- Chimera-users - RBVI Mailing Lists

transparent surfaces
by Charles Midgett 05 May '08

05 May '08

I want to make a transparent surface in volume viewer that can be drawn in POVray. It appears the *.pov and *.ini files produced by Chimera cannot be read by other POVray renders. Is there some work around that will allow me to ray trace a transparent surface displayed by the volume viewer? Charles

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areaSAS_areaSES
by De Nicola, Gian 05 May '08

05 May '08

To whom it may concern I would like to calculate the areaSAS and areasSES using Chimera.This is what I do Load the structure tools Surface Binding Analysis area/volume from web I choose the type of surface I want. Click apply then Ok As an output I get " unexpected output from struc tools server" . What am I doing wrong? Regards Gian

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surfaces, electrostatic coloring
by Elaine Meng 03 May '08

03 May '08

On May 2, 2008, at 8:04 PM, James Fethiere wrote: > > Another wquestion. I managed to display separate surfaces for 2 > chains in a single model using the surfcat command you've > recommended last time. Is this command accessible through the menu? There is no menu equivalent to "surfcat," sorry. > > However, I can't color each surface separately according to > electrostatics. I know that chimera does not calculate > electrostatics. What I tried is to go to tools/surface binding/ > electrostatic surface coloring, set the palette to radius and set > the full range. What I get when I color is a gradation from red to > blue with no atom type discrimination. When you choose "radius" the coloring is by distance from a point, not electrostatics.. To actually color by electrostatics, you would have to open an electrostatic potential map and then choose it from that menu (the one with "radius" in it). Also, your two surfaces would be two separate entries in the menu listing the surfaces. You would have to choose one, color, and then choose the other, color again. Perhaps it is misleading to call this tool "Electrostatic Surface Coloring" when it is really identical to the "Surface Color" tool: it includes options to color by distance from a point, axis, or plane. The radial coloring is used (for example) to color a virus capsid by the distance from its center to highlight the contours of its surface; see the figure in the man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html Another possibly confusing thing is that in older versions of Chimera, after you use Surface Color, it can be tricky to change the color of the surfaces. In current versions (recent daily builds), you should just be able to color the surface with the menu (Actions... Color) or commands (color, rangecolor) regardless of whether this tool had been used. > So I go to the attributes of this map in the model panel, and color > source atoms. Great, I get red for acidic and blue for basics. > Now for the other chain, it doesn't work. At the color source atoms > step, the whole surface takes one single color. The other thing is > that in the model panel I do not have the small color icon for the > two maps!! Is there a better way to do this? The two surfaces would again be listed separately in the Model Panel, and have their own separate attributes dialogs. I don't know what you mean by "doesn't work." Did you try to use the menu or commands to color the surface? Also, I don't know what other things you did in the session, but the red and blue you were seeing were probably just the element colors: surfaces of oxygen atoms (red) and nitrogen atoms (blue). Maybe you had colored the atoms of one chain and not the other. In any case, you could proceed to color the surfaces with the menu and/or commands as mentioned above. If you don't have an electrostatic potential map and don't want to color by distance from a point, axis, or plane, there is no reason to use Surface Color. For example, to show the element colors on the surface for the two chains in 2zcp: open 2zcp surfcat one :.a & protein surfcat two :.b & protein surf one surf two col byatom (or "col byhet" to not change carbon color) Or, instead of using the atomic element colors, you could color :asp,glu residues red and :his,arg,lys residues blue. > > Can you also tell me how to make the surfaces smoother. Whatever > vertex density I give, I see pretty rough edges and it's not very > nice. The vertex density is the only way I know of for making the surface smoother. I am surprised it is not doing that in your case - it definitely works in the molecular surfaces I have tried: 5.0 is a lot better, 10.0 even better. Did you press return? The main drawback I ran into is that it can take a long time to calculate, rotate, etc. Maybe increasing the probe radius would improve your surface's appearance. I hope this helps, Elaine

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Sec structure loss
by James Fethiere 02 May '08

02 May '08

Hi, I'm seing something strange with secondary structure assignments in peptides. Two examples: PDB 1axc has a peptide bound to PCNA with beta strand interactions and chimera doesn't pick it up as a strand. In the other example, 1rxz, it picks up the strand in a similar peptide but the strand disappear when I run matchmaker with 1ul1 (which also has a strand at the c-terminus that is not picked up. Is there any explanation? Are the criteria for secondary structure assignments to strict? One more thing that may have been asked already!! how does one keeps the NH and CO of the peptide bond displayed in the ribbons view? Thanks James

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automated rebuilding of side chains?
by Ian Yarbrough 02 May '08

02 May '08

Hi, A model that I am working with has several missing or partial side chains, and I'm dealing with about 80 subunits of this protein (organized into 3 chains). I am trying to repair these, but don't want to go through the task of finding every broken chain. Is there a way to get chimera to locate the broken ones and repair them all? I've seen the dock prep feature, but don't want to change them all to alanines. Thanks for you help. Ian Yarbrough Texas A&M University

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adding metal ions
by Carlo Zambonelli 01 May '08

01 May '08

I have a pdb file with the coordinates of an apo-enzyme. I know Fe3+ and Zn2+ are essential for catalysis; I also know some of the residues involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in the structure so that they are correctly oriented relative to the coordinating residues? My ultimate goal is to create a PDF file containing also the metal ions. Thanks, Carlo

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adding metal ions
by Carlo Zambonelli 01 May '08

01 May '08

I have a pdb file with the coordinates of an apo-enzyme. I know Fe3+ and Zn2+ are essential for catalysis; I also know some of the residues involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in the structure so that they are correctly oriented relative to the coordinating residues? My ultimate goal is to create a PDF file containing also the metal ions. Thanks, Carlo

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Moving an ensemble of molecules together
by Thomas Goddard 01 May '08

01 May '08

Hi Miguel, If you have two molecules each surrounded by additional molecule copies that make crystal contacts you can align the two crystal lattices as follows. Align the two original molecules (e.g. using Match Maker dialog or match command). Then choose all copies of the first molecule in Model Panel and use the Transform As button. You'll be asked to choose the molecule to transform these as, so choose the aligned molecule. That will bring all the crystal contact molecules surrounding the aligned molecule into correct locations around the aligned molecule. This method assumes you have saved the crystal copies to a PDB file and have opened that file. If you simply use the new crystal contacts option to make the molecule copies then the Transform As will move all those copies to the exact same position as the original molecule -- not what you want. This is because the crystal contacts tool is placing the surrounding molecules by adjusting their transformation matrices rather than changing their atom coordinates. If you save all copies to a PDB file and read it back in then the atom coordinates of the copies will be adjusted and all of the molecules will have the same transformation matrix and the above alignment procedure will work. Tom Miguel Ortiz-Lombardía wrote: > Hi again! > > I had tried this, yes. But the problem is that when I want to compare > crystal packings the procedure is: > > 1. Generate the two ensembles around "central" molecules > 2. Superpose the "central" molecule (submodel if saved as you say) of > the first ensemble to the "central" molecule of the second one > > Doing it this way only the central submodel of the first ensemble moves, > not the whole ensemble, as I wish... A single molecule with various > chains would move as a whole, as I want. I see the 62 chains limitation, > but normally we don't have such enormous amount of molecules contacting > an asymmetric unit (of course, with viruses may be different). So, it > would be nice (to me, I don't know how generally) to have a way to > transform an ensemble of models into an ensemble of chains. > > Thank you for your help! > > > Miguel > > 2008/4/30 Tom Goddard <goddard(a)cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>>: > > Hi Miguel, > > You mentioned that you would like to be able to save the crystal > contact asym units in a single PDB file as separate chains. Why not > save them as multiple models in a single PDB file? You can do this > currently with the Chimera menu entry File / Save PDB.... Making > separate chains requires making new chain names and since only one > letter names are allowed in PDB format this is limited to about 62 > chains (a-z, A-Z, 0-9). > > Tom > > > > > -- > http://www.pangea.org/mol/spip.php?rubrique2 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Je suis de la mauvaise herbe, > Braves gens, braves gens, > Je pousse en liberté > Dans les jardins mal fréquentés! > Georges Brassens

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pretty nice article on PDB website about Chimera
by Eric Pettersen 30 Apr '08

30 Apr '08

http://www.rcsb.org/pdb/general_information/news_publications/ newsletters/2008q1/education_corner.html

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Initial window size
by Bernard Heymann 30 Apr '08

30 Apr '08

Where is the initial graphics window size set? I did not see any preference for that. I would like to change that to have Chimera open with a bigger window. Thanks Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

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