- Chimera-users - RBVI Mailing Lists

Protein Design
by Jared Adolf-Bryfogle 13 Jun '11

13 Jun '11

2 1

Re: [Chimera-users] [chimera-dev] Protofibril model
by Elaine Meng 09 Jun '11

09 Jun '11

Dear Lihong and others, The Multiscale Models tool in Chimera is meant for this purpose --- it shows low-resolution surfaces, which are often preferred for large complexes. In Chimera I tried opening 1ei3, then started Multiscale Models (in menu under Tools... Higher-Order Structure), then clicked the "Make models" button at the bottom of the multiscale dialog. This shows the structure with low-resolution surfaces and automatically uses different colors for the different chains. You can adjust the colors, surface resolution, etc. in the dialog. Click the dialog's Help button to see its manual page. There is also a copy here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu…> I also tried it with 1m1j, which also worked fine on my computer. 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 Jun 9, 2011, at 12:13 PM, Russell M. Taylor II wrote: > Dear Lihong, > I am glad to hear that Chimera let you start down this path. > I'm CCing the Chimera developer mailing list in case they know of a better solution. > You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there. > > The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this. > > Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. > This launched the Python Molecule Viewer. > Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. > Clicked to turn off the red dot under the CPK label so that we only see the surface. > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file. > > I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality. > > I attach the resulting coarse model (inside a Zip file) to this email. > Russ > > [Things below I tried that didn't work] > > (Fine surface) > Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). > Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified. > > VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps. > > NOPE: > > You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. > To turn off the little axes display, select Display/Axes/Off > To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button. > > Open Blender (available from blender.org) Press delete to get rid of the cube that is created by default. > Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ" > > At 10:18 AM 6/7/2011, lihong huang wrote: >> Dear Dr. Taylor, >> >> I am postdoc working in Dr. Susan Lord's lab. According to your suggestion, we set up the protofibril model using UCSF Chimera program which is very nice. Now we want to move on to make small fiber model, however, the program run very slowly when we add more fibrinogen molecules. We are thinking if we could make the fibrinogen molecule lose more details, maybe the program could run easily. Do you know which program could do this? We just want to show the basic shape of fibrinogen, no needs to show very detailed part, such as alpha, beta and gamma chains. Thanks a lot for your help. >> >> Lihong Huang, >> Postdco >> Pathology and lab medicine > > --- > Russell M. Taylor II, Ph.D. taylorr(a)cs.unc.edu > CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr > University of North Carolina, Voice: (919) 962-1701 > Chapel Hill, NC 27599-3175 FAX: (919) 962-1799 <protofibril.zip>_______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Contacts
by George Tzotzos 07 Jun '11

07 Jun '11

Hi everybody, I'm trying to analyse AMBER trajectories of protein/ligand complexes. The objective of my exercise is to find out contacts/interactions between the ligand and the receptor in the course of the trajectory. Is there a way of doing this DIRECTLY in Chimera? Or one has to first perform clustering of structures and then work out clashes/contacts on the representative structures that are dumped from the trajectory. Best regards George

2 1

mac default directory
by Dougherty, Matthew T 06 Jun '11

06 Jun '11

Hi- Where is the default directory for movie images on the mac? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

2 1

coordinate rotation measuring
by Jeffrey Hu 06 Jun '11

06 Jun '11

Hi, I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)? -Thanks!

3 2

Smooth edge when masking volume data
by Tom Goddard 03 Jun '11

03 Jun '11

> Thanks, Tom. That helped a lot. However, is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge. This is true whether I am masking directly, or the inverted view. > > Kelly Hi Kelly, When you mask volume data in Chimera using Volume Eraser or the mask command it sets the density values to zero outside the surface. In places where high density crosses the surface the masked result looks horrible -- volume contour surface is jagged with stair-steps following the pattern of the volume grid. I don't have any trick to make that surface look smooth. I have two ideas about how to approach the problem. One is to not have the density fall to zero immediately outside the surface. If it rolled off gradually the contour surface of the masked data would look better. I'm not optimistic that that will produce a good result. The second approach is to do something different from masking. Instead clip the volume surface with the sphere surface and cover the resulting holes with patches of the actual smooth sphere surface. I think this would look very nice and the patches of sphere could be a different coloring which would give a nice visual indication that you have cut through high density. I have not implemented either of these two ideas. Just last week I had a lengthy discussion on this problem with Greg Pintilie and Ernesto Arias. Greg said he might try the gradual fall-off technique. I include that email discussion below. Tom -------- Original Message -------- From: Greg Pintilie To: Tom Goddard Date: 5/24/11 6:10 PM > Right - it's numpy to the rescue; I'll give it a shot... I think if we > use a smoothing filter with relatively high width the staircase effect > may not be as bad as you think... though then the boundaries may > become exceedingly smooth; so it will be a fine balance. Will let you > know how it goes! > > Greg > > > > On Tue, May 24, 2011 at 7:42 PM, Tom Goddard wrote: >> Hi Greg, >> >> It's an interesting idea. But it seems to me there will still be a >> discontinuity in map values. For example imagine you have a box shaped >> region with density values 1 inside and 0 outside. The Gaussian filter of >> that will give values approximately equal to 0.5 at the surface (if the >> Gaussian is half in the 1 region and half in the 0 region). So I think the >> drop from 1 to 0.5 on the surface is likely to give the same ugly artifacts. >> That said, implementation would be trivial. Just compute the Gaussian >> smoothing and copy it only where the original map has zeros (can be done >> with a line or two of tricky numpy Python code). >> >> You know Gaussian smoothing is what the heat equation produces. If you >> modify your idea so the non-zero density points are fixed temperature >> sources, and the heat flows to the zero grid points (by averaging neighbor >> temperatures) then you would get a continuous fall-off. Again it is a >> pretty easy calculation in Python/numpy. But I'm not optimistic about the >> results. The trouble is we've created this horrible stair step surface and >> it will take pretty long range smoothing to get rid of the stair steps. I >> think a good smooth cut is going to require stepping back and not producing >> the stair steps in the first place -- you need a boundary definition that is >> smooth instead of discretized. For instance when we make a contour surface >> we trilinear interpolate the 8 nearest grid points and the surface comes out >> smooth. Not quite sure how to do the equivalent for watershed regions. >> >> Tom >> >>> Sounds good - thanks for all those insights, Tom. I agree that >>> solution is not ideal, but I'm glad it helps at least a bit. I just >>> got an idea that might be interesting to try - I mentioned that you >>> can Gaussian-filter the masked map, which would lessen that huge drop >>> in density values at the boundary, but this removes good detail from >>> the actual map as well. What I'm thinking to try is to do the filter, >>> but only apply it to voxels with 0 density values (the masked >>> portion); that way the original density map gets left alone, and the >>> boundary no longer has a drop from some density value to 0... what do >>> you think Tom, could there be an easy way to implement this using >>> current functions? Done voxel by voxel in python would probably be >>> exceedingly slow... >>> >>> Greg >>> >>> >>> >>> On Tue, May 24, 2011 at 7:04 PM, Ernesto Arias >>> wrote: >>>> Hi, >>>> >>>> I tried and is working. The problem is that I'm visualizing the volume >>>> close >>>> to the noise level, so the segmentation at lower thresholds could be >>>> trickier, but I think I'll can deal with it. >>>> >>>> I really appreciate your help. >>>> Ernesto. >>>> >>>> >>>> >>>> >>>> On Tue, May 24, 2011 at 4:20 PM, Tom Goddard wrote: >>>>> Hi Ernesto, >>>>> >>>>> Yes, now I understand. The Segger regions only include grid points >>>>> above the contour level that was displayed when you made the >>>>> segmentation. >>>>> So when you mask to one of those regions, then use a contour level that >>>>> is >>>>> the same or lower (or even a little higher) than the Segger contour >>>>> level >>>>> you get a horrible surface because the density has been set to zero >>>>> everywhere below the segmentation contour level. The solution is to use >>>>> a >>>>> low contour level when you do the segmentation -- a contour level >>>>> substantially lower than what you plan to use to actually view the >>>>> masked >>>>> regions, so that the zero density values are not near the eventual >>>>> contour >>>>> surface you will be displaying. The Color Zone approach is effectively >>>>> doing this, since it includes all the density out to a specified >>>>> distance. >>>>> >>>>> Tom >>>>> >>>>> Hi, >>>>> >>>>> I see what you mean, but I'm not sure why I get different results. Maybe >>>>> I'm not explaining well what I'm doing There are attached some images >>>>> and >>>>> volumes to illustrate it better. >>>>> >>>>> When I segment the map using segger, mask the original map using the >>>>> segger "Regions->mask map with selected" I get the segger.mrc map or the >>>>> segger_masked_region.png that I'm attaching. >>>>> However, when I place some markers around the same region of the >>>>> original >>>>> map, color the map using Color Zone, and do the Split map option I get >>>>> much >>>>> better results (color_zone.mrc and color_zone_masked_region.png). >>>>> >>>>> One thing I noticed is that the histograms of segger.mrc and >>>>> color_zone.mrc are completely different. The segger.mrc volume has a >>>>> sharp >>>>> cutoff at low threshold values whereas color_zone.mrc has a more >>>>> continuous >>>>> histogram. Could it be the problem? >>>>> >>>>> Thanks so much for your help. >>>>> Ernesto. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 24, 2011 at 10:10 AM, Tom Goddard wrote: >>>>>> Hi Ernesto, Greg, >>>>>> >>>>>> The Color Zone splitting tool uses the same method of setting density >>>>>> values to zero outside the region. So the jagged surface appearance >>>>>> should >>>>>> be every bit as bad looking as the Segger ones. If color zone really >>>>>> does >>>>>> look better you'd have to show me an example. It shouldn't look any >>>>>> better. >>>>>> >>>>>> The problem is fundamentally that Segger defined the boundary between >>>>>> regions by saying which grid point are in the region and which are >>>>>> outside >>>>>> the region. So the surface has stair steps matching the volume grid >>>>>> points. >>>>>> I don't have a good idea of how to smooth this jagged surface out. >>>>>> Ideally >>>>>> I'd want to see the jagged surface as smooth, but colored differently >>>>>> from >>>>>> the other parts of the surface. I'd like the different coloring >>>>>> because at >>>>>> this surface patch you have cut through high density -- it is an >>>>>> artificial >>>>>> boundary. When you hide that by masking it makes misleading images. I >>>>>> have >>>>>> an idea about how to achieve both these goals but it is not implemented >>>>>> yet. >>>>>> Basically I don't mask the volume. Instead I intersect the volume >>>>>> surface >>>>>> with the masking surface. By "intersect" I mean I show the mask >>>>>> surface >>>>>> wherever it lies inside the volume surface, and the volume surface >>>>>> wherever >>>>>> it lies inside the mask, and hide everything else. The mask surface >>>>>> and >>>>>> volume surface can have two different colors. Another way to think of >>>>>> this >>>>>> idea is that I clip the volume surface using the mask surface. We >>>>>> already >>>>>> allow you to clip a surface with a plane in Chimera. This is just a >>>>>> generalization where you can clip a surface with some arbitrary other >>>>>> surface. This isn't too hard to implement, but I want the boundary >>>>>> where >>>>>> the volume surface and the mask surface meet to be a smooth curve. >>>>>> That >>>>>> requires cutting up the the triangles of the original surfaces. I've >>>>>> been >>>>>> meaning to try this for years now. I think it would look great. >>>>>> >>>>>> One further comment. Segger makes its region surfaces using the list >>>>>> grid points in the regions, so how does it make the surface look >>>>>> smooth? >>>>>> The main trick it uses is "surface smoothing", 5 iterations with >>>>>> smoothing >>>>>> factor 0.25. You can enable this for the volume surfaces using the >>>>>> Surface >>>>>> and Mesh Options panel and see if it helps. Segger also rebins the >>>>>> grid >>>>>> points which may help the appearance and that is possible but not so >>>>>> easy to >>>>>> duplicate with a volume surface using standard Chimera features. >>>>>> >>>>>> Tom >>>>>> >>>>>>> Hi Ernesto, >>>>>>> >>>>>>> That is a good point, I'm not completely familiar with how the color >>>>>>> zone tool splits out a subsection of the map, so I am cc-ing Tom >>>>>>> Goddard, who I think wrote that tool, and is a developer of Chimera >>>>>>> and co-developer of Segger. Tom, could you look at the message Ernesto >>>>>>> sent and my reply, both below? Let us know if you have any further >>>>>>> insights into how we can make segmented-region-masked maps have nicer >>>>>>> boundaries... >>>>>>> >>>>>>> Greg >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sun, May 22, 2011 at 8:26 PM, Ernesto >>>>>>> Arias >>>>>>> wrote: >>>>>>>> Hi Greg, >>>>>>>> >>>>>>>> Thanks so much for answering my question. Everything is crystal >>>>>>>> clear. >>>>>>>> For illustrating the segmentation results I can use the segmented >>>>>>>> regions, >>>>>>>> but I wanted to make a morphing and some movies using the segmented >>>>>>>> regions >>>>>>>> and I would be easier if I could save the maps without loosing >>>>>>>> details. >>>>>>>> I >>>>>>>> tried to use a lower threshold and also to filter the volume before >>>>>>>> segmenting it, but the results are not much better. >>>>>>>> >>>>>>>> I'm not a programmer so I'm sorry if I say nonsenses. Using Chimera >>>>>>>> "Color >>>>>>>> zone" tool you can color different regions in the volume using >>>>>>>> markers >>>>>>>> or >>>>>>>> atoms, and it has the option of splitting the colored regions into >>>>>>>> different >>>>>>>> maps and save them. In that case I don't notice a a coarser surface >>>>>>>> in >>>>>>>> the >>>>>>>> manually segmented maps. Could I use the segger information to color >>>>>>>> the >>>>>>>> volume with Color zone, and use the split map option to segment the >>>>>>>> map? >>>>>>>> >>>>>>>> Thanks again for your help, >>>>>>>> Ernesto. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, May 20, 2011 at 7:50 AM, Greg Pintilie >>>>>>>> wrote: >>>>>>>>> Hi Ernesto, >>>>>>>>> >>>>>>>>> Sorry for the slow response - but thanks for the message and the >>>>>>>>> question. I believe the artefact you are noticing is that when you >>>>>>>>> mask the map with the segmented region, the map densities are set to >>>>>>>>> 0 >>>>>>>>> everywhere except inside the region. Hence instad of a gradual >>>>>>>>> decrease in density at the boundary, making the surface smooth, as >>>>>>>>> you >>>>>>>>> can see in your original map, now there is a sudden drop from some >>>>>>>>> density value to 0 in the segment-masked map. This manifests itself >>>>>>>>> as >>>>>>>>> a coarser surface (as you describe it, the triangles look bigger >>>>>>>>> because you can actually see them). I've sort of know about this >>>>>>>>> problem for a while, but I'm not sure I know yet a good way to >>>>>>>>> address >>>>>>>>> it. I've tried, for example, to extend the segmented regions by a >>>>>>>>> small number of voxels when masking the map, however this looks even >>>>>>>>> worse (it sometimes looks like little fragments coming out of the >>>>>>>>> surface). As long as you know why this happes (let me know if it's >>>>>>>>> still not clear, and I'll try to explain more), I hope at least it >>>>>>>>> seems reasonable. If you have any ideas on how to address it, please >>>>>>>>> let me know! Meanwhile, here are some things you might try to get >>>>>>>>> around this issue: >>>>>>>>> >>>>>>>>> 1) filter the masked map - use the Volume Data / Volume Filter tool >>>>>>>>> - >>>>>>>>> this will remove some signal from your map, but it will make the >>>>>>>>> boundaries smoother as well >>>>>>>>> >>>>>>>>> 2) if you're mainly concerned about illustrating the segmentation >>>>>>>>> results, re-segment the masked map, and use the segmented region for >>>>>>>>> illustration - the segmented region is always smooth as you might >>>>>>>>> have >>>>>>>>> noticed... >>>>>>>>> >>>>>>>>> I hope this helps, and again let me know if you have any ideas... >>>>>>>>> >>>>>>>>> Greg >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, May 17, 2011 at 6:51 PM, Ernesto >>>>>>>>> Arias >>>>>>>>> wrote: >>>>>>>>>> Dear Greg, >>>>>>>>>> >>>>>>>>>> My name is Ernesto and I'm a postdoc in James Berger's lab at UC >>>>>>>>>> Berkeley. >>>>>>>>>> I'm using segment 1.6 built in chimera 1.5.3 and is working >>>>>>>>>> remarkably >>>>>>>>>> well. >>>>>>>>>> I have a question and I'd be grateful if you could answer it. >>>>>>>>>> I want to save in individual mrc files the segmented regions of my >>>>>>>>>> map, >>>>>>>>>> but >>>>>>>>>> when I do it and open the volume of the subregion region it seems >>>>>>>>>> like >>>>>>>>>> the >>>>>>>>>> triangle size is bigger than in the segmentation and in the >>>>>>>>>> original >>>>>>>>>> volume. >>>>>>>>>> I tryed to save the segmented volumes using the "File->save" >>>>>>>>>> options >>>>>>>>>> of >>>>>>>>>> segger as well as "Regions->Mask map with selected", but I get the >>>>>>>>>> same >>>>>>>>>> results. >>>>>>>>>> I don't know if I'm explaining myself clear enough, so I attach two >>>>>>>>>> pictures >>>>>>>>>> to try to illustrate what is happening. >>>>>>>>>> Do you know how can I save segmented regions without this loss of >>>>>>>>>> quality? >>>>>>>>>> >>>>>>>>>> Thanks very much for you help, >>>>>>>>>> Sincerely, >>>>>>>>>> Ernesto. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>> >> >> > Thanks, Tom. That helped a lot. However, is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge. This is true whether I am masking directly, or the inverted view. > > Kelly > > On Mon, 16 May 2011 12:18:01 -0700 > Tom Goddard wrote: >> Hi Kelly, >> >> There is no command to position the volume eraser sphere using typed coordinates. >> >> If you want to erase a spherical region centered on the center of a virus map use the shape and mask commands: >> >> shape sphere radius 120 center 0,0,0 coord #0 color blue >> mask #0 #1 invert true >> >> The first command makes a spherical surface of radius 120 Angstroms at center 0,0,0 (Angstroms) in the map #0 coordinate frame colored blue. The second command copies the region of map #0 outside the sphere #1, making a new volume data set. >> >> The main trouble here is figuring out the coordinates of the center of virus map. The virus map origin is set in the Volume dialog Coordinates panel where you specify the grid index for position (0,0,0). In the above example I've got the map origin set to the center of the virus (EMDB 1058, grid index 87 for a size 175 map, base index is 0). You can use >> >> shape sphere radius 120 center #0 color blue >> >> which puts the center at the center of the bounding box of the displayed surface for map #0. But that doesn't in general give you the exact center of symmetry. So it is better to find the exact grid point that is the center of symmetry used when the map was calculated. >> >> Tom >> >>> Hi, >>> >>> I would like to place the origin of the eraser to correspond with the >>> center of my map but haven't found a way to define its position based on >>> coordinates, only by moving it with the mouse. Is there a line command >>> or other menu option that allows me to set the position more precisely? >>> >>> Thanks, >>> Kelly

1 0

Secondary Structures in MD data
by Simon Sham 01 Jun '11

01 Jun '11

Hi, I am interested in analysizing the secondary structures from a period of MD trajectories. Is it possible to do that in Chimera? Thanks for your insight. Best, Simon

2 2

Asymmetric partial charges on symmetric atoms
by Brian Fochtman 31 May '11

31 May '11

Hi, When adding partial charges (AM1-BCC) to small molecules in chimera, we observed that atoms in symmetrical groups are not assigned the same partial charge. Specifically, the two oxygens in a carboxyl group are not assigned the same partial charge. See excerpt from mol2 file below: carboxyl: 20 C20 23.4850 19.6920 64.8870 C.2 1 BCZ 0.9226 21 O21 22.2660 19.7760 65.0340 O.co2 1 BCZ -0.9253 22 O22 24.2040 20.8120 64.7970 O.co2 1 BCZ -0.7643 There is a significant difference in partial charge between the two carboxyl oxygens (0.161). This problem was observed in both older (with mopac) and newer (with sqm) versions of chimera. The molecule is peramivir from the pdb1L7F crystal structure. Similar problems were observed for other molecules that inhibit Neuraminidase for example those 1L__ pdb structures. This problem is also observed when assigning am1bcc charges to the mol2 file using antechamber/sqm directly. Best Regards, Brian Fochtman, Trent Balius, Sudipto Mukherjee

2 1

Chimera with 50000 pdb files
by mselvaraj＠mbu.iisc.ernet.in 31 May '11

31 May '11

Dear all, I have some 50000 pdbs obtained from a md simulation of my protein. I would like to calculate ellipsoid (with 'measure inertia' command) around the protein molecule in each pdb and get their axes. Is there a provision/script in chimera to run multiple pdbs and get the axes in a file separately? Any suggestions on this will be helpful. Thanks in advance. yours truly, M. Selvaraj, Graduate student, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

Molecular representation & FindHbond
by George Tzotzos 31 May '11

31 May '11

Hi everybody, I've successfully loaded my protein. It is represented in ribbon. I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them. I follow the procedure below: 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds 2. show sel 3. repr bs sel 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein. I'd appreciate your guidance how to deal with this. Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons? Thanks in advance for your advice Regards George

2 2

Re: [Chimera-users] An ellipsoid around a protein
by Elaine Meng 30 May '11

30 May '11

Dear M, Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC'd here). In Chimera you can calculate and display the inertia ellispoid for any set of atoms with the command "measure inertia." For example, you could open the protein structure in Chimera, show the command line (from Favorites menu) and then enter the command: measure inertia protein The principal axis information is given in the Reply Log. There are other keywords, such as to control the color of the ellipsoid. See: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia> 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 May 29, 2011, at 9:45 PM, mselvaraj(a)mbu.iisc.ernet.in wrote: > Dear sir, > I would like to calcualte an ellipsoid with its principle axis for a > protein molecule,given its PDB. I came across your discussion on > chimera-users discussion.. Do you have a program that can calculate the > ellipsoid and its principle axes. It would be very help ful for my > analysis. Thanks in advance. > > yours sincerely, > M. Selvaraj, > Graduate student, > Molecular Biophysis Unit, > Indian Institute of Science, > Bangalore 560 012 >

1 0

system freeze completly with ubuntu 10.10
by Mario Dejung 27 May '11

27 May '11

Hello, I have some trouble with chimera on my old laptop. My complete system is freezing after a few seconds. I can not restart X server or switching to a console or anything, even the mouse pointer is not moving. I tried 32 bit chimera 1.5.2 and 1.5.3, both have the same problem. I have 64 MB graphical memory available, but the maps I am loading are very small, like less then 4MB and the system crashs also, even if I open just one map. Does anyone has a good suggestion? Since the whole system is freezing, I am not able to switch back to a terminal to look for error messages or similar. Kind regards Mario

2 1

Import IMOD models into Chimera
by Thomas Heuser 27 May '11

27 May '11

Hi all, Is it possible to open IMOD model files in Chimera? I have used IMOD (with imodmesh) to generate a model of my structure and would now like to load this IMOD model file (.mod) as a volume into Chimera. Is that doable? Thanks a lot in advance and big cheers, Tom -- XXXXXXXXXXXXXXXXXXXXXXX Thomas Heuser Nicastro Lab Rosenstiel Center, MS029 Brandeis University 415 South Street Waltham, MA 02454-9110 Phone: (+ 1) 781 736 2608

2 1

question about "measure rotation"
by Bobby Laird 25 May '11

25 May '11

I am using the measure rotation command in chimera to calculate the degree of rotation between two dimers, which make up a tetramer. I am using the following commands to accomplish this: mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/ab-aligned.pdb close #1 open #1 /tmp/ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #0 #1 I have noticed that when I use the "measure rotation" command that can get two different answers. I realize that the two answers are the result of an arbitrary decision made by the measure tool that result in a +/- of the same angle (i.e. 6 versus 174 degrees). Since I am looking at more several crystal structures, is there a way to force "measure rotation" to always make the same decision so that I know what relative direction the rotations are in to each other? Thanks _______________________________ Bobby W. Laird

2 1

installation of headless chimera
by bharat gupta 24 May '11

24 May '11

Hi, I am new to chimera and I am trying to install it on fedora core 6 . After followng the instructions given in installation manual nothing happens in my system. Can anybody tell me how can I install the headless version of chimera .. Thanks in advance for help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46010(a)yahoo.com

2 2

Re: [Chimera-users] Proline sidechain broken (with backbone as a ribbon)?
by Visvaldas K. 24 May '11

24 May '11

I'm very sorry, I take my question back. Actions->Atoms/bonds->Show will do the trick. Vis

2 1

Proline sidechain broken (with backbone as a ribbon)?
by Visvaldas K. 23 May '11

23 May '11

Hi, I really like the default view of a loaded PDB file, where the whole protein is shown as a ribbon, but also the sidechains next to the heterogroups are shown. Proline shows up in this representation as a sort of rhomboid (or kite) shape, which is okay. However, I cannot achieve the same effect for proline when I select proline manually. If I do Actions->Atom/bonds->sidechain/base->show, the proline sidechain appears as a broken rhomboid, which looks more like a hook, i.e. a one of the bonds is missing to close the loop. How do I obtain a "closed" proline sidechain look? Thank you, Vis

1 0

centering a volume to an atom's coordinate
by Roni Rayes 23 May '11

23 May '11

Hi, I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file. When I created the volumes I made sure that their center is in the middle of the box containing the volume. I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided. Any idea on how to do that? Thank you Roni

2 1

PipesAndPlanks
by George Tzotzos 23 May '11

23 May '11

Hi everybody, I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. Obviously, I'm missing something. Your guidance will be greatly appreciated. Have a good weekend George PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list.

3 6

Pack molecules in Unit Cell
by Joe Osmundson 20 May '11

20 May '11

Hi everyone, I would like to transform a pdb so that it fits nicely in the unit cell, which seems to be described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.… as "Pack molecules in unit cell". However, this is not an option when I bring up the options in the Unit Cell tool (although literally everything else that should be there IS indeed there). Is there a glitch in the most recent version? Is there an easy way to script this to essentially move the model (and its crystallographic mate) into the center of the unit cell? Thanks, Joe Osmundson Darst Lab Rockefeller University

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Completely reinstall chimera
by Daniel Hitchcock 20 May '11

20 May '11

Hi, I want to completely uninstall chimera and remove all the settings from the program. I notice though if I uninstall and reinstall though, it still has all the settings and history from before. How can I completely remove Chimera from the computer so I can return to default settings? Thank you -daniel

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solid-cylinder representation of helices
by Francesco Pietra 19 May '11

19 May '11

HI: Is any plan about a solid-cylinder representation of protein helices? It would be very useful to represent pathways of ligands inside a protein (in combination with centroid). Helices allow a less defined 3D perspective, especially when all is projected into a screen or paper. Thanks francesco pietra

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Visualising PDB files from AMBER
by George Tzotzos 18 May '11

18 May '11

Hi everybody, I've generated a average pdb structure from an AMBER trajectory. The structure contains one water molecule (named: WAT). I fail to visualise it in Chimera despite the fact that I can select it. I'm using Chimera 1.5.2 on OSX 10.6.7 Any ideas explaining this behaviour? I'm attaching the relevant file. Thank you in advance for your help Best regards George

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Re: [Chimera-users] Pseudobonds disappearing during morphing movie
by Elaine Meng 17 May '11

17 May '11

Hi Alan, Sorry, there isn't currently a command to apply residue class, only scaling (ribscale) and style (ribrepr): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon…> Some possibilities: - save session with morph already calculated and residue class applied. Your script would then restore the session, play the trajectory, and record the movie. I agree this is not as nice, since then you are saving two files instead of one, and the session file is large. You wouldn't have to wait for the morph to recalculate, however. - use a small python script to apply the residue class. Your Chimera script could open that python file, which automatically executes it. One of the other developers would have to supply the python (beyond my skill set, sorry), and that also requires having two files, albeit much smaller than a session file. In general when playing a morph with ribbons that show secondary structure, consider whether you need to recalculate the secondary structure assignments with "ksdssp" at each frame. To execute a set of commands at each frame, one would use the "perframe" command in combination with "alias": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> For example, your script could contain something like: alias ^redefine ksdssp #2 perframe redefine movie record coordset #2 1,21; wait 21; ~perframe I hadn't used ksdssp/perframe in my examples since (perhaps fortuitously) the secondary structure didn't change that much. If you are just displaying a tube or licorice which doesn't show secondary structure with different widths, it doesn't matter, however. You're right that the shape tube surface will not automatically morph along with the structures, but it might work to destroy/recreate it at each coordinate frame using "perframe". Interesting idea... I haven't tried it, though! I hope this helps, Elaine On May 13, 2011, at 6:10 AM, Alan Cheung wrote: > Thanks Elaine! Yes, the reported thickness was 3.333 (pixels?) and that seems to match the width of the pseudobond i see on the video. The width isn't too bad, and i can live with it. > > Thanks for the explanations and tip too. > > One last question : can I apply a saved residue class (from the ribbon style editor) via a command? I'm morphing a mixture of ribbon and side chain atoms and (for a leucine residue) the CA-CB bond is unrealistically long, but seems ok if i remove the orientation atom (O) from the residue class. I saw the "shape tube" feature in the documentation that draws a tube through CA atoms, but i guessed it's not morphable (and might also not include my precious pseudobond ;) ) > > Many thanks again for the quick replies! > > Alan > > On 12/05/2011 19:22, Elaine Meng wrote: >> Hi Alan, >> Never mind about the PDBs, I made up my own by deleting parts of the structures in my favorite morph test case. >> >> I think I answered all of your issues except for the pseudobonds completely disappearing with "morph movie nogui true" -- I did reproduce that problem, and it seems like a bug, albeit mysterious. I'll file a report about that one, but in the meanwhile I hope you will be able to manage without using that option. >> >> One minor thing is that I generally recommend adding a few more wait frames to the recording after the morph plays, to avoid any "motion blur" effect at the end you might get as a result of encoding. I didn't see much of that effect in my test case proteins using your script, however. It may be because the morph is spread out over 50 frames so there is less differences between adjacent frames, but I was also using different PDBs than you. >> Best, >> Elaine >> >> On May 12, 2011, at 9:25 AM, Elaine Meng wrote: >> >>> Hi Alan, >>> I haven't tried the whole script yet (can you send me the PDB files? I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions: >>> >>> (A) lines thinner in saved movie. In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size. You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling. The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera). If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit. Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display. You could try using lower supersampling. Also make sure you are using a recent version (1.5.3 candida > te ! >>> or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago. >>> >>> (B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g). Individual pseudobonds don't have a linewidth attribute, it is set at the group level. All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths. If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups. The balloon help will give the attribute name and allowed values. >>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelattrib.html> >>> >>> I will try to look at your other issues and get back to you, >>> 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 May 12, 2011, at 8:54 AM, Alan Cheung wrote: >>> >>>> Hi there - i'm scripting a complex movie and am having problems with >>>> pseudobonds during morphing. Script is pasted at the end. >>>> >>>> Part of the movie contains a morph between two structures, both of >>>> which are missing the same amino acid segment. Loading the two >>>> structures show the pseudobond for the missing residues and the >>>> resulting morph also contains the same pseudobond. >>>> >>>> I've been changing the thickness of the pseudobond with : >>>> >>>> setattr g lineWidth 8 >>>> >>>> and while the two static structures and the morph in the chimera >>>> window have a thicker pseudobond, the resulting movie (encoded to >>>> .mov) does not. Am i doing something wrong? >>>> >>>> Alan >>>> >>>> p.s. incidentally, when morphing by script, if one includes "nogui >>>> true" with the "morph movie" command, pseudobonds aren't kept in the >>>> morph at all. A bug? >>>> p.p.s. can someone explain to me the difference between "setattr g" >>>> and "setattr p"? I've read the manual but i don't understand why only >>>> the former seems to work for me. >>>> >>>> ## movie script >>>> >>>> open model1.pdb >>>> open model2.pdb >>>> morph start #0 frames 50 name morph1 method linear >>>> morph interpolate #1 name morph1 >>>> morph movie name morph1 >>>> coordset #2 1,1 >>>> setattr g lineWidth 8 >>>> ~modeldisplay # >>>> >>>> movie record supersample 3 directory ~/TEMP/ >>>> modeldisplay #2 >>>> coordset #2 1,51 ; wait 51 >>>> movie stop >>>> movie encode output morph1.mov >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > -- > Alan Cheung > Gene Center > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: cheung(a)lmb.uni-muenchen.de

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labeling residues
by Daniel Gurnon 16 May '11

16 May '11

Hi all, A student of mine wants to make a wire sculpture of a protein, and I'm thinking of ways Chimera could make the task easier. Ideally, I would create a script that would display any protein in wire-form, with residue positions clearly and unobtrusively labeled. I'd like to use the command line to display a backbone as a licorice ribbon with residue numbers and 1-letter codes at the alpha carbon of each residue. so starting out, I would use: ribscale licorice; ribbackbone; rlabel @ca; But instead of "ALA 24.B", I want "A 24". Though I can get what I want using the Actions menu, I can't find a way to create custom rlabels via the command line. Is there a way to do this? If possible, I would also like to position each label near the spot on the ribbon closest to the alpha carbon (the "primary atom"). I can see how to do this with the molecule attributes panel, but I'm having difficulty setting the placement through the command line. And while I'm at it...is there a way to color a spot on the ribbon closest to the alpha carbon a different color than the rest of the ribbon? Thanks for the help! Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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