- Chimera-users - RBVI Mailing Lists

emulation of threee button mouse not working
by Geeta Narlikar 21 Aug '08

21 Aug '08

Hi, I'm having problems with the three button mouse emulation feature. My OS is Mac X Leopard and I turned on the "emulate three button" mouse feature in X11. But that does not seem to work. My version of Chimera is 1.2509. Is there any other setting I should change? Thanks for your help. Geeta Narlikar

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Re: [Chimera-users] density maps in chimera- question
by Thomas Goddard 21 Aug '08

21 Aug '08

Hi Sarah, You can use the keyboard shortcut "bv" to create a new map that covers your PDB model. To enable keyboard shortcuts use Tools / General Controls / Keyboard Shortcuts and turn on "Enable keyboard shortcuts" in the dialog. Select the atoms of your PDB model. If you have more than one map open make sure the highlighted one in the volume dialog is the crystal map for the selected atoms. Then type the "bv" shortcut to create a new map covering the select atoms. This assumes that the starting map is a full unit cell. If you don't want to go to the trouble of enabling keyboard shortcuts, you can use the command "ac bv" which runs the shortcut (accelerator) bv. You can save the covering map with volume dialog File / Save Map As.... Tom Sarah Boyce wrote: > Hi Tom- I was told you might be the person to ask about the density map > features in chimera. I'm trying to display crystallographic electron > density maps and I've run into a problem aligning some of the maps to > the protein model. When I load the map and model it looks as though the > map is of the symmetry related molecule, but when viewed using Coot it > automatically centers the map on the model. So far the only tool that > I've found to do this is by hand alignment, which doesn't work at all > for an atomic level model (or at least when I've tried it it is too much > of a pain). Is there an automated tool in chimera that will > automatically center the map on the model similar to the way Coot > handles it? > > > Thanks, Sarah

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(no subject)
by charles marchand 21 Aug '08

21 Aug '08

Greetings, I was wondering if someone could tell me how to select multiple sequences in the sequence viewer. I am trying to select different regions of RNA to visualize, but Chimera has not allowed me to pick to sequences that are separate. Is there a way to do it through the sequence viewer? Thank you, Charlie

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Re: [Chimera-users] CHARMM PBEQ calculations
by Tom Goddard 21 Aug '08

21 Aug '08

Hi Fabian, The OpenDX file you sent has a small but important error. It is missing the words "data follows" at the end of the header line that says "object 3 class array..." so Chimera never reads the data. The misleading error message comes about because the last line of the file is blank and Chimera still thinks it is reading the header. The header line object 3 class array type double rank 0 items 378885 has to be object 3 class array type double rank 0 items 378885 data follows Hopefully Sunhwan can update the phi2dx.py script to include the very important "data follows". The OpenDX format is described in Appendix B of the OpenDX User's Guide: http://opendx.npaci.edu/docs/pdf/userguide.pdf Tom Fabian Glaser wrote: > Dear Elaine, > > I am afraid it's still giving the same error when I try to open the dx > file, even when the first line is removed or # starts it. Here is the > message: > > Opening /media/data/WORKSPACE/PROJECTS/DanCassel/COP/step2_pbeq.dx > Error reading file step2_pbeq.dx, format apbs > Incorrect format: blank header line. Comments must begin with # > character. > > And the dx file is attached, probably I am doing something wrong.... > > THanks a lot, > > Fabian > > > Elaine Meng said the following on 19/08/08 19:19: >> Hi Fabian, >> Well, the error message says the format is wrong. Based on the >> message, you could try removing the blank line at the top of the file >> or adding # in front of it. >> >> If that still doesn't work you could send me the file to look at, but >> it is probably just a simple fix such as the above. >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> >> >> >> >> On Aug 19, 2008, at 7:03 AM, Fabian Glaser wrote: >> >>> Dear Sunhwan >>> >>> Thanks a lot for your kind answer and for the script. The script run >>> fine, but when I try to upload it to chimera I get an error: >>> >>> Opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> Error reading file step2_pbeq.dx, format apbs >>> Incorrect format: blank header line. Comments must begin with # >>> character. >>> Done opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> >>> Which maybe perfectly chimera problem, so I am CCing this email also >>> to Elaine Meng from the CHIMERA team. >>> >>> Any help will be very appreciated, >>> >>> Thanks a lot, >>> >>> FAbian >>> >>> Sunhwan Jo said the following on 19/08/08 15:25: >>>> Dear Dr. Glaser, >>>> >>>> I'm afraid CHIMERA is not able to read CHARMM phi80 format. But simple >>>> search guided me that CHIMERA can to read dx format file, which I >>>> have a >>>> converting script. So, please find the script in the attached file. >>>> We've been >>>> using this script to read our potential data in Pymol, so I believe >>>> this should >>>> be working fine with CHIMERA as well. >>>> >>>> usage: >>>> python phi2dx.py step2_pbeq.phi80 > step2_pbeq.dx >>>> >>>> Please feel free to contact me, if you have a further problem. >>>> >>>> Thanks, >>>> Sunhwan >>>> >>>> >>>> On Tue, Aug 19, 2008 at 4:53 AM, Fabian Glaser >>>> <fglaser(a)technion.ac.il> wrote: >>>> >>>>> Dearl CHARMM team, >>>>> >>>>> have been trying to upload the electrostatic potential calculated >>>>> by CHARMM PBEQ routine to the CHIMERA viewer, since the java >>>>> viewer you use is very good but at least in my machine does not >>>>> work. But despite I have been trying to upload it to chimera there >>>>> seems to be some stubborn problem (or I am doing something wrong). >>>>> What I am trying to do is to color the pdb by the potential in >>>>> chimera so I can freely manipulate it and compare it with other >>>>> calculations. >>>>> >>>>> If you have any suggestion I'll be very grateful, >>>>> >>>>> Best regards, >>>>> >>>>> Fabian Glaser, PhD

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clipping planes question
by William Jeffrey Triffo 20 Aug '08

20 Aug '08

I know of the hinder and yon clipping planes, and also the per-model clipping plane that allows individual model clipping. I have a current imaging session where I have already used per-model clipping on several models, but would like to trim off some material from the side of the entire combined model - I don't suppose there is an arbitrary clipping plane that applies to the whole scene, like hinder-yon but from any user-defined direction? For now, I was just going to crop the resulting image. But this will result in an abrupt end to the background color (I can adjust the image border clone the background in photoshop/etc, but would be nice to be able to do that within Chimera) thanks, -Jeff

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saving nol2 files
by 吴超 20 Aug '08

20 Aug '08

Hi, dear folks, I have some doubt about how chimera determines the atom type when you save mol2 files from ligand pdb files. Because when I opened the saved mol2 files, I found there were some mistakes about atom type. Does Chimera use the same procedure that Sybyl uses to determine the atom type? -- Chao Wu

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MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
by Darrell Hurt 20 Aug '08

20 Aug '08

Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> 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] Distance and Angles
by Thomas Goddard 19 Aug '08

19 Aug '08

Hi Andy, To show a distance between atoms select the two atoms and use menu entry Tools / Structure Measurements / Distances and press the Create button. You can show distances for multiple pairs of atoms. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… Not sure what you mean by the angle between two density map surfaces. The surfaces intersect in many places making different angles. You could place 3 markers with Volume tracer and measure the angle made by those 3 markers using the Angles/Torsions tab of the Structure Measurement dialog. Tom Anindito Sen wrote: > Hi Tom > > Probably this question is already answered before- > > How do I show multiple distances between different amino acids of two > molecules from two different parts of the density map. > > Also do can I determine the angle between two surfaces? > > Thanks > Andy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

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saving maps generated with molmap - origin?
by Grigore Pintilie 19 Aug '08

19 Aug '08

Hello, I'm wondering why when I generate a density map from a pdb structure (using the molmap command) and then save it, once I reopen it it seems to have shifted with respect to the structure. I'm noticing that before saving it, the generated map has a certain origin (shown in the Coordinates pane in the Volume Viewer), and then when I reopen it the origin appears as 0 0 0. If I copy the origin shown initially and then paste it into the origin of the opened file, this shifts the map to the correct position, but why isn't the right origin saved with the file? I'm using alpha version 1 build 2509 2008/05/01, platform win32 Many thanks, Greg

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How to Create Isopotential Contours, not Surfaces, with Chimera
by Charles Letner, Ph.D. 19 Aug '08

19 Aug '08

Hello all, I have a map of electrostatic potentials. Using volume viewer I am able to display the surfaces at any potential value I would like (as well as multiple values by having multiple bars in the volume viewer histogram). Now, I would like to be able to take a slice through that potential surface and see a line associated with a given value of the potential in that slice - call that the contour. I would like to have multiple potential contours, each with a different constant value in that contour (-10 for one contour, -20 for the next, -30 for the third, and so on- call these the iso-potential contours). This would allow the contours of potential to be seen in a single plane. Seems like I am so close using planes but that just isn't working. Am I approaching this right and if so any hints would be appreciated? If I am off base with the approach, I sure would appreciate a nudge in the right direction? Cheers, Chuck

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Flipping between alternate conformations (depiction/movie)
by David Chenoweth 19 Aug '08

19 Aug '08

Dear Chimera team, Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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Question about Measure Volume and Area
by Patrick Redmill 18 Aug '08

18 Aug '08

Hi all, I am using the the calculate "Area and Volume" option in Chimera to estimate the SASA and excluded volumes of a family of fullerene materials. I need to calculate the area and volume using two different probe sizes (1.4 and 2.0, to be specific). For most of my particles, you see that the volume and area are relatively insensitive to a change in probe size (which I would expect). For one particle, however, I find the results to be quite different and unintuitive. For instance: 1.4: Area: 1174 Volume: 3534 2.0: Area: 1692 Volume: 2493 My (perhaps wrong??) assumption is that the area calculator uses a Connolly algorithm. If that is the case, I can't understand why a larger probe would give a larger area (smaller probes samples more surface). Also, why would a larger probe give a larger volume? Again, I thought the volume calculator used a Voronoi algorithm, which, to me seems independent of probe size. Any idea what may be wrong about my understanding? I've attached a .pdb of the molecule in question if you'd like to take a gander. Thanks in advance! ~Patrick

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stereo
by Matthew Dougherty 16 Aug '08

16 Aug '08

I have been using chimera/macAqua with sequential stereo with no problems on a CRT. I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT. On other packages I activate a left/right image swap to get around this. Is there something I can do to achieve this on Chimera? Matt National Center for Macromolecular Imaging

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Fwd: Question about Measure Volume and Area
by Elaine Meng 15 Aug '08

15 Aug '08

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: August 15, 2008 12:11:33 PM PDT > To: Patrick Redmill <patrickredmill(a)gmail.com> > Cc: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Question about Measure Volume and Area > > Me again, I just wanted to quickly reiterate that if you want > analytical values, just look in the Reply Log after first showing/ > creating the surface. That will report the analytical values, and > not just the totals but also the values for each component > (disconnected blob, so outer surface and inner surface are two > components), and also both SAS and SES areas even though only the > SES is actually displayed in Chimera. > > So for molecular surfaces, there isn't really any reason to use > Measure Volume and Area or Measure and Color Blobs. Those tools are > mainly needed for other, nonmolecular surfaces. I didn't present > this clearly in the previous messages, sorry. > Best > Elaine

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Re: [Chimera-users] quick angles question
by Tom Goddard 15 Aug '08

15 Aug '08

Hi Jeff, Here is a Python script to report the angles made by bonds attached selected atoms. Just select the atoms, then open the script. Output will be printed to the reply log. Tested in Chimera 1.2548 but should work in much older versions. Tom Jeff Triffo wrote: > hi Tom, > > if I have a Chimera marker file full of interconnected markers, is > there a quick/easy way to report all the angles formed in the > meshwork? (screenshot attached) > > I figure the easiest way is to cycle through the markers and survey > the angles it makes with each attached marker, but I don't know how to > do that (but it sounds like something that is probably straighforward > in python) > > thanks for any input there, > > -Jeff > # ----------------------------------------------------------------------------- # Report all angles made by bonds originating from selected atoms. # from chimera import selection, angle atoms = selection.currentAtoms() print '%d atoms selected' % len(atoms) c = 0 for a in atoms: bonds = a.bonds for b1 in bonds: for b2 in bonds: if b1 < b2: a1 = b1.otherAtom(a) a2 = b2.otherAtom(a) t = angle(a1.coord(), a.coord(), a2.coord()) print ('Angle %s %s %s = %.3f degrees' % (a1.oslIdent(), a.oslIdent(), a2.oslIdent(), t)) c += 1 print '%d angles reported' % c import Accelerators.standard_accelerators as sa sa.show_reply_log()

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Re: [Chimera-users] midas/6155 (Chimera error)
by Eric Pettersen 14 Aug '08

14 Aug '08

On Aug 14, 2008, at 1:23 PM, Christine Deillon wrote: > Hi Eric, > > I try to save a movie of a collagen molecule (cylinder shape) > just moving around its major axis (along the molecule) for about > 15 secondes, then I would like to play the movie in the microsoft > power point program > is it possible to do that with chimera? > > Christine Hi Christine, Yes, absolutely you can do that. There is a Chimera tutorial that covers movie-making in good detail here: Movie Making in Chimera The "Spin Movie" section of the tutorial is almost exactly what you are asking for. Issues with embedding movies into PowerPoint are at the very end of the Movie Recorder documentation page: problems in PowerPoint --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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version 1.2540 stability
by James Fethiere 14 Aug '08

14 Aug '08

Hi, I just upgraded my May version with the last version of Chimera for PC and am having stability problems. Every now an then (every 10' or so), chimera freezes and the cursor flickers for a couple of seconds; then all goes back to normal. Sometimes, it just crashes completely. Is this last version more demanding on memory? Thanks James

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Re: [Chimera-users] calculation of volume
by Elaine Meng 14 Aug '08

14 Aug '08

Hi Navnit, Sorry, I don't know of a way to calculate the van der Waals volume in Chimera. You can see the VDW volume, of course, by simply displaying the atoms in the sphere representation, but that does not give the volume value. In theory, you could get values closer to the VDW volume by calculating molecular surface with smaller and smaller probe radius. In practice, this tends to increase the number of surface calculation failures, and currently the smallest allowed probe radius value is 0.5 angstroms. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 14, 2008, at 7:01 AM, Navnit Kumar Mishra wrote: > Hi Elaine; > > Thank you for so detailed description. I am interested in measuring > the compactness of the complex during the simulation, I think the > calculation of the ratio of molecular volume to van der waals volume > provides the compactness. I have tried the procedure as you > suggested to calculate the molecular volume, the value in replylog > file is in two digits precision, for these calculation can I get the > value in four digits precision. I am using latest chimera version > 1.2540. I can calculate the total van der waals volume using the van > der Waals radii for each atom excluding the hydrogen atoms. Is there > a way in chimera to calcualte the van der waals volume. I would be > thankful to you for any suggestions. > > with regards, > navnit

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Color zone with transparency
by Tom Goddard 14 Aug '08

14 Aug '08

Daniel Wilson wrote: > Hi Tom, > > ... > > The other thing I noticed is that you lose transparency on a whole volume when you color zone one region of it? or am I making something wrong? Is it not possible to have a single volume with two different colours and transparent? > > Thanks for you advice and kind offer, > regards > Daniel > Hi Daniel, When I make a transparent surface for a volume by pressing the volume dialog color button and making opacity 0.5 and then use color zone to color part of the surface (using a PDB model), the transparent part far from the zone remains transparent. Also works if select the volume surface and use the Actions / Surface / Transparency menu then color zone. What are the exact steps you use when it fails to preserve transparency? Tom

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Two transparent models
by Tom Goddard 14 Aug '08

14 Aug '08

On Aug 11, 2008, at 12:15 PM, Daniel Wilson wrote: > Dear Elaine, > > I realise that there have already been requests about fixing the bug > in Chimera for displaying two transparent maps at the same time, so I > guess I am just asking whether this is likely to be fixed anytime > soon? We are desperate to use this function for a figure for a paper :) > > THanks, > Daniel > > Dr. Daniel N. Wilson > > Gene Center Munich > Department of Chemistry and Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > 81377 Munich, Germany Hi Daniel, The incorrect transparency in Chimera when 2 or more models are transparent is very difficult to fix and will not be fixed any time soon. The trouble is that Chimera draws each model separately and it is not possible to correctly handle transparency without intermixing the drawing of parts of models (in depth order). If you use Chimera image saving in the POVray raytracing mode it will correctly show multiple transparent models. The trouble is that this takes a long time to render and adjusting the levels of transparency many times to get the right appearance may be tedious. It would be possible to make a script that combines the currently displayed map surfaces into a single model and hides all the original models so that multimodel transparency would appear correct on-screen. But the combined model would not update when you changed the transparency, color, ... settings of the separate maps. It would require rerunning the script that makes the single model. This would be tedious to use. But if you think it worth trying I can write the script and send it to you. It would not work for transparent molecular models (ribbons and atoms), just surfaces. Tom

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Hydrogens in proteins
by Walter Novak 13 Aug '08

13 Aug '08

Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H. The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle." Unfortunately, the point of my project is to see the hydrogens!!!! Thanks for any help you can offer, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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opening CASTp results
by Walter Novak 13 Aug '08

13 Aug '08

Hi all, How can I open my own CASTp results easily? The fetch command works great, but I need to submit some modified structures, and I don't see CASTp under file type in the open window. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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calculation of volume
by Navnit Kumar Mishra 13 Aug '08

13 Aug '08

Hello all; I am trying to compute the molecular volume of a complex. Chimera first computes solvent-excluded surface area using MSMS. I see it does not compute the surface area of ligand. I am wondering if I can add the extra parameters or atom types for my ligand in some file. I would like to calculate the molecular volume from amber trajectory. Can some one suggest me how to automate the computation of surface area and molecular volume for each snapshot. If you know, please point out the article which describes the procedure for the volume calculation. with regards, Navnit

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representing 70s ribosome in ribbon
by Bong-Gyoon Han 12 Aug '08

12 Aug '08

Hi, I am tring to show the full 70S ribosome structure (PDB id: 1GIX and 1GIY) in ribbon representation with EM experimental density together. These PDB data consist of backbone atoms only (single alpha carbon for each a.a and single phosphate for each nucleotide). Ribbon option does not generate any ribbon (due to the incomplete information in the PDB?). Is there any way to show this molecule in ribbon format? I assume that backbone atoms must be enough to generate ribbons. BGHan

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IMOD model reader question
by William Jeffrey Triffo 12 Aug '08

12 Aug '08

I have an IMOD model (just a bunch of contours, representing filaments) that I tried to load into Chimera, but it threw some errors. This was odd, because it was a model I had augmented (added more contours) from a previous model that did load correctly (and I re-verified after the load error). is it helpful to forward the model file in question? best, -Jeff

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