summer Researchassistant Jensenlab California Institute of Technology, HHMI Mail code 114-96 1200 E. California Blvd. Pasadena, CA 91125 626-395-8848 (phone)

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about the command: match
by 韩晓东 05 Sep '13

05 Sep '13

Dear sir, it is no doubt the UCSF chimera is a very excellent software. However, when i use the command: match iterate 2.0 site2 site1, a problem appeared as follows: unequal numbers of atoms chosen for evaluation. would you kindly share me the skill to deal with this problem. thank you very much for your time. sincerely yours, xiaodong han.

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Re: [Chimera-users] Chimera hbond
by Elaine Meng 05 Sep '13

05 Sep '13

On Sep 5, 2013, at 2:40 AM, Neha Gandhi <n.gandhiau(a)gmail.com> wrote: > Hi Elaine, > > I was going through your response on chimera mailing list regarding > saving h-bond analyses during MD ensemble/movie. Either one can write > files every nth frame or save log files. Is there a way to put all the > output of the frames one by one in one single file? > > Your help is appreciated. > > -- > Regards, > Dr. Neha S. Gandhi, > Curtin Research Fellow, > School of Biomedical Sciences, > Curtin University, > Perth GPO U1987 > Australia > LinkedIn > Research Gate Hi Neha, Writing the information to the Reply Log does not save a file. You can accumulate multiple sets of results in the Reply Log and then, at the end, save the Reply Log contents to a single file. The "findhbond" command has two separate options to write results to a file ("saveFile true") and to write results to the reply log ("log true"). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html> You can save the contents of the Reply Log (in menu under Favorites) to a file with its Save button. 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 P.S. please send chimera questions to chimera-users(a)cgl.ucsf.edu (CC'd on this message) instead of to me directly - thanks!

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display atom by coordinates
by Bala subramanian 03 Sep '13

03 Sep '13

Friends, I am trying to visualize the md movie of a channel protein. In every frame, i want to display only those ions whose Z coord ranges from -10 to 35 (zcoor of the channel) to make the movie. Is there any simple way ?. Precisely displaying atoms with a condition. Thanks in advance, Bala -- C. Balasubramanian

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Linking two chains in a PDB file
by Maxwell Cherf 03 Sep '13

03 Sep '13

Hi Sir/Madam I have a PDB file of three proteins bound together (in one model). I would like to fuse the N terminus of one protein to the C terminus of another protein by adding a peptide linker between the termini. Is it possible to do this using Chimera? So far, I have built a linker and joined it to one of the termini, but doing that combined the linker and all proteins in the file into one model. Now, I can't connect the free end of the linker to the other terminus because they are part of the same model. Any help would be much appreciated! Best, Gerald Cherf, PhD candidate Cochran Lab Bioengineering Department Stanford University

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problem with SwissSidechain plugin installation
by Thomas Evangelidis 03 Sep '13

03 Sep '13

Greetings, I have a problem with SwissSidechain Chimera plugin in Linux 86_64 (Centos 6.3). I followed the instructions yesterday and could use it to create a D-peptide: http://swisssidechain.ch/visualization/chimera.html However today I can't. I tried to add it several times to Preferences->Tools->Locations without any luck. I even did a fresh install of the current stable release and rebooted but I still can't use it. I remember I encountered similar problems in the past. Do you know what's wrong? Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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help
by rajan sreekanth 30 Aug '13

30 Aug '13

Hi, I had morphed two conformations (open and close) of my protein using 'Morph Conformations' tool. I want know whether we can save the coordinates capturing the intermediate states? Something like an NMR ensemble consisting of the open-intermediate states-close conformations as a single PDB file? Thanks Sreekanth

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Re: [Chimera-users] building a peptide
by Elaine Meng 30 Aug '13

30 Aug '13

Hi Kumud, You would just specify the phi and psi angles for "turn" when building the peptide. You can specify a different phi and psi for each residue if you want, in the peptide building dialog. You do not have to use the values supplied for alpha and beta, you can enter any values, as described in the instructions: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Also, in a peptide structure that already exists, you can change phi and psi for each residue, either ...by rotating the bond interactively (see the Adjust Torsions tab in Build Structure): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> or ...by changing the "phi" and "psi" attribute values in the Selection Inspector (select an amino acid residue in a peptide or protein, click green magnifying glass near bottom right of Chimera window to open the Inspector, Inspect: "Residue" and change the values for "phi angle" and "psi angle") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> However, it is up to you to specify reasonable values. You can check the Ramachandran map by using the "Ramachandran plot" function in the Model Panel (under Favorites in the menu). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/rama…> Although it is possible to build a whole protein with different secondary structures, it would probably have many severe problems (packing etc.) and the basic peptide-building in Chimera is *not* intended for this purpose. You might want to look into using some other program to predict structure instead, or modify an existing protein structure instead of building the whole thing from scratch. There are probably hundreds of programs and dozens of web servers to predict protein structure, but it is beyond the scope of the chimera-users list and my knowledge to discuss the possibilities. 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 Aug 29, 2013, at 11:50 PM, Kumud Agarwal wrote: > Hi, > Thank you for your help. > Is there any way to build a beta sheet in Chimera? How can I introduce > turns in between the strands in beta sheet using the build structure > option in chimera?

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Chimera VTK file reader
by Tom Goddard 29 Aug '13

29 Aug '13

Hi Andrew, I added a VTK file reader -- in tonight's Chimera daily build. It handles vtk structured points files in ascii format like the one you gave me. Your file had many -32768 values which seem to indicate regions where you don't have data and normal data values in a range 0 to 55. This makes the histogram display of data values in Chimera worthless because the data range is 33000 but the meaningful range is 55. Chimera is only able to show the whole range. You might want to use some other value to indicate "no data", like -1 if negative values are not valid. Tom > On Aug 6, 2013, at 10:09 AM, Andrew VanBenschoten wrote: > >> Hi Elaine, >> I hope all is well! Quick question for you: I have a 3D .vtk file (attached) that I want to be able to view in Chimera. This is one of the diffuse scatter maps that we discussed earlier: nearly identical to X-ray diffraction patterns except that the data values are applied to entire voxels as opposed to points. Any suggestions as to what I could try? Thank you so much! >> >> -Andrew >> <out.vtk> > >

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building a peptide
by Kumud Agarwal 28 Aug '13

28 Aug '13

Hi I am very new to Chimera. I am using Chimera version 1.8. I am trying to build a peptide in chimera in beta strand conformation using build structure option but the generated peptide did not show beta strand. Why is it so? Thanks, Kumud Agarwal IIT Bombay India

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Make bonds in a large polypeptide
by Francesco Pietra 27 Aug '13

27 Aug '13

Hello; Is there a limit in the number of atoms when using the function "make a bond"? I was trying that in a polypeptide of 450 standard residues (I made it a single model) and it did not work. Just to not be cryptic, that need arises from having modeled by special techniques the initial portion of the polypeptide. Now I would like to replace that portion with the modeled one. I had restrained with rmsd-colvars the dihedrals of a short stretch of alpha helix, so that I could align the modeled portion with the polypeptide. thanks francesco pietra

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some questions about new features, in particular MD
by Lionel Nauton 24 Aug '13

24 Aug '13

Hello I was very pleasantly surprised to discover a molecular dynamics module in the latest version of chimera, I used already "MD movie" to see the dynamics with NAMD made, but the ability to make dynamic from chimera is a real plus, thank you for that. in spite of this, one thing I do not understand why the minimization phase is parallelizedin the dynamics module and is not in standard mode, is a planned evolution, I'm too impatient? Second, in the latest version (21-08-2013), I can not read trajectories files from GROMACS , I saturate the RAM (16 GB and 7 GB swap) and the program exits.the same dynamics made with NAMD in .dcd formatworks well, any idea ? that's all thanks for your very good job.

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