- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] mac pro theoretical question
by Tom Goddard 29 Jan '08

29 Jan '08

Hi Jeff, I don't know much about any of the current Apple graphics cards (Radeon HD 2600 XT 256Mb, Nvidia GeForce 8800 GT 512Mb, Nvidia Quadro FX 5600 1.5Gb). My first concern would be whether bugs in the drivers for these cards are going to cause trouble in Chimera. We have a web page that lists problems with graphics drivers observed using Chimera: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards There was a recently reported problem (squashed atom spheres) with GeForce 8800 GTX (not GT) on Windows. The Apple driver may be much different. The Quadro FX 4500 which was Apple's high-end offering before the 5600 crashed with solid volume rendering. Don't know if the current 5600 would have the same problem -- but there is a fair chance it does. Chimera uses many different OpenGL calls and I'd guess 1 in 10 drivers exhibit bugs of varying severity when using Chimera. Some of Chimera performance is related to graphics card speed and memory, and some is related to CPU speed and memory. When the displayed models rotate slowly that is the graphics card except if you are using transparent volume surfaces or meshes which are sorted by depth on the CPU for every new view angle. Everything else is the CPU, main memory, memory cache performance, and hard-drive speed. Solid style volume rendering makes a lot of textures which usually will be stored in graphics card memory. More graphics card memory could make larger volume rotate faster because they fit on the card. 256^3 volumes (16 million voxels, 4 bytes per voxel) typically rotate at 10 frames per second with graphics memory sizes 128 Mb and up. Textures have to have power of 2 sizes so just knowing that can get you better performance if you trim your 550x550x100 region to 512x512x100 you'll get a factor of 4 speed-up. I don't know if a single application using one display can use more than one graphics card in Apple's multicard options. Chimera has no special code to do that. For large volume data, hard-drive speed, main memory size, and CPU speed are likely to be noticable factors in Chimera performance, each of about equal importance to graphics card speed. Tom > hi Tom, > > if you were considering a Mac Pro at some point in the future, what > graphics card would you pick when thinking of chimera (if you don't > mind peeking at some point at the list at > http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/9354001/wo/… > > > are rendering bottlenecks in chimera largely a processor-limited thing > (and thus one of the 'lower end' cards listed would be fine), or > something that benefits dramatically from spending $2000 on a graphics > card (I am not in that kind of market, just wondering what kind of > decision you would make if evaluating that platform) > > best, > > -Jeff > > >

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average vs ensemble
by Rachel Scherer 29 Jan '08

29 Jan '08

Given that chimera doesn't calculate average NMR structures, this query may be outside the groups interests, but can anyone suggest what the appropriate protocol is when making aa-substitutions into an NMR structure: should an "average" be calculated (by averaging the atom coordinates across all the models in a PDB file that predates inclusion of the average into the database entry) or, should one use a representative from a cluster generated with "ensemble cluster" be chosen? Or an average of the representatives of the clusters? Or, the cluster representative that best matches the calculated average? -- Rachel Scherer rachel(a)bio.umass.edu Biology Department (413)545-2825 vox UMASS Amherst (413)545-3243 fax

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coordinates
by hsosa＠aecom.yu.edu 25 Jan '08

25 Jan '08

Hi, I am trying to rotate a molecule around a 3D density map. I had already saved the coordinates of the molecule relative to the map. However if I rotate the pdb file (creating a new pdb file with the rotated molecule) by rotating the coordinates around the origin (0,0,0) the new molecule is rotated around a a center that does not coincide with the center of the map. So I am confused about what are the relative positions of the origin for the map and pdb file. If I have an atom with pdb coordinates 0,0,0 should this atom appear at the center of the density map ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] Save a transformed density map
by Thomas Goddard 24 Jan '08

24 Jan '08

Hi Keren, Chimera has a resampling capability for extracting regions of a map that aren't aligned with the axes. It doesn't work well in the case you want. So I've made a Chimera command that will do what you want. If your the map you wish to save in the new orientation has id number 0 (listed next to the name of the map in volume dialog), and the map you fit into has id 1 you would use the command: vop #0 resample onGrid #1 The vop stands for "volume operation". (Use menu Favorites / Command Line to type commands.) This will create the new map which will appear in the volume dialog and can be saved with the volume dialog File / Save map as... (or using a command like "volume #2 save /tmp/newmap.mrc"). The vop command with the resample operation will be in tonight's builds of Chimera (assuming they succeed). http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Keren Lasker wrote: > hey Tom, > > I need to save the transformed map for other calculations. Is there a > resampling option in chimera? if not I guess that I can use the output > transformation matrix generated by fit map2map - right? > > thanks, > Keren. > On Jan 24, 2008, at 3:27 PM, Thomas Goddard wrote: > >> Hi Keren, >> >> You can save the Chimera session to preserve the orientation of one >> map fit into another. >> >> If you want to write a new map so that when it is loaded in Chimera >> and other software it will be at the correct place in the map it was >> fit into that is harder. The problem is that none of the map file >> formats provide for a positioning transformation in the header. So it >> would be necessary to resample the map that you fit on the grid of the >> map you fit into. Resampling interpolates data values and can degrade >> map quality. Do you want to do that? >> >> Tom >

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volume visualization
by Enrico Malito 24 Jan '08

24 Jan '08

Hello, I am trying to visualize a map as Volume (ccp4 format map calculated with VOIDOO in NEWZD then converted with MAPMAN) and somehow the map in chimera results shifted with respect to the corresponding pdb model (in a completely different place). If I open same pdb and map file in other visualization programs they are actual in the right position (map into the cavity of the enzyme). I'm opening the map from the Volume Viewer-->File-->Open map Am I doing something wrong? Thanks, EM -- Enrico Malito Ben-May Department for Cancer Research Center for Integrative Science, W423J The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637 Tel: 773-702-4608 Fax: 773-702-6260 http://home.uchicago.edu/~emalito

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Save a transformed density map
by Keren Lasker 24 Jan '08

24 Jan '08

hello, How can I save a transformed map after using the fit map2map option? The "save map" option saves it in its original transformation. thank you, Keren.

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Chimera batch surface exporter
by Trent Grover 24 Jan '08

24 Jan '08

Hi Everyone, I'm pretty new to Chimera, but I'm working on an animation project that requires quite a few proteins and molecules. To speed up the process, I'd like to create a batch converter/exporter script to do the following: Open a PDB file Generate a multiscale model at a specified resolution Export the model out as a VRML or OBJ file I think I can do this using a Chimera command file, but I was hoping someone could point me in the right direction for some of the relevant command line syntax. Is it possible to control the multiscale model tool via command line (I know I can launch the dialog, but can I change the parameters and execute)? Is there a reference somewhere for the command line parameters for the multiscale models tool? What is the command line export command? Where can I find an OBJ exporter (there are references to it in the mailing list archive)? Any help would be greatly appreciated. Thanks, Trent BTW - I have a suggestion for improvement of Chimera. Add a command history window (or modify the existing one) that echoes out the command line text that is equivalent to any command executed via the Chimera user interface. Maya has this functionality and it is wonderful for anyone who is trying to figure out how to script a process that they know how to execute via the various menus.

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Re: [Chimera-users] Surface representation
by Elaine Meng 24 Jan '08

24 Jan '08

> Hi, > I would like to know if there is a way to build a surface > representation from a pdb file of a dummy atom saxs model in > chimera. The file consist only of CA atoms. I could simulate this > by increasing the vdw radius but the model becomes way to big. > Thanks > James Hi James, You can use Multiscale Models to make a contour surface that encloses the "atoms." The tricky part may be adjusting the contour surface parameters to get the desired smoothness and enclosed total volume. At least in my tests, Chimera did not like the columns in your file after the B-factor column, so I made a version with those removed and opened it with "File... Open" before proceeding. I will send you that file in a separate message. (1) for purposes of comparison to the surface, I displayed the atoms as spheres with the radius 3.75 (this value was given in comments in the file) using the following commands: setattr a radius 3.75 rep sphere You can show the command line with Favorites... Command Line. (2) started Multiscale Models (under Tools... Higher-Order Structure), clicked the "Make models" button near the bottom. This generates the contour surface but hides the spheres. To also show the spheres, Ctrl-click on the surface to select it, and then in the "Style" line of the dialog, choose "Show also.. Spheres". To see spheres inside the surface, make it transparent; set Transparency to some fraction, say 0.3. (3) Then you can fiddle with the contour surface parameters in the Multiscale Models dialog. Many are hidden but can be shown by checking the box next to "..." I got a fairly decent enclosure of the spheres with all default parameters except setting the "Threshold atom density" for "CA only" to 0.0006 instead of the default 0.002. You could also fiddle with the smoothing parameters and resolution if that is not good enough. If you have some idea of what total volume the surface should enclose, that can be evaluated with Measure Volume and Area (under Tools... Volume Data). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Chimera-users Digest, Vol 57, Issue 24
by Jonathan Hilmer 22 Jan '08

22 Jan '08

POV-Ray also works extremely well as a distributed job. This site has some basic discussion of some of the distributed POV options: http://columbiegg.com/httpov/?p=why Jonathan > Today's Topics: > > 1. (no subject) (jean-francois menetret) > 2. Re: Flip handedness of map (Tom Goddard) > 3. VRML alpha vs 1-alpha (Nils Becker) > 4. Re: VRML alpha vs 1-alpha (Greg Couch) > > > ------------------------------ > > Message: 4 > Date: Tue, 22 Jan 2008 10:37:54 -0800 (PST) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] VRML alpha vs 1-alpha > To: Nils Becker <nils.becker(a)ens-lyon.fr> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0801220934340.1761700(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Tue, 22 Jan 2008, Nils Becker wrote: > > > Hi, > > > > I found information on the web site that VRML models use > > 1-alpha blending for transparency, and that that looks ugly. > > I agree. > > > > Now I have externally generated VRML files including transparency. > > > > Is there a way to get nice (normal) transparency rendering of these > > models in chimera? > > > > e.g. editing the vrml files, converting them to another format or some > > option inside chimera? > > > > Thanks for any help, cheers, Nils > > The VRML transparency is 1-alpha, because alpha is an opacity value. So > that is just an alternative way of saying that same thing, and is not the > reason it is worse. > > The reason VRML transparency is worse is that there is no sorting within > the VRML shapes, so the blending of transparent objects has to be > drawing-order independent, so VRML uses additive blending. > > The simpliest solution would be to live with chimera's current depiction > and use the Save Image dialog to generate a ray-traced version. The > ray-traced version will be much nicer (and take a lot longer to compute, > try using the POV-Ray 3.7 beta on a multi-core computer to speed things > up). > > The other solution, is to write some Python code and use the _surface > module's Surface_Model and Surface_Group classes. That is, convert each > VRML object into a triangulated surface, a Surface_Group, and put all of > the Surface_Groups into one Surface_Model. All surfaces within one > Surface_Model are sorted so that the transparency is correct for more than > one overlapping surface (unlike the transpareny in chimera between > models that only works for one level of transparency). You can see > examples that use the _surface module in the GraspSurface, IMOD, > Icosahedron, and Intersurf modules (and others) in the CHIMERA/share > directory of your installation. > > If you have any questions about the _surface module, please ask them on > the chimera developers mailing list, chimera-dev(a)cgl.ucsf.edu. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 57, Issue 24 > ********************************************* >

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VRML alpha vs 1-alpha
by Nils Becker 22 Jan '08

22 Jan '08

Hi, I found information on the web site that VRML models use 1-alpha blending for transparency, and that that looks ugly. I agree. Now I have externally generated VRML files including transparency. Is there a way to get nice (normal) transparency rendering of these models in chimera? e.g. editing the vrml files, converting them to another format or some option inside chimera? Thanks for any help, cheers, Nils

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(no subject)
by jean-francois menetret 21 Jan '08

21 Jan '08

In older versions of Chimera, it was possible to change the handedness of a map with a minus sign for the pixel size of the axis. How do you do that in the newer version ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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visualizing density map
by francesco zonta 20 Jan '08

20 Jan '08

Good morning. I have some problem in visualizing a ccp4 density map with chimera. I can see only a small slab of the map, but i need to visualize a larger reagion. How can I enlarge the visualized volume? thank you for the help Dr. Francesco Zonta

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Re: [Chimera-users] visualizing density map
by Tom Goddard 18 Jan '08

18 Jan '08

Hi Francesco, Your map contains only the crystal asymmetric unit. Coot is able to replicate that asymmetric unit (using the 4 space group symmetries and unit cell translation symmetries) to show the map for a bigger region of the crystal. http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC… Chimera is not able to do that replication. Chimera can only display the part of the map present in the file. You might be able to export a map from Coot that covers a larger region but I do not know how. This replication of the crystal asymmetric unit is a nice feature and I'll add it to the list of requested features for Chimera. Tom francesco zonta wrote: > Hi thomas, here is how I can see the map with coot > This is a cubic box of 60 angstrom. [Image deleted] > The problem I have is probably that with chimera I can not see a > bigger volume, but I do not know why. > > Francesco

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VRML rendering options?
by Nils Becker 18 Jan '08

18 Jan '08

Hi, I have been using Chimera for a while and find it great software. Now I am trying to include my own VRML models and show them together with PDB data. I succeeded in opening an externally generated VRML 2.0 file. Since the VRML file contains colored boxes, the standard smooth rendering is not appropriate. Is there a way to influence the rendering style? Also, is there a way to switch on a fixed transparency (alpha value) for the whole VRML model, on a per-model basis? Any help would be appreciated! Cheers, Nils

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Fwd: Re: Bug (?) with EnsembleCluster
by Francesco Pietra 17 Jan '08

17 Jan '08

Yes, the two behave differently, and not only as to importing pdb. I had opened my combined trajectories (protein+ligand in a lipid membrane) in VMD while looking at either the ligand or the protein: both highly distorted at each one of the 550 frames. I only got nearly reasonable structure for the ligand by averaging the frames. That was most discouraging in the last few days. Did the same for the equilibration and got the same discouraging results. This last analysis was not fitting the analysis with ptraj, Therefore I have now done the same for the MD trajectories with Chimera, which runs more slowly along the frames, and surprisingly, "at the naked eye" both the ligand and the protein save their correct structure along the 550 frames, with only the internal displacement on/back that one expects from MD. I repeated without hiding the membrane and water, and "at the naked" the ligand was not wandering around. I looked at RMDS Maps(Start frame 1; End 550; Step size 2; RMSD map of trajectory against itself; Lower rmsd threshold 2.9, higher 3.9: RMSD varied from 0.194 to 1.810 for the ligand and from 0.612 to 2.420 for the protein. Is that variation too much for accepting this MD for good (or fair) and continuing it with same settings? If it is a too large a range, that explains why the ligand encountered so many protein residues when the mask was used. I was unable to find how to get a plot of RMSD against time. I would like to do that for the ligand (which is a single big residue) and selected residues of the protein. Thanks francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Tue, 15 Jan 2008 06:44:21 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Re: [Chimera-users] Bug (?) with EnsembleCluster > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > CC: chimera BB <chimera-users(a)cgl.ucsf.edu> > > Got FMI, thanks. That seems a reasonable rationalization. Though, if I > understand, importing pdb files without saturating memory (may be importing > one > "model", analyzing it, and then removing it from memory before importing next > "model", or any other better idea) is something to overcome in order to have > Chimera carrying out cluster analysis. Or I do not understand or cluster > analysis is of minor interest, both equally possible. > > francesco > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > Just FYI, when you open a 5000 MODEL structure with Chimera's normal > > File...Open, you get 5000 completely separate models (and will likely > > exhaust memory unless its a small molecule). Each model can be > > colored individually, moved, mutated, closed, etc. individually. > > When you open the same 5000 MODEL file with the MD Movie extension > > you get _one_ model with 5000 sets of coordinates, which takes much > > less memory. On the other hand, each frame shares colors and so > > forth with all the other frames, cannot be moved with respect to the > > other frames, etc. VMD undoubtedly uses the latter approach. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > > On Jan 11, 2008, at 3:04 PM, Francesco Pietra wrote: > > > > > Yes, 5365. What happened will be discovered. Up to the stage on > > > amber_score_everything, all was perfectly OK. Minimization and > > > heating was also > > > OK. As to MD, the situation could not be clarified so far. > > > > > > In view of your comments below, I carried out a check with proven > > > MD. I went to > > > Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the > > > related prmtop, > > > and fed the two files to Chimera, last Daily Building. After all > > > 5000 steps had > > > been acquired, saved pdb, all frames. Quit MD Movie. Try to open > > > this pdb. > > > Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb > > > could not be > > > opened: rapidly the memory was exhausted and to get control of the > > > computer I > > > had to kill gnome. With vmd, this pdb developed rapidly with all > > > 5000 frames. > > > Exactly as with the pdb from MD with my protein. This does not mean > > > that my MDs > > > are OK. I'll look for what may be wrong there. > > > > > > Thanks > > > francesco > > > > > > > > > > > > > > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > > > >> 5365 atoms? Given average atom counts in protonated protein residues > > >> that means your ligand came in close contact with ~340 residues over > > >> the course of the trajectory -- so it's wandering all over the > > >> place. I can see why you want to use cluster analysis. Oh well, I > > >> guess we're stuck until I have time to coordinate with Conrad and > > >> integrate his clustering code with MD Movie. > > >> > > >> --Eric > > >> > > >> On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote: > > >> > > >>> Eric: I followed previous route from combined mdcrd from ptraj. > > >>> > > >>> Removed remaining water. > > >>> > > >>> select ligand z<2.5 > > >>> > > >>> as Chimera command; (this was the minimum, selecting 244 atoms, 118 > > >>> of which > > >>> for the ligand; with z<2.0 the ligand only is selected) > > >>> > > >>> On playing the pdb (saved for selected atoms only) (with LOOP > > >>> deselected) the > > >>> atom selection increased, reaching 5365 atoms at the last (549) > > >>> frame. In > > >>> another run, with z<4.0 the course of atom selection was similar, > > >>> reaching 5993 > > >>> atoms at frame 549. > > >>> > > >>> This huge number of atoms proved problematic for opening pdb. For > > >>> the z<2.5 > > >>> case I left the computer on for 4h and half, with python occupying > > >>> 98% of the > > >>> available MEM (nearly 1GB). I had to kill gnome to recover command. > > >>> > > >>> May be with much more MEM it will work, though I can't check that > > >>> now. > > >>> > > >>> I did not try to combine the trajectories with Chimera as I have no > > >>> indication > > >>> that those from ptraj are faulty. The pdb files for both z<2.5 and > > >>> z<4.0 open > > >>> in vmd. > > >>> > > >>> francesco > > >>> > > >>> --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > >>> > > >>>> On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote: > > >>>> > > >>>>> In the "Define script.." I defined "select ligand z<10", then OK > > >>>>> and a BUG > > >>>>> window was presented. Attached is the reply log (bug). I tried > > >>>>> with > > >>>>> z<4 with > > >>>>> the same result (actually, I don't remember if attached bug file > > >>>>> refers to z<10 > > >>>>> or z<4). > > >>>> > > >>>> In the script-definition dialog you need to have "Interpret script > > >>>> as" set to "Chimera commands". You had it set to "Python". > > >>>> > > >>>>> Still found difficulties in loading more than one mdcrd, though > > >>>>> this should be > > >>>>> my fault. I was not sure if the list of mdcrd is to be given at > > >>>>> beginning or if > > >>>>> the other mdcrd files after the first one are to be given > > >>>>> subsequently from the > > >>>>> menu. I tried with the "list" option but only the first mdcrd was > > >>>>> opened. > > >>>> > > >>>> When you run MD Movie and the dialog comes up where you specify the > > >>>> prmtop/trajectory files, you can use the "Add..." button to add as > > >>>> many trajectory files as needed. I think this means you "give > > >>>> it at > > >>>> the beginning" rather than "subsequently from the menu" in your > > >>>> terminology. > > >>>> > > >>>> You can also just list the files in a "metafile" for the command > > >>>> line. For instance, this file works for me: > > >>>> > > >>>> amber > > >>>> leap.top > > >>>> md01.crd > > >>>> md02.crd > > >>>> md03.crd > > >>>> md04.crd > > >>>> md05.crd > > >>>> md06.crd > > >>>> > > >>>> Note that there _still_ seems to be something funky with Amber > > >>>> compressed trajectories, so don't use them for now but I should > > >>>> have > > >>>> things fixed in a day or so with that. > > >>>> > > >>>> --Eric > > >>>> > > >>>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> ____________________________________________________________________ > > >>> __ > > >>> ______________ > > >>> Be a better friend, newshound, and > > >>> know-it-all with Yahoo! Mobile. Try it now. http:// > > >>> mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > >>> > > >> > > >> > > > > > > > > > > > > > > > ______________________________________________________________________ > > > ______________ > > > Looking for last minute shopping deals? > > > Find them fast with Yahoo! Search. http://tools.search.yahoo.com/ > > > newsearch/category.php?category=shopping > > > > > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

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MolMol file format for electrostatic potentials
by Esther Bullitt 16 Jan '08

16 Jan '08

Hi, Is there a way to import into Chimera the results of MolMol's calculation for electrostatic potentials? I like MolMol because it shows the charge without the surface hydrogens (so the results show the same thing as with, the hydrogens, but 'more strongly'), and equally important, the program is very easy to use. Is there a format conversion script, or would it be possible to make one? I can send sample files, if this would be helpful. thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

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coloring by property
by Elaine Meng 15 Jan '08

15 Jan '08

Hi everybody, There is another set of possibilities I neglected to mention. These simply categorize residues into discrete sets which could be colored differently, as opposed to coloring continuously over a numerical range. There are amino acid categories that can be specified with "Select... Residue... amino acid category... [category-name]" where category- name is hydrophobic, positive, negative, etc. These names could also be used in the command line, e.g.: color blue positive color red negative We took the default categorizations from a paper, http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/aacat.html but you can change which residues are in which category as well as create entirely new categories with the ResProp tool. The new categories will show up in the menu and can be used in the command line too. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/resprop/ resprop.html A similar approach is to use the "alias" command, for example: alias myres :phe,tyr,leu col hot pink myres alias thezone ligand z<4 rep stick thezone Aliasing can use any type of specification and is not limited to amino acids like ResProp. To color by some continuous numerical property, however, attributes would definitely be the way to go. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Questions about homology modelling
by Elaine Meng 15 Jan '08

15 Jan '08

Hi Jim, You can color by any attribute, once it is assigned. New attributes will be listed in the Render by Attribute (coloring) tool. You can create attributes arbitrarily with Define Attribute, as mentioned, and various different tools in Chimera create tool-specific attributes: (1) A "charge" attribute could be created by reading in a Mol2 file with charges or by running the Add Charge tool (an example of use is included in the Attributes tutorial). This uses Cornell et al. AMBER charges for standard residues and calculates charges for nonstandard residues with Antechamber. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/ addcharge.html You could use Attribute Calculator to create a residue attribute from those atom attributes, or if you used the Define Attribute approach, you could define the residue charge directly. That would be quite simple to do for the standard amino acids, for example. (2) Electrostatic potential: Currently Chimera does not calculate the potential for you, but reads several formats of maps. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp If you have opened an electrostatic potential map and a structure, you can use the "Values at Atom Positions" tool to create an atom attribute of the potential value at its position. This can be used with other kinds of maps as well, such as electron density. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ density.html Alternatively, you could color a surface directly by potential or density without going through atomic attributes. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html (3) Docking scores: the ViewDock tool automatically assigns whatever DOCK scores are in the ligand file as attributes. (4) Residue conservation: if you have a sequence alignment and associated structure(s) open in Chimera, the structure residues get various conservation attributes according to the columns in the alignment. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/framemav.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#mavAttributes There are probably additional examples, but that may already be more than you wanted to know. I would be happy to provide more specific assistance with whatever you would like to do - let me know, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 15, 2008, at 12:01 PM, Nicholson, Jim wrote: > Elaine: > > Thanks for the reply. My comment about coloring refers to using a > table > of residue hydrophobic index to color atoms or surfaces. I used it > all > the time for docking. I also want to color things by residue > charge or > electrostatic field. Most modelling packages offer something like > that, > and, I couldn't find it in Chimera, so, I thought would ask. > > -Jim Nicholson >

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Questions about homology modelling
by Nicholson, Jim 15 Jan '08

15 Jan '08

Hi: I still love Chimera (if you remember my last message), but, I need to do some homology modelling. I was using Insight/Homology, but, access to that software has been taken away. I'm wondering if anyone on the Chimera project is using an interface to Modeller or has any recommendations commands that might be usefull, like adding amino acids from a sequence, extending the protein, etc. Also, the coloring schemes I can see look a little limited. I regularly color by charge or hydrophobicity. I was wondering if there might be something I'm missing in Chimera? -Jim Nicholson Program in Neuroscience University of Maryland 685 W. Baltimore, St., MSTF 5-11 Baltimore, MD 21201 410-706-3418 410-804-5872 (cell)

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Bug (?) with EnsembleCluster
by Francesco Pietra 15 Jan '08

15 Jan '08

I was trying to carry out a cluster analysis from three mdcrd trajectories from Amber 9. I reported here yesterday that I was unable to input more that one mdcrd (in gz form) to Chimera. Therefore, I combined the mdcrd files with ptraj in Amber 9, while stripping all water molecules, all lipid, and box information, leaving only the protein with ligand. That combined mdcrd loaded perfectly into Chimera MD Movie saving a pdb file (there was no option "save all frames" suggested by Elaine's email; I did not select anything else than "untranformed coordinates") Opened successfully this pdb into Chimera, Tools, MD/EnsembleAnalysis, EnsembleCluster, select the new file, finally click on OK: that resulted in Chimera Error. This was a first trial, though I have right taken the opportunity to submit an alleged bug from the window inviting to do so. From a perusal of Reply Log, I was unable to grasp the nature of the failure. In particular, lacking documentation for ksdssp, I was unable to run it (to assign the lacking secondary structure of the protein) with different parameters from used energy cutoff -0.5 minimum helix length 3 minimum strand length 3 and commands as from Log. Perhaps I should also mention that lack of secondary structure is typical of the long procedure through different programs to carry our (1) model building, (2) docking, (3) MD. Thanks francesco ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

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A features-related question
by Dmitri Pavlov 14 Jan '08

14 Jan '08

Dear friends and colleagues, I have not really tried the product yet, but was wondering whether it is possible to "edit" a protein's structure by introducing one or two single mutations with the follow-up minimization using Chimera. If so, could you please hint to the algorithm of actions. Thanks a lot in advance! The project is burning :-( Dmitri

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transparent background
by Krepkiy, Dmitriy (NIH/NINDS) [F] 14 Jan '08

14 Jan '08

Hi, Is it possible to make background transparent? Thanks, Dmitriy ************************************** Dmitriy Krepkiy, Ph.D. Room 3B213 Building 35 - Porter Bldg, 35 Convent Dr Bethesda, MD 20892

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Fit model in map algorithm
by Tom Goddard 14 Jan '08

14 Jan '08

Christopher Akey wrote: > Tom- > > I was wondering how the fit model into map works? Is it calculating a > ccf and if so how since a pdb and a map file are quite different > entities. > > > cheers C Akey Hi Christopher, The Chimera fit model in map capability does a rigid rotation and translation to maximize the sum of the map values at the atom positions. It reports the average map value at the atom positions. It doesn't report a correlation coefficient. That would require calculating a simulated map from the PDB at the desired resolution and Chimera currently cannot do that. I would like to add that capability since correlation values are the standard measure of goodness of fit that is reported in the literature. The fit model in map code uses a gradient ascent iterative method to maximize the sum of map values. The Chimera fit map in map capability will report a correlation value. So you could run some external program to compute a simulated map (I've used pdb2mrc from the EMAN package) then fit that simulated map into your experimental map with the fit map in map dialog and get a correlation value. Or you could use the Chimera fit model in map to fit the PDB, then open the simulated map, register it with the fit PDB (using Model Panel / Transform As button), and then have the fit map in map dialog report the correlation without optimizing the simulated map placement. I'd expect very similar results from fitting the PDB versus fitting the simulated map. The fit map in map algorithm maximizes the "overlap" between maps. That is not the same as the correlation. It is a sum of the pointwise products between the two maps at grid points within the contour surface of one of the maps. That differs from the correlation in that it is not normalized by the sum of the squares of each maps' values within the surface. This has important consequences. The Chimera "overlap" optimization will move the map into a nearby high density region even if the pattern of highs and lows in the density does not match. The correlation normalization eliminates the tendency to move to higher density -- instead just optimizing the match of the highs and lows in the density. Both are useful and I will in the future add an option to optimize the correlation. The Tools section of the Chimera User's Guide describes the map and model fitting methods: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodel… http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht… Tom

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Re: [Chimera-users] suppressing warning messages
by Eric Pettersen 08 Jan '08

08 Jan '08

Hi Ryan, Perhaps other Chimera developers can chime in, but I don't know of any good way to selectively suppress the non-status messages that Chimera generates, particularly the "duplicate atom serial number" messages which are being put on standard error by code in the C++ layer. What I can suggest in your situation is that you have your print statements go to standard error (so that they flush through pipes immediately) and that you prefix them with some unique string that you can grep for. Something like: from sys import __stderr__ as stderr print>>stderr, "OUTPUT", "my result:", r and run Chimera with: chimera --nogui myscript.py |& grep OUTPUT --Eric On Jan 8, 2008, at 12:19 PM, Ryan Pavlovicz wrote: > Are there ways just to suppress the chimera output? I'd still like > to see some of my print commands that are part of my python script, > so i can easily debug, follow a process, etc.? > > On Jan 8, 2008 1:24 PM, Eric Pettersen < pett(a)cgl.ucsf.edu> wrote: > Well to suppress all output you would use normal shell redirection > to /dev/null. For csh-style shells, something like this: > > chimera --nogui >& /dev/null > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Jan 8, 2008, at 9:28 AM, Ryan wrote: > >> The --nostatus option will suppress messages like: >> >> "Executing xxx.py... Opening xxx.pdb..." >> >> but still, messages like: >> >> "Model 0 (xxx.pdb) appears to be a protein with noe secondary >> structure assignements. Computing assignments..." & "warning: >> duplicate atom serial number found..." >> >> are still printed to the screen. Are there ways to suppress these >> messages as well? Thanks again, >> >> ryan >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Re: [Chimera-users] suppressing warning messages
by Ryan 08 Jan '08

08 Jan '08

The --nostatus option will suppress messages like: "Executing xxx.py... Opening xxx.pdb..." but still, messages like: "Model 0 (xxx.pdb) appears to be a protein with noe secondary structure assignements. Computing assignments..." & "warning: duplicate atom serial number found..." are still printed to the screen. Are there ways to suppress these messages as well? Thanks again, ryan

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