- Chimera-users - RBVI Mailing Lists

Coloring selected residues based on B-factor
by Mahendra B Thapa 07 May '15

07 May '15

Dear Chimera users, While using Chimera to study a protein with 511 residues, I colored residues 1- 274 'dark grey', residues 274-417 'tan' and residues 418-511 'dark khaki'. I want to color residues, say, 313,350,412,415,485,503, from blue to red with an increasing order of B-factors, say respective B-factors are 40,13,2,21,33,6 without altering the color of other residues. I manually put these B-factors values for the corresponding residues; rest residues have no b-factor values as the structure is obtained from a simulation. I tried some unsuccessful attempts visiting some previous posts (sorry if I missed such posts close to my query). Any comments and suggestions might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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aborting a volume command
by Dougherty, Matthew T 07 May '15

07 May '15

I issued this command, which works correctly. volume #2 planes z,1,100,1,10 I try to abort it around slice 50 using freeze, which does not terminate. Is there a way to abort it? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Displaying and calculating protein surface enclosed pockets
by Matthias Fellner 07 May '15

07 May '15

Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software. Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question. I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket. How can I display the "negative" (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details. If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed. Thank you Matthias Fellner

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listen selection command
by Mungo Carstairs (Staff) 07 May '15

07 May '15

Hi, I am trying out a REST listener for selections in Chimera and need help. I can talk to Chimera over REST. I can start an Http listener in Jalview - and verify it in my browser. I have sent this command to Chimera: listen start selection rest http://134.36.162.131:64745/ Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification. I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel. I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection. What have I missed or how can I diagnose what I am doing wrong here? Thanks, Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

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Re: [Chimera-users] [chimera-dev] VolumeEraser
by Tom Goddard 06 May '15

06 May '15

Hi Alex, Surfnet in Chimera does not produce a volume, only surfaces. It calculates the volume but then computes surfaces and deletes the volume. If you would to measure the enclosed volume of the disconnected pieces produced by surfnet, first make those pieces independently selectable with command sop split #0 where #0 is the id for the surfnet model (use Favorites / Model Panel to find the correct id number). Then select the piece of interest (ctrl click on it), then get its enclosed volume with command measure volume sel To type commands to Chimera use menu Favorites / Command Line. This question belongs on the chimera-users mailing list, not the chimera-dev list which is for programming issues. Tom > On May 6, 2015, at 8:18 AM, Alex wrote: > > Dear Sirs, > I recently started using chimera, please apologise my lack of knowledge. > In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? > If you know, please point out the article which describes the procedure for this kind of volume calculation. > > Best regards, > Alex > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>

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PC shut down automatically while using Chimera
by kzhang＠mrc-lmb.cam.ac.uk 06 May '15

06 May '15

Dear Chimera Developers, Recently, I found something really annoying when I was using Chimera. The problem is that when I use chimera to display CryoEM maps(400X400X400, 32 bits), my computer shut down automatically. I don't think there's something wrong with the hardware and coot or pymol is fine. This is not just an accident. It happened quite a few times, especially when I suddenly zoom in, computer is suddenly shut down. Later there would be some error massage related to the instability of the power, CPU self protection "£$%^&# ... when I turned on the computer again. But I don't think there is anything wrong with the power as well, I've run other softwares without any problem. Also, it happens to both Window 7 and CentOS 6.5 in the same PC. So it's obviously hardware level issue related to Chimera. My guess is that there might be something in Chimera that activated the self-protection of CPU or similar things. Any ideas why this occurs and how can I solve it? Best wishes Kai

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imod
by Dougherty, Matthew T 04 May '15

04 May '15

I have recently been getting some imod segmentation files and have been noticing three problems 1) when I read the MRC and imod files I am having a scaling problem, and the datasets do not integrate. For example, if the MRC voxel size is 31.22 31.22 31.22, and the origin index is 0 -114 0, I have to change the the voxel size to 3.122 3.122 3.122 , and the origin index to 0 0 0 so that graphics match correctly. Since there are number of people in the data chain before it gets to me, I thought it might check to determine if this is known problem before going upstream to unknown people to figure out if they are getting the imod output settings correct. 2) The graphics performance with imod segmentation files is sluggish in chimera, not sure what it is in imod. I assume that the format defines the vertices at the highest resolution corresponding with the MRC file. Is there a way to improve the performance on the chimera side? I am not using contouring, just reading the file in default mode. 3) The segmentation has a lot of components, such as vesicles and microtubules, that have different colors. Is there a way to break apart the components so they can be manipulated seperately? E.g., display/hide, change colors, translate and rotate. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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running script + recording movie
by Dmitry 04 May '15

04 May '15

Dear colleagues, Does anybody know how to run the script in chimera - *.cmd (from windows) and in the same time record everything that script does as a movie? Sincerely, Dmitry

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chimera meeting tomorrow
by Greg Couch 29 Apr '15

29 Apr '15

The agenda is available in advance! Thank you Conrad! Conrad says "feel free to add items" :-) https://plato.cgl.ucsf.edu/trac/chimera2/wiki/2015-4-30

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Auto dock Vina Increasing Exhaustiveness
by Tunc Morova 29 Apr '15

29 Apr '15

Hello! I am using UCSF Chimera, Autodock Vina extension for obtaining conformations of my protein and ligand. In this interface, As you know, I can change the exhaustiveness value between 1-8. However, since my system is more than 30x30x30 A, I need to get my exhaustiveness value more than 8 for getting more accurate results. But I can’t make it more than 8 through Auto dock Vina interface in Chimera. How can I increase this exhaustiveness value ? Btw, Instead of using Opal web service, I am using vina locally. Thank you many times for your help Best Regards Tunc Morova

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Converting sdf file into mol2 format
by Mahendra B Thapa 29 Apr '15

29 Apr '15

Dear Chimera users, I am trying to convert sdf file ( downloaded from* diversity set* data from 'http://scs.illinois.edu/htsf/compound_collection/nci.php') into mol2 format. When I ran the command chimera --nogui processSDF.py as given the previous posting ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html) I got the following error messages: Cannot find consistent set of bond orders for ring system containing atom #0.73:1@N1 --- Unknown redo atom type: N3 Traceback (most recent call last): Any suggestions for correcting these errors will be a good help for me. Thank you, Mahendra Thapa University of Cincinnati,OH

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Create an artificial bond between ribbons for 3D printing
by David Bhella 28 Apr '15

28 Apr '15

Dear Chimera users, I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long. The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported. Any suggestions would be gratefully received. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Delete Bug?
by Korbin West 27 Apr '15

27 Apr '15

Hi all, I'm running some code on Chimera to select only certain chains and nearby aspects, but when I try to delete the extraneous information, Chimera freezes up. I'll detail the commands I use below, and for reference I'm interested in the H chain of 1CT1, but it doesn't seem to work with any of its chains. open 1CT1 zonesel :.h 3.5 extend true select invert del sel It then freezes on del sel. I've tried this with other pdb files and it works fine, but for some reason it stops on this one. For example, it works fine on 1PZ3 for its A and B chains. Is this some kind of bug or is there a work-around to this issue? We looked at the residues and couldn't find anything out of place, so we are not sure what is happening. Much thanks in advance. Best, Korbin West? Wabash College

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Making a composite residue
by Repic Matej 23 Apr '15

23 Apr '15

Hello, I wonder if it is possible to construct a composite residue from two existing residues in Chimera? What I would like to do is concatenate residues ALA100 (mid chain) and GLY200 (end of chain) to make a composite residue AGL100. Chimera won't let me set the same residue number via the "resrenumber" command. Preferably, the composite residue would have all the atoms listed where ALA100 was in the original pdb. While I realize there are trivial text editor-based workarounds I would like to know if there is a native way. Thank you all, ---------------------------------------- Matej Repic Ecole Polytechnique Fédérale de Lausanne SB - ISIC - LCBC BCH 4108 CH - 1015 Lausanne ----------------------------------------

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about volume viewer
by 张雷 21 Apr '15

21 Apr '15

Hi, the experts of Chimera, I am a new user of Chimera and have a question to consult you. When I display a 3D model in the volume viewer, I found that there was an original value of the level, as the attached figure shown. If I increased and decreased the values of level, the densities of 3D models were different. Therefore, how to deternime the right value of level for a protein. It is known that the average density of proteins is 1.35 g/cm3; If a protein has a molecular weight of 1350 kDa, and 1 Da = 1.66054E-27 kg; therefore, the protein volume is 1661 nm3.If I want to display the volume of 1661 nm3 in chimera, how can I decide the value of level? In another words, how can I calculate the value of level from the actual volume of a protein? Thank you! Best wishes! Lei Zhang Peking University, Beijing, China

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Re: [Chimera-users] coloring individual segments of a protein
by Greg Couch 21 Apr '15

21 Apr '15

To get a different resolution than 72 dpi, you need to turn on the "Use print units" option in the Save Image dialog, and set the "Print resolution" and pick the image width and height. Or you can use a program like Adobe PhotoShop or GIMP to edit the DPI if you already have an image that you like. HTH, Greg On 04/21/2015 03:01 PM, A G Szabo wrote: > Greg > > Thanks for your reply > > > I had just sent Elaine another question that perhaps you might be able to > answer. > > I am currently writing a book and the editor would like the protein > structure images saved with at 300 dpi. When I saved an image of > Ribonuclease, PDB 5RSA, both as a png file and a Jpeg file the editor > indicated that the resolution was not sufficient and was only 72 dpi. > > Suggestions? > > Thanks > > ags

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Residue Numbers vs. Residue Codes
by Korbin West 21 Apr '15

21 Apr '15

Hi all, I'm trying to determine uncommon ligands in pdb files using a python code, but have run into an odd dilemma. In my code, I open a pdb in Chimera, select the ligand, and write out the residue list. However, the formatting of this list changes depending on how I run the program. If I run the program through xterm, it will print out only residue numbers. If I run the program though Chimera's Idle, however, I will get the residue codes and the residue numbers. For example, I ran this with 3VKG, you can see the results in the attached files, where I show a sample code of what I'm using, the xterm results and the Chimera results. I want to do this for a large number of pdbs, so I'd like to do this --nogui through xterm, but I need the residue codes. Has anyone else ran into this problem or know of a work-around? Thanks in advance. Best, Korbin West Wabash College

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coloring individual segments of a protein
by A G Szabo 21 Apr '15

21 Apr '15

How do I use Chimera to color a protein in the following way: for example: Helix 1 - red Helix 2 - yellow Helix 3 - magenta Strand 1 - dark blue Strand 2 - cyan Etc. A G Szabo

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keyboard accelerators
by Dougherty, Matthew T 20 Apr '15

20 Apr '15

Hi, had a few questions about the documentation. A click in the graphics window may be required. Sometimes it is necessary to click in the graphics window to take back focus from some other dialog so that accelerator or command keystrokes will register. >> is there a way to send accelerators through the Viewing-Side View? I have been dedicating one monitor for the 3D graphics and the other for control, menus, etc. using various USB devices sending accelerators. Would prefer not put to the focus/mouse cursor on the 3D graphics. Accelerators could be shown on menu entries. The keyboard shortcuts could be shown on the corresponding menu entries to make them easier to learn.? >> How? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Help in MD movie
by Ankit Agrawal 18 Apr '15

18 Apr '15

Hi I have trajectory file from gromacs and opened in chimera. Now I am doing inertia calculation. I wrote a python script to show the ellipsoid. But this script is showing only the ellipsoid. I want ellipsoid as well as the molecular structure of that frame, i.e. both ellipsoid and the molecule. so that I can show the how molecule is changing its position. This is like a structure overlay but I want it with ellipsoid. thanks regards Ankit Agrawal

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Reducing the map to a cubic box
by Sushree Tripathy 17 Apr '15

17 Apr '15

Hi, I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. Please help. Thanks Sushree. Sushree Tripathy Graduate Student Department of Physics University at Buffalo

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Generating a map from atomic molecule
by Tom Goddard 17 Apr '15

17 Apr '15

Hi Zhihai, The reason your map surface shows the triangulation is because the grid spacing is large. You made the map with molmap with 30A resolution. By default molmap sets the grid spacing to 1/3 of the requested resolution, so 10 Angstroms in this case. Apparently this is too coarse for your needs. So spedify a finer grid spacing in the molmap command. For instance molmap #0 30 gridSpacing 3 to produce 30 A resolution with 3 A grid spacing. Here is the molmap documentation http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html> Tom > On Apr 16, 2015, at 8:45 PM, 李智海 wrote: > > Hi Tom, > It seems that the low-resolution (about 30A) map generated from atomic model by “molmap" has many artifacts on its surface (see first attached figure), and I can see many rectangle signatures of it in Fourier space (see 2nd attached figure) so that I can not use it as the start map for further reconstruction. > Please tell me how can I get rid of this. Thank you! > > Best wishes! > > > Zhihai Li > > <molmap_30A.png><FFT.png> > > Zhihai Li > > Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. > School of Life Sciences, Xiamen University. > Xiang'an Road(South), Xiang'an District, Xiamen City, > Fujian Province, China. > >> On Apr 15, 2015, at 1:28 AM, Tom Goddard wrote: >> >> Hi Zhihai, >> >> If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid. If #0 is the atomic model and #1 the reference map. >> >> molmap #0 8 edgePadding 50 >> vop resample #0 onGrid #1 >> >> Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map. >> >> Tom >> >> >> >>> On Apr 13, 2015, at 9:00 PM, 李智海 wrote: >>> >>> hi, >>> here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. >>> I have met some questions to successfully finish these work. >>> >>> 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. >>> >>> 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. >>> >>> >>> Thanks in advanced! >>> >>> Best wishes! >>> >>> Zhihai Li >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >

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on script which can be read and executed by chimera
by Smith Liu 17 Apr '15

17 Apr '15

Dear All, Will you please introduce to me a web link on how to compile and edit scripts which can be read and executed by Chimera? I am looking forward to getting your reply. Smith

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the "select" funtion of mouse is disable
by sunyeping 16 Apr '15

16 Apr '15

Dear all,I find the "select" funtion of mouse in Chimera is disable. I can not use "ctrl+left mouse button" to select any item in the structure. Have you met this problem before? My systems is windows 7 and the Chimera version is 1.10.1. How to solve this problem? Do I need to change some setting?Best regards,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Re: [Chimera-users] Reducing the map to a cubic box
by Tom Goddard 15 Apr '15

15 Apr '15

In Chimera “atoms” means an atomic model, for example from a PDB file, not a density map. If you want to reduce your map to a cube by cropping and it is size 54,36,51 use command volume #0 region 0,0,0,35,35,35 That gets the lower left corner. To get the center part volume #0 region 9,0,7,44,35,42 The 6 numbers are imin,jmin,kmin,imax,jmax,kmax where i,j,k are indices along the 3 map axes. You can also do this with the Volume Viewer dialog menu entry Features / Region Bounds, or interactively with the mouse using Features / Subregion Selection. For more info about map manipulations http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom > On Apr 15, 2015, at 1:17 PM, Sushree Tripathy wrote: > > Hi, > > Thanks for your prompt reply. What I am trying to do is I have a map which I have loaded in chimera as #0. Now I want to reduce it to cubic size. Since the syntax is "vop boxes <> volume-spec atom-spec <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> size d", so I am choosing #0 for my volume and all the atoms in that volume. so #0 again. Please correct me if I am wrong. > > > Thanks > Sushree. > > Sushree Tripathy > Graduate Student > Department of Physics > University at Buffalo > > On Wed, Apr 15, 2015 at 4:13 PM, Tom Goddard wrote: > Hi Sushree, > > Why does your "vop boxes” command use model #0 for both the map and the markers? That can’t be right. If your marker(s) are in model #1 you would need “vop boxes #0 #1 size 36”. What are you trying to do? > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes> > > Tom > > > >> On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote: >> >> Hi, >> >> I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. >> >> Please help. >> Thanks >> Sushree. >> >> >> Sushree Tripathy >> Graduate Student >> Department of Physics >> University at Buffalo >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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