January 2008 - Chimera-users - RBVI Mailing Lists

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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Chimera-users January 2008