January 2008 - Chimera-users - RBVI Mailing Lists

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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suppressing warning messages
by Ryan 08 Jan '08

08 Jan '08

Is there a way to suppress warning messages when using Chimera in a python script (--nogui option)? Additionally, is there a way to suppress the additional non-warning Chimera output that prints to screen when running via python script? Thanks, ryan

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How to input more than one mdcrd file
by Francesco Pietra 07 Jan '08

07 Jan '08

I was unable to input more that one mdcrd file to MD Movie (to get a single pdb file for EnsembleCluster). I tried by either giving the files one to one, or with the following prod.meta: amber my.prmtop prod1.mdcrd.gz prod2.mdcrd.gz prod3.mdcrd.gz Always, I got prod1 trajectories alone. I used compressed coordinate files also when fed one to one. I did not try with non compressed files. Thanks francesco pietra ____________________________________________________________________________________ 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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Chimera-users January 2008