September 2013 - Chimera-users - RBVI Mailing Lists

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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Chimera-users September 2013