- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] transform coordinates of multiple volumes
by Elaine Meng 03 May '12

03 May '12

On Apr 27, 2012, at 9:26 AM, Ludovic Renault wrote: > Hi Elaine, > I have 120 or so 3d volumes (EM maps). They are all equivalent and are centered at the same position. > I would like to move each one of these 120 volumes by a specific value in terms of euler angles and shift (in pixels I assume). I can use the 'trAnsform coordinates' tool but then if I save the map, it is not saved with the new coordinates. > So > 1- How to (Or can I) save the new coordinates for each volume? > 2- Can I use command lines to automate the process for example by giving the command a text file with the specific coordinates for each volume? > > I did do the rotation with spider software, but the shifting doesn't work because the volume(s) go outside of the box. So if all the above is not doable, is it possible to increase the volumes boxe size in chimera, then I could use the shift function in spider? > > I hope I'm clear enough. > Thanks, > Ludovic Hi Ludovic, It is recommended to send Chimera questions to the chimera-users list (CC'd) -- I'm not the top expert on volumes, so others may have better answers! I think the shift in Transform Coordinates is not in pixels but in units of length. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor…> How the volume grid units map to units of length can be viewed by using Features...Coordinates in the Volume Viewer menu. Chimera has commands for translation (move) and rotation (turn) in X,Y,Z coordinate systems, but I don't know of a command to apply Euler rotations. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> About saving a transformed map: The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map. The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> The resampling of one map onto the grid of another can be done with command "vop resample", for example: vop #1 resample onGrid #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> To save the new resampled volume to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. However, I see that "vop resample" is most pertinent for saving a map that has been fitted to another. In your case you are simply transforming the map, so it is unclear on what grid you could resample. Maybe there is some way to make a "dummy" grid in the right place. Although "vop cover" extends a map, it assumes periodicity of that map, whereas I assume you want zeroes in the expanded parts. Perhaps expanding a map with zeroes could be done using "vop add" to add a dummy zero map to your data set of interest. Sorry I couldn't give a more complete solution, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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About resolution and origin
by Yuhong Li 02 May '12

02 May '12

Hi friends, Firstly, I was wondering how to know the resolution of my map since one day I opened volume viewer...tools...fit to segments. And I found that there displaying "density map resolution". So my question is whether that number is the correct resolution of my map? Secondly, in the volume viewer...corrdinates I can know the origin index, but how can I know the origin? These questions may seem to be stupid, but I just want to know. So hope to hear from you very soon! Best Wishes, Yuhong Lee

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changing map dimensions
by Elaine Meng 01 May '12

01 May '12

On Apr 30, 2012, at 6:56 PM, Yuhong Li wrote: > Hi Elaine, > Thanks for your help, now I've understood what those numbers mean. But I was wondering if you could tell me how I can change those gird points, such as change 88 66 94 to 94 94 94 or any cubic numbers ? > Best Wishes, > Yuhong Lee > Hi Yuhong, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Those numbers are the size of your input data file, so I'm not sure what you mean. You can't just change the numbers arbitrarily. It is possible to make a new data set by cutting off part of the original data set. One way to do that is to use the "volume" command to save a new map file, using the "saveSubregion" option to include only part of the original map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> However, it sounds like you want to make a new data set that is bigger than your original map. There is a "vop cover" command that will make a bigger map, but it assumes periodicity of the input map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> If instead you wanted values of zero at the additional grid points, however, I don't know how to do that -- maybe the others have ideas. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Just want atom distances
by Patricia LiWang 30 Apr '12

30 Apr '12

Hello users group, I don't want anything complicated-- I just want to get some rough distances between atoms. So I go to Tools Structure Analysis Distances A window comes up with an empty table. (No instructions on how to pick atoms) A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms But no matter how often I click and click and click, it never gives me anything. I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table. I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking" So I figure I'll just use the command line. But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms. There is documentation on how to get distances between something and a "plane". Why do they make this so hard? Surely this is the main "simple" thing people want to do with this program. Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance? Or better yet, please tell me the exact command line command I can use to get the distance between Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"? Thanks! Patti ---------------------------------------------------------------------------

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Measure contact between copies of the same map
by Giovanni Cardone 30 Apr '12

30 Apr '12

Hi, I can use the tool measure contactArea on the surface models of two different maps, but I can not make it work when using it on two copies of the same map: no matter how much I move one map with respect to the other, the first surface listed in the command line will always be entirely colored in red (using offset 0). It looks like the command ignores the transformation. Is this the expected behavior? I can work around it by resampling the maps after the transformation (vop resample # onGrid #), but I liked more the idea of doing the measure without this additional step. Tested it with the latest alpha version 1.7 (build 36320). Thank you, Giovanni

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Contour mapping
by Nikolay Igorovich Rodionov 30 Apr '12

30 Apr '12

Hi all, I was wondering if anyone could help me create an accurate contour map based on surface charge. I've tried rendering my molecule by charge, then using the surface clipping, capping, and the color zone tools. However, the coloring varies based on how I orient the plane. Does anyone know a better and more accurate way to creating a contour map? Nikolay Rodionov

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gaussian filter
by Mike Strauss 30 Apr '12

30 Apr '12

Hi, I've been using the gaussian filter for a number of years to help me display my noisy data. I'd like to understand what it's doing a bit better, and so I need help with the following code: ijk_linewidths = map(lambda step: linewidth / step, g.step) what is the resulting length of ijk_linewidths? I can't seem to figure out what type of data type g.step is. Is it a feature of the image itself, or where does it come from? Best Regards, mike

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About volume viewer in chimera 1.6.1
by Yuhong Li 30 Apr '12

30 Apr '12

Dear Chimera developers, Hi! I am a student from Sun Yat-Sen University. I recently began using the Chimera for my study, but I have a problem about how to read the displayed information in volume viewer. Here I attach a picture and inside the picture there are two places I've point out with arrows which represent two different map files in mrc fornat. Now I was wondering if you could spare some time to explain it to me that what do those different numbers mean? Hope to hear from your reply in very soon. Best Wishes, Yuhong Lee

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addaa command
by Mahendra B Thapa 27 Apr '12

27 Apr '12

Dear chimera users, I also added an amino acid residue at the N-terminus of a small protein following the posting: [Chimera-users] Using addaa at the N-terminus?*[ posted date:Fri Sep 30 10:36:31 PDT 2011]* The residue is added at the n-terminus but the added residue is not connected to rest of the protein structure in the graphical display [i.e, a little gap between the added residue and the rest of the protein at N-terminus]. Is this due to wrong command ? Thanks, Mahendra Thapa Graduate student Department of Physics University of Cincinnati, OH

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Per model clipping not working ?
by Damien Larivière 27 Apr '12

27 Apr '12

Dear all, I try to use the Per-Model clipping tool but this error is returned, whatever the PDB file: Model cannot currently be clipped [no valid bounding box] Do I make something wrong? I use Chimera version 1.6.1 (build 35849). My configuration is Windows 7 64bits, ATI Mobility Radeon HD5650. Many thanks for your help! Damien

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loading trajectories with no box line
by Michael F. Bruist 25 Apr '12

25 Apr '12

Is there a way to load trajectories that do not have box lines? I have trajectories from which most solvent and ions have been stripped. They were written with ptraj as amber coordinate files with the "nobox" option. I cannot get these to stay in register for MD movie. I do not have this problem for trajectories for which the box line has not been removed. Mike Bruist Dr. Michael F. Bruist Associate Professor of Biochemistry Department of Chemistry & Biochemistry Griffith Hall 147 University of the Sciences in Philadelphia Philadelphia, PA 19104-4495 Phone (Office & Voice Mail): (215) 596-8530 Department Phone: -8839 Department Fax: -8543 E-mail: m.bruist @usp.edu web page: http://tonga.usp.edu/bruist

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saving transformed map
by Elaine Meng 25 Apr '12

25 Apr '12

On Apr 25, 2012, at 9:04 AM, Ariane Briegel wrote: > Dear Elaine, > I have been using chimera to align several EM maps in respect to each other. > These maps are generated by imod (mrc format). I know I can save the transformed maps in chimera when I use the 'save session' command, but that only allows me to use the transformed maps inside chimera. I would like to save the individual transformed maps- either in mrc or CCP4 format. > I tried to find any info about that in the manual, then checked the old chimera list comments. I found a similar question from the year 2006 (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000864.html) but at that time your conclusion was it is not possible. > Do you know if there is a way to do this now? > Thank you so much for your answer, > Ariane Hi Ariane, The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map. The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> The resampling of one map onto the grid of another can be done with command "vop resample" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> For example: vop #1 resample onGrid #0 To save the resampling result to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Chimera-users Digest, Vol 108, Issue 25
by Boaz Shaanan 24 Apr '12

24 Apr '12

Hi, Elaine is correct in that newly deposited structures (since a year or so?) have to have their TLS information converted to aniso B and have those values in the appropriate place on the ATOM card. However, this was not the case for the older entries. The 1ss8 entry seems to have been refined by refmac5 from the ccp4 package. In this package there is a program called tlsanl which will do the job of converting the TLS infotmation to B-aniso. (a several seconds job) So maybe Steve could use it and thus solve his problem? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Tuesday, April 24, 2012 7:19 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 108, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: remote session (Greg Couch) 2. Rendering TLS information in Chimera ? (Steven Ludtke) 3. Incomplete chain contain many dotted lines while displaying (Junfeng Huang) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Apr 2012 12:05:41 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] remote session Message-ID: <4F95A805.1080609(a)cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" The error is that the OpenGL library is looking for a NVidia-specific extention to the remote protocol and failing when it is not there. That is a driver bug -- it shouldn't matter what graphics driver you have on either of the systems. There are two things I'd do to try and fix it: (1) try updating the NVidia driver on the remote computer that is running chimera (not the computer displaying chimera), and (2) try uninstalling the NVidia driver on the remote computer, and reverting to the software implementation of OpenGL (mesa). The first option is preferable if it works, because the proprietary (NVidia/AMD) drivers have been faster and less buggy than the mesa driver for most uses. Good luck, Greg On 04/20/2012 02:25 PM, Hernando J Sosa wrote: > > Hi > > I used to be able to run chimera remotely from a machine with an X- > windows server (the one that comes with Cygwin in this case). But now > I get the following error: > > Xlib: extension "NV-GLX" missing on display "localhost:10.0". > > X Error of failed request: BadRequest (invalid request code or no > such operation) > > Major opcode of failed request: 148 (GLX) > > Minor opcode of failed request: 181 () > > Serial number of failed request: 12779 > > Current serial number in output stream: 12784 > > I t does work fine if run directly from the computer where chimera is > installed. Any idea what the problem could be? > > Thanks > > Server computer: > > Chimera v 1.5 (similar problem with 1.6) > > OS: Linux OpenSuse 11.3 64b > > Client computer: > > OS: Windows 7 64. > > Graphics: ATI Radeon HD 5450 >

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electron density ven diagram
by Terry Lang 24 Apr '12

24 Apr '12

Hey Guys, I am interested in making kind of a ven diagram between two maps for electron density (see attached). What I would like to do is where the density is above a certain threshold for both maps, color the map grey, and where it is above the threshold for map A only, color red, and for map B only, blue. Plan #1 --superimpose maps (have this working) --create a third map (have this working) --do a direct < > = point-by-point comparison between map A and B and reset the values of the third map to be -1 (map A only), 0 (both maps) or 1 (map B only) --color the map using the histograms PROBLEM: The maps are not gridded the same. After some careful thought, I don't think I actually can get them gridded the same for technical reasons. Plan #2 --superimpose maps (have this working) --create copy of map A (coarser map) with map A gridding (have this working) --use interpolation function to interpolate map B (finer map) onto map A gridding --create copy of map A and do a direct < > = point-by-point comparison between map A and interpolated map B and reset the values of the fourth map to be -1 (map A only), 0 (both maps) or 1 (map B only) --color the map using the histograms QUESTION: Is there an easier way to do this with tools that already exist in Chimera? If not, can I get a little bit of info on how the data is stored in the ccp4 style maps (eg start at origin and loop over x, loop over y, loop over z or something else?) Let me know if you need more details or clarification on this rats nest. Thanks! Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Incomplete chain contain many dotted lines while displaying
by Junfeng Huang 24 Apr '12

24 Apr '12

Hello Everyone， I have a problem while display PDB file. I extract the residues from protein-protein interface by ligplus into a new PDB file, and want to display and analysis it. As the file contain only the residues form interface, they are discontinuous. While display with pymol, it is OK. However, While using Chimera, there are many dotted lines between the residues. I know what the dotted lines are, but I do want to hide all these lines, can somebody please give me some hints? I sent two figures in the attachment. It's the first time I used mail-list, if it doesn't support figures, please check here: Interface display by pymol http://bbs.sysu.edu.cn/attach/Pictures/1335235173.JPG Interface display by Chimera http://bbs.sysu.edu.cn/attach/Pictures/1335235254.JPG Thank you very much!

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Charge data
by Nikolay Igorovich Rodionov 24 Apr '12

24 Apr '12

Hi everyone, I know chimera does not produce PQR files, but I was wondering if it is possible to create a data text file with the atoms' three dimensional coordinates and charges after applying the amber forcefield? Sincerely, Nikolay Rodionov

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Rendering TLS information in Chimera ?
by Steven Ludtke 24 Apr '12

24 Apr '12

Hi. A question about rendering B-factor information: Over the last decade, rather than simple anisotropic B-factors, it has become increasingly common to represent local "motion" using the translation-libration-screw (TLS) model, which provides for anisotropic representation of such motions. Is there a good way to represent this data in Chimera ? Here is an example. If you render the PDB structure 1OEL as atoms, and color the atoms by B-factor, you can immediately observe regions of high variability in the apical domain. This same data was later re-refined using a TLS model as PDB structure 1SS8. When you render this structure in Chimera in the same way, you see high B-factors only for a few specific sidechains. The overall large-scale variability is gone, presumably because the TLS parameters have absorbed it, and the "B-factor" is now only a residual B-factor. However, I can't see any obvious way of rendering the TLS information. Any tips ? ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu) Co-Director CIBR Center (www.bcm.edu/research/cibr) Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem) Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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remote session
by Hernando J Sosa 23 Apr '12

23 Apr '12

Hi I used to be able to run chimera remotely from a machine with an X- windows server (the one that comes with Cygwin in this case). But now I get the following error: Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 148 (GLX) Minor opcode of failed request: 181 () Serial number of failed request: 12779 Current serial number in output stream: 12784 I t does work fine if run directly from the computer where chimera is installed. Any idea what the problem could be? Thanks Server computer: Chimera v 1.5 (similar problem with 1.6) OS: Linux OpenSuse 11.3 64b Client computer: OS: Windows 7 64. Graphics: ATI Radeon HD 5450

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Displaying atoms within a distance
by Nikolay Igorovich Rodionov 21 Apr '12

21 Apr '12

Hi everyone, I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I've looked at the chimera manual and I am still confused on how these commands function. Thank you, Nikolay Rodionov

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Charge calculations PDB2PQR
by Nikolay Igorovich Rodionov 20 Apr '12

20 Apr '12

Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov

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Volume Viewer Mesh
by Terry Lang 19 Apr '12

19 Apr '12

Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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modeller interface
by Sadler, Evan 19 Apr '12

19 Apr '12

Hi, I'm trying to construct what I think should be a simple homology model and it's failing as below whether I use the web server or run modeller locally: Target seq: VWF_CK Template structures: 2TGI.pdb (#0)Run locally, the Modeller binary location: /Library/modeller-9.10/bin/mod9.10 Now, modeller is running locally... <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <function command at 0x17982770> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerDialog.py", line 579, in Apply veryFast=self.veryFastVar.get(), tempPath=self.pathTempOpt.get().strip(), **kw) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: <type 'exceptions.UnboundLocalError'>: local variable 'loopData' referenced before assignment UnboundLocalError: local variable 'loopData' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: See reply log for Python traceback. My version of Chimera is alpha version 1.7 build 36205, running under Mac 10.6.8. Do you have any advice? Thanks, Evan Sadler -- J. Evan Sadler, M.D., Ph.D. Chief, Division of Hematology Department of Medicine Washington University 660 S. Euclid Ave., Box 8125 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler(a)wustl.edu

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How to save high resolution image?
by Yogendra 19 Apr '12

19 Apr '12

Dear Sir, I am a new user of Chimera software. I am using this software for academic purposes (i.e. research publications). I am trying to save the image with more then 600 dpi but every time i am ending up with an image of 96 dpi. I am using the POV-Ray method for image improvement but everything is going to the drain when taking the final print of the document. Can you please help me ho can i save a high resolution image? I am briefly describing my protocol of image generation: 1) I am making a density map of particular PDB file. 2) loading in the Chimera and adjusting the volume by volume viewer option 3) Coloring it using described colors 4) Using Pov-Ray for increasing effects on plane 5) Increasing the pixels to about 5000 in the pixel option 6) finally trying to save an image with 600 or 1200 dpi. But at the end of this, i am just getting an image of 96 dpi every time. Can you please help me out to make an image of higher dpi (600, 1200 or more if possible). It will be very much helpful for me if can do it. I am stuck at this point.I am badly waiting for your reply whether i can do it or should i look for some another software. Regards Yogendra S Rathore Research Scholar ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

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Methanesulfinamide Stability and Synthesis
by Nancy 19 Apr '12

19 Apr '12

Hello All, I would greatly appreciate it if anyone has information on the stability of methanesulfinamide (SMILES: C[S](=O)N([H])[H]), as well as it's stability in water. Thank you.

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Command line "Render by attribute"
by rswett＠chem.wayne.edu 18 Apr '12

18 Apr '12

So, I"m wondering if there's a way to call "Render by Attribute" command line for movie making purposes. I have several Defined Attributes and i'd like to be able to recolor surfaces by the various attributes at different points in a movie. What would the format for that type of command be? Thanks for any help you guys have! ~Rebecca

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Check Marks in 2D Labels
by Paul Cernek 17 Apr '12

17 Apr '12

Hello, I'm having trouble inserting a check mark (Unicode page here: http://www.fileformat.info/info/unicode/char/2713/index.htm) into a 2D label, using the Chimera Daily Build from April 10 2012 on Windows Vista. I know that you can reference a special character via its Unicode escape sequence (in this case \u2713). Indeed, when I specify such text from the command line, or when I copy/paste the check mark into the text box of the 2D Labels window, it displays exactly what I want IN THE 2D LABELS WINDOW. However, in the main Chimera model display window the check mark is NOT properly depicted in the label. Instead, I get that empty square you get whenever a program encounters an unrecognized character. Other more conventional symbols (such as the Greek letter 'alpha') display normally. Why would the "2D Labels" window display the check mark properly, while the main display window does not? Any assistance in this matter is very much appreciated. Thanks, -Paul

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APBS maps
by Rebecca Swett 12 Apr '12

12 Apr '12

Hey guys, i'm working with some electrostatic potential maps and am interested in doing a difference map. Two nearly homologous proteins with nearly identical surface shapes, and radically different electrostatics. I"m thinking a difference map would illustrate the differences well, but in looking at the APBS output I have no idea how to do that manually. Does anyone here have an idea about how to do that in chimera?

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Re: [Chimera-users] [Dock-fans] Help with antechamber
by Trent E. Balius 10 Apr '12

10 Apr '12

Hi Brad, I am cc'ing this to the chimera list. I think that you should write a python script to run DOCK prep on the command line. See the following: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html For other example scripts see the following: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html You should not have to specify the AMBERHOME path. This is done internally to chimera. as an aside, It is unnecessary to run antichamber with sudo. I hope this helps, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/ -----Original Message----- From: Brad Ridder <clustro(a)gmail.com> To: dock-fans <dock-fans(a)docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber Hi Dockfans, My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University. We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI. Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens. Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running: sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/3GLRcharged.mol2 -fo mol2 Which returns the error: Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder. Here is what I have in my .bash_profile file in my home folder. export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6' I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect. I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem. I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files. What am I doing wrong that is preventing antechamber from executing correctly? -- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University _______________________________________________ Dock-fans mailing list Dock-fans(a)docking.org http://mailman.docking.org/mailman/listinfo/dock-fans

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vector of axis
by Gwo-Yu Chuang 09 Apr '12

09 Apr '12

Dear all, I am trying to figure of the principal inertia axis of a protein domain using Chimera. Is there any way to get the vector of the axis (the values), besides just showing it on the screen? Many thanks Yours Sincerely, Paul

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Morph with Cofactors
by Marco Jost 06 Apr '12

06 Apr '12

Hi, I am trying to morph two conformations of a protein that includes multiple cofactors. While the protein structure is morphed just fine, the cofactors are not included in the morph (or in the output PDB). I numbered the cofactors identically in both files and everything else should be consistent as well. Does anybody know how to include cofactors in the morphing and have them be written into the output PDB? Thanks! Marco Jost Ph. D. Student, Department of Chemistry Massachusetts Institute of Technology

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Re: [Chimera-users] [Open Babel] UCSF Dock mol2 files
by Scott Brozell 06 Apr '12

06 Apr '12

Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ? thanks, scott On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 > http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek(a)wojcikowski.pl > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff(a)geoffhutchison.net> napisał: > > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff

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Selecting submodels when they are density maps
by Javier Velazquez 05 Apr '12

05 Apr '12

Hi, I am interested in generating a map from a PDB with 2 chains, and color each chain differently. I can do it very easily using the graphical interface, but I couldn't figure out how to do it from the command line. Here are my commands: molmap #0:.A 7 molmap #0:.B 7 And now adding color is simple: volume #0 color red But this adds color to both maps. Is there a way to specify a submap, so I can add color separately. I am looking for something like this: volume #0:.A color red which I tried and didn't work. Thank you for your help. Javier

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Merge the protein sequences of two different chains
by Hsih-Te Yang 05 Apr '12

05 Apr '12

Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te

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Solvate models
by Nikolay Igorovich Rodionov 05 Apr '12

05 Apr '12

Hi all, I was wondering if some could explain to me the differences between the water models available under the solvate option. * POL3BOX - POL3 water model * SPCBOX - SPC/E water model * SPCFWBOX - SPC/Fw water model * QSPCFWBOX - qSPC/Fw water model * TIP3PBOX - TIP3P water model * TIP3PFBOX - TIP3P/F water model * TIP4PBOX - TIP4P water model * TIP4PEWBOX - TIP4P/Ew water model Thank you all in advance, Nikolay Rodionov

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Coloring distance labels
by George Tzotzos 04 Apr '12

04 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

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Coloring distance labels
by George Tzotzos 04 Apr '12

04 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

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color by RMSD
by Thomas Evangelidis 04 Apr '12

04 Apr '12

Dear UCSF Chimera users and developers, Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them? thanks in advance, Thomas

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Re: [Chimera-users] [Chimera] #10638: heme not included in morph trajectory
by Elaine Meng 04 Apr '12

04 Apr '12

Hi Francesco, There is some progress... in the newest daily build (Apr 4) I can run the commands below to successfully show a morph of 1hho and 2hhb that includes heme and iron. 1hho only has two chains, so it is necessary to delete C,D from 2hhb before morphing. To include heme and iron, it is necessary to delete all the other het residues that may be different between the structures. I hope this helps, Elaine Here between "----" are contents of Chimera command file, which you could save as plain text file named something.cmd and open in Chimera to execute the commands. Lines starting with # are just comments/explanation and don't do anything. ------------- open 2hhb open 1hho # # delete 2hhb chains C,D # delete #0:.c-d # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose the structures; I used "mm" with defaults but it could be # done with options, or MatchMaker GUI, or "match" command, # or manually with mouse # mm #0 #1 # # create morph trajectory which will be model #2 # morph start #0 frames 25 morph interpolate #1 frames 25 morph movie ~modeldisp #0,1 --------------------- Then I tried to get fancy and make a tetramer of 1hho so that the morph could be from tetramer to tetramer. However, then only the heme/iron from A and B were included, not from C and D. I don't know why, because they are all in the input structures!! Here is that script in case it might be useful: --------------------- open 2hhb open 1hho # # make 1hho tetramer; #1 is original, #2 additional copy # sym #1 # # combine #1,2 dimers into tetramer model #3, close #1,2 # combine #1,2 name 1hho-tetra newchainids true close true # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose #0 and #3 # mm #0 #3 # # create morph trajectory which will be model #1 # morph start #0 frames 25 morph interpolate #3 frames 25 morph movie ~modeldisp #0,3 ---------------------

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occupancy field
by Darjan Andrejc 03 Apr '12

03 Apr '12

Hey, Is it possible to change occupancy field to 1.0 in Chimera? I need a pdb file of my protein for docking and the file needs to have an occupancy field 1.0. Thanks for the help Darjan Andrejc, Mpharm PhD student, Department of Biotechnology National institute of Chemistry, Ljubljana, Slovenia

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Minimize with fixed atoms
by Hurt, Darrell (NIH/NIAID) [E] 02 Apr '12

02 Apr '12

Hi there, I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to <5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms. Am I in a local minima? Is that why nothing moves? The energy is very high (from the Reply Log): Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps Any ideas? I do have some hetero atoms... Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Re: [Chimera-users] morphing
by Elaine Meng 31 Mar '12

31 Mar '12

Hello Francesco! First make sure you are hiding the input conformations, so that you are seeing only the morph (for example, you could show Model Panel from Favorites menu, then uncheck the S(hown) boxes for everything except the morph results). I say that because if you see something not moving, it might be the original structure. As explained here, the morph should contain all of the atoms in the protein chain that are included in all of the input structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p…> Since your input structures are the same protein, if each one includes the sidechain atoms, the morph should contain all the same sidechains and they should move from one position to the other during the morph. They may not be displayed automatically, however. Try displaying all atoms (again better to hide the other structures first) to make sure of what is there. About the ion: even if the ion is in both structures, it may not be in the morph if you are using an older version of Chimera. However, there have been some fixes, and I believe if you are using Chimera 1.6 or newer, the ion should be included. The fix I'm thinking of was 6 months ago and is described here: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9886> If you try Chimera 1.6 and the suggestions above but you believe there is a bug, you could use Help... Report a Bug in the menu and describe how to reproduce the problem, attaching session file if necessary. 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 Mar 31, 2012, at 5:24 AM, Francesco Malatesta wrote: > Hello from Rome! > I'm trying to morph 2 different conformations of the same protein. I get a very very nice movie, but I can't get amino acid side chains or heteroatoms (heme iron) to move also. > Is there any way to do this? > thank you for help > Francesco

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How to save VIPER transformation matrix
by snoze pa 30 Mar '12

30 Mar '12

Dear Chimera Users, Is it possible to save the coordinates after the VIPER transformation (xyz-2 fold symmetry) in Chimera. I can create a multiscale biological molecule in chimera but it is not saving the viper matrix in pdb file. Please note that this pdb is a model not the crystal structure and I am trying to save the viper matrix for this pdb. Thank you, S

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Chimera is not loading properly
by Andrea Edwards 27 Mar '12

27 Mar '12

I have not used Chimera in awhile. I just downloaded the new version for Mac-OSX-64-bit and when I open it, none of the buttons on the gui are visible. There are ovals and things where there should be buttons, but not words on them. How can I fix this? attached is a screenshot. Thanks, Andrea

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PDB model merging
by Nikolay Igorovich Rodionov 27 Mar '12

27 Mar '12

Hi all, I'm working on a project that requires me to merge models created through PDB BIOMT records. I have been using the copy&combine feature in the model panel to merge all of my models, and then writing a new PDB of only the combined model. I've noticed that this method deletes a large amount of information about the structure, including secondary structure records. Is there a way to merge models without losing such data? If it is relevant, I am merging 90+ models.

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Trajectory analysis: hbond
by George Tzotzos 26 Mar '12

26 Mar '12

I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works. Or dumb values to a file. Many thanks in advance for any suggestions Regards George

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Re: [Chimera-users] Electrostatic Potential using APBS .dx file
by Tom Goddard 26 Mar '12

26 Mar '12

Hi Soca, Sounds like you are doing everything right. That makes me suspect that something is wrong with your APBS file -- like all the potential values are zero. To see what the distribution of the potential values are, open the APBS file and then use menu Tools / Volume Data / Volume Viewer, and click on the histogram (empty rectangle in the middle of the volume dialog). That will show a histogram of the potential values. You can move the vertical bar on the histogram to see what the potential value is at that position. Check if -5 to 5 is a reasonable range. Tom > Hello, > > I have been attempting to generate a electrostatic surface map in > chimera using an external potential file generated from APBS (.dx). > > I understand that Chimera has an internal surface calculation protocol > via Coulombic Surface Coloring, however, I would like to use the > Electrostatic Surface Coloring. > > However, when I open my molecule (PDB), show surfaces, and choose its > MSMS main surface to color by electrostatic potential using the .dx > file, the surface map is not the red, white, blue that I have set in > my parameterts under Surface color. Everything turns to grey. My other > parameters include: > > red -5, white 0, blue 5. Colors 3. Palette Red-Blue. Surface offset 1.4. > > I feel as though I am missing something trivia that would allow me to > generate the surface image I want, however I am lost after may > searches for advice through the forums and tutorials. > > Please let me know what I am missing. > > Thanks > > Soca > > -- > Ardian Soca Wibowo, Ph.D. > Postdoctoral Associate > Dann Research Group > Department of Chemistry > Indiana University

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Dimethyl Sulfoxide Electromagnetic Absorbance
by Nancy 25 Mar '12

25 Mar '12

Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy

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RMSD plot
by lecan 23 Mar '12

23 Mar '12

Hi everybody. I am interested in plotting RMSD values vs time from molecular dynamics. Is there a way to extract the RMSD values from a the RMSD map in the analysis tool of MD movie. Or maybe exists another way to do this with Chimera. Thank you in advance Luis L.

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how to measure the volume of the active site
by Thomas Evangelidis 23 Mar '12

23 Mar '12

Dear UCSF Chimera developers, I am interested in measuring the volume of the active site of a kinase. I have searched through the documentation and the only thing I found was how to measure the enclosed volume of a surface object. Is it possible to do what I want with UCSF Chimera? Could you please point me towards the relevant commands? Thanks in advance for any help. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Multi-PDB fitting question
by Tom Goddard 21 Mar '12

21 Mar '12

> Dear Tom, > > ... > Currently we are trying to use a lot of PDBs (hundreds!) to fit one > density map and trying to find out the best fitted PDB, and we found > that fitting the PDBs one by one manually was very time-consuming and > low-efficiency. So we are wondering that if there is any advanced way > or batch file that can speedup this process? > > Thank you so much and we are looking forward your reply. > > Best Regards, > Lei > Hi Lei, Ok, I added a new "eachModel" option to the Chimera fitmap command so that one command can independently fit many molecules in the same map. For example, fit #1-50 #0 resolution 13.5 eachModel true listFits true will fit PDB models with id numbers 1 to 50 into map with id #0 and list the fits in a dialog. Each of the fits is done independently (no account for clashes between molecules). Details on each fit are given in the Reply Log dialog (menu Favorites / Reply Log). This will be in tonight's Chimera daily builds (run at midnight) if they succeed: http://www.cgl.ucsf.edu/chimera/download.html#daily Here is the fitmap command documentation which will be updated later this week or next week. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html You will probably find that you can't open hundreds of PDB molecules in Chimera because it takes too much memory. But you can fit them in a few batches if this happens. Tom

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