- Chimera-users - RBVI Mailing Lists

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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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 crashes my linux 64 bits PC
by jean-francois menetret 07 Jan '08

07 Jan '08

After I rebooted my linux 64 bits PC this morning, chimera crashes the machine. I tried older versions of chimera ... same result :-( How can I fix that situation ? 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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mean structure
by sette＠uniroma2.it 07 Jan '08

07 Jan '08

Hi, I don't know if someone already ask for this... It is possible to calculate an average structure having a bundle of structures? I loaded from the pdb a file containing 30 NMR structures but I would like to use only the mean structure... Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Slow dealing with pdb files
by Francesco Pietra 03 Jan '08

03 Jan '08

I am dealing with the average structure (a protein complex embedded in a POCP membrane and water solvated) derived with Amber's ptraj from a 1.5 ns MD. Opening this pdb file in 1.2470 Chimera has become extremely slow. The file is 6.4MB. First, below the screen it is warned "Ignored bad PDB record found on line #", for lines from 1 to 114154. This may take some 10 minutes. The pdb records read as in the following examples: For the lipid: ATOM 20 2C21 POP 1 25.569 20.201 48.492 0.00 0.00 For the protein: ATOM 10915 HB2 ALA 117 44.211 74.567 28.832 0.00 0.00 For water: ATOM 22264 O WAT 1771 25.558 39.417 16.580 0.00 0.00 ATOM 22265 H1 WAT 1771 25.582 39.432 16.549 0.00 0.00 ATOM 22266 H2 WAT 1771 25.569 39.482 16.611 0.00 0.00 After that, the warning message changes to "Computed secondary structure assignments (see reply log)" which lasts for longer than 1 hour and 20 minutes. During this time, "top" command shows that python is using 12% MEM and 99% CPU. Then, the graphics appears, with the membrane-protein-complex not centered in the water box. During all that time, I had to avoid doing anything else with the GNOME interface. A second terminal for "top" had to be opened before launching Chimera on another terminal window. Otherwise, spurious graphics become superimposed to the Chimera window. I could then carry out rapid mapping of the protein residues around the single-residue ligand (select protein & :ligandname z<#), which was what I wanted to do. The same events occurred with shorter trajectories. At ca 0.7ns the time taken by Chimera to work out the average-structure pdb was about 15 minutes. Clearly, there is an exponential trend. I can in part compare these events on VMD: the pdb file from 1.5ns MD is opened in VMD in less than 1 minute and the resulting membrane-protein-complex is centered in the water box. Is all that caused by the not-updated atom naming by Amber? Or could the execution be accelerated by calling some C routines by python? Chimera was run on a modest desktop: Athlon 1GHz, RAM 1GB, a poor main board (product: K7S5A, vendor: ECS, version: 1.0), Debian Linux i386. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Fwd: Re: Slow dealing with pdb files
by Francesco Pietra 03 Jan '08

03 Jan '08

Must add that alternatively to "average structure" I tried a cluster analysis with MMTSB. The program refused to work on my trajectories for unclear reasons: the program is installed correctly and the input is correct (as verified by the program author). Therefore, I am eagerly waiting for Chimera being able to carry out cluster analysis (if I understood correctly your message to this regards) francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Wed, 2 Jan 2008 23:04:40 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Re: [Chimera-users] Slow dealing with pdb files > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > CC: chimera <chimera-users(a)cgl.ucsf.edu> > > Eric: > Thanks a lot for this lesson, surely useful to many other guys, too. > > Whether looking at an "average structure" or some other output structure was > a > problem I got no clarification from the Amber mailing list. Unfortunately, Pr > Brozell is not active in this period on Dockfans to ask him. My question was, > is the "average structure" representative of the interactions occurring > between > the protein and the ligand as resulting from the MD carried out? Although > DOCK6.1 does that with amber score, it is only for implicit medium > surrounding > the complex. Ideally, I would have liked to estimate the free energy of > interaction in the presence of explicit surrounding medium but Amber does not > appear to have a way to that for a complex in a membrane (or anyway for a > non-standard ligand). Therefore, what I am relying on, is the distance > between > the protein residues and the ligand. The closest the protein residues are to > the ligand, the more they are considered to be relevant. > > At any event, given the problem Chimera has encountered with an average > structure, do you believe that mapping the protein environment around the > ligand with Chimera's "zone" is correct? From your "lesson" I understand YES. > > I would appreciate any comment or suggestion about that. > > francesco > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > On Jan 1, 2008, at 1:44 PM, Francesco Pietra wrote: > > > > > I am dealing with the average structure (a protein complex embedded > > > in a POCP > > > membrane and water solvated) derived with Amber's ptraj from a 1.5 > > > ns MD. > > > > > > Opening this pdb file in 1.2470 Chimera has become extremely slow. > > > The file is > > > 6.4MB. First, below the screen it is warned "Ignored bad PDB record > > > found on > > > line #", for lines from 1 to 114154. This may take some 10 minutes. > > > > These are for the water ATOM records where the atom serial number and/ > > or residue number were "****" (what FORTRAN inserts when a number > > won't fit inside a field width). > > > > > After that, the warning message changes to "Computed secondary > > > structure > > > assignments (see reply log)" which lasts for longer than 1 hour and > > > 20 minutes. > > > During this time, "top" command shows that python is using 12% MEM > > > and 99% CPU. > > > > Due to the fact that this is an "average" structure, Chimera's > > estimation of the connectivity is bad for many parts of the structure > > -- particularly the POP residues in the membrane. This creates a > > rat's nest of intra-residue connectivity which the ring-finding > > algorithm (designed for "reasonable" structures) takes a long time to > > operate on. Normally Chimera wouldn't run ring-finding as a > > structure opens, but due some interesting naming of hydrogens in the > > POP residues (e.g. RH16) it assigns some of the hydrogens to be other > > elements (e.g. rhodium, as per PDB atom naming rules). Since rhodium > > is a metal, it wants to depict it as a sphere, which means it needs > > to know the radius, which in turn depends on the atom type, which > > needs to find rings... > > > > > Then, the graphics appears, with the membrane-protein-complex not > > > centered in > > > the water box. > > > > This is due to the "****" waters being ignored. > > > > > I could then carry out rapid mapping of the protein residues around > > > the > > > single-residue ligand (select protein & :ligandname z<#), which was > > > what I > > > wanted to do. > > > > If you only care about the protein and ligand in your analysis, you > > should just edit your file to strip the waters and lipids. When I > > did this with the file you sent it only took moments to open. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > > > > > > > ____________________________________________________________________________________ > Never miss a thing. Make Yahoo your home page. > http://www.yahoo.com/r/hs > ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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selection
by Sara Bowen 03 Jan '08

03 Jan '08

Hi, I've been going through the chimera tutorial, but I'm having some trouble selecting anything. I can select atoms, and the bottom corner of the window lists what I've selected, but there is no green highlighting in the image. Then if I try to move anything, the image will move in the side view but not in the main window. It seems frozen. If I select everything or select nothing, I can still only get the image to move in the side view...not the main window. Then if I make the main window full screen, the image is just fuzzy colors like snow on a out of tune t.v. Does anybody know what's going on and how I can fix it? Thanks, Sara B. at ASU

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coloring protein structure according to Order parameters
by rama krishna 03 Jan '08

03 Jan '08

Dear Friends, I need to Paint a protein structure according to generalized parameter values. Is there any way to do that in UCSF-Chimera. Kindly suggest me. Regards Ramakrishna, Dr Ashish Arora Lab, Molecular and Structural Biology lab, Central Drug Reseach Institute, India

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Opening compressed trajectories
by Francesco Pietra 02 Jan '08

02 Jan '08

I found comfortable to deal with mdcrd compressed (gz) files directly in Amber's ptraj. This saves much disk space. I wonder whether this could be made available for Chimera. The scope would be twofold: other that saving disk space, shorted times of ssh transfer from the computing machine to the desktop with Chimera. Happy 2008! francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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saving complex structure
by bala 02 Jan '08

02 Jan '08

Dear chimera friends, I have a protein-RNA complex pdb structure. I want to remove the RNA in the crystal structure and put my RNA molecule in to the binding site. Since my RNA is very big around 20bp long, i prefer to manually dock my RNA followed by a big simulation than a automated docking. I tried in chimera and i saved the complex structure with the option "save the displayed atoms". But when i see the pdb structure, it has the coordinates of RNA molecule but not the protein. Also when i open the pdb in chimera, it shows me the protein structure. Kindly write me your comments on using chimera i) for such a manual docking and also ii) how to save the complex structure. Wish you all a happy new year, Bala

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Command for volume and area calculation
by shengzhiya＠nibs.ac.cn 27 Dec '07

27 Dec '07

Dear all, May I know if there is some command in chimera for measuring volume and area like in the menus: “Tools…Surface/Binding Analysis…Measure Volume and Area”? Thanks in advance! Happy new year and have a nice holiday! Zhiya

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formal charge or net charge
by snoze pa 25 Dec '07

25 Dec '07

Dear Chimera Users, Is it possible to calculate the net charge or formal charge of unknown residues using chimera. I have a large set of molecules for which i am trying to calculate the net charge on each molecule. Thanks in advance s

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rmsd cluster analysis
by Elaine Meng 24 Dec '07

24 Dec '07

Hi Francesco and others, People with MD trajectories can also use this new EnsembleCluster tool (available in the most recent daily builds) by: - viewing the whole trajectory with the "MD Movie" tool, or at least all the frames you want to cluster - from the MD Movie dialog menu, choosing File... Save PDB and saving "all frames" to a file - quitting from MD Movie and opening the new file with File... Open - choosing Tools... MD/Ensemble Analysis... EnsembleCluster, clicking the line that shows that new file, then OK I just tried this to make sure it works. The clustering calculation may take a while, but eventually another dialog with results should appear. This tool is still under development and may change, but this will at least allow users to try it on trajectory ensembles as well as NMR ensembles. 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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Transparent background
by Abbas 20 Dec '07

20 Dec '07

Hi, One feature I really appreciated about chimera was the ability to make pictures without a background, however recently i realized this is not possible anymore I checked out under the effects dialog under tools>viewing controls and it give me an error saying this wasn't supported. I haven't changed my computer since i first started using chimera I have updated to the latest version of chimera available for OSX 10.4, I wonder if this is the cause of the problem. I would really like to have pictures without backgrounds like I used to, I know PyMol lets you do it, but I dislike this program. In any case I would greatly appreciate any help/pointers on this issue. Thanks in advance. abbas.

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Re: [Chimera-users] fitting models into maps
by Tom Goddard 20 Dec '07

20 Dec '07

Hi Dan, The Chimera fit model in map tool doesn't give a correlation value. To get a correlation requires you have two maps to compare, so first a map needs to be calculated from the PDB model that matches the resolution of the experimental map. Although I'd like to have that in Chimera, it is not currently there. I have used the EMAN pdb2mrc program to compute the map. Then you can use the Chimera fit map in map tool to get a correlation value, or you could use fit model in map, then open the map calculated for the PDB and find the correlation for the orientation obtained for the PDB model. You're right that reported correlation values depend on some often unreported parameters. First there is the method used for producing a map from the PDB model. Then the correlation depends on the part of the volume used. I would guess this is typically the portion within a certain contour level of the PDB map. What contour level? Something like 1 standard deviation is not sensible since it depends on the size of the map (the extent of padding). Probably a contour level that encloses a given volume -- maybe the volume enclosed by the solvent excluded surface of the PDB model with a reasonable probe radius. Would be nice if Chimera automated this calculation starting from the fit model in map position -- some day, hopefully in 2008. Reporting average density value at the atom positions would only make sense if the map is normalized. Maybe reporting that value in standard deviations. But the standard deviation depends on how much empty volume surrounds the structure, so that is not very satisfactory. Chimera reports that number so you can compare different fits in the same map -- only relative values are meaningful. Another value I have seen reported is the number of atoms outside a certain contour level of the experimental map. The fit model in map tool reports that in the reply log (Favorites / Reply Log). Of course it depends on how you set the contour level. Again if you set that as some number of standard deviations that depends on the map size. Alternatively you could set the contour level so the experimental map encloses the expected volume. Menu entry Tools / Volume Data / Measure Volume and Area can help set such a contour level. Seems correlation is the most meaningful number. You can calculate the standard deviation of a map from its mean in newer versions of Chimera with menu entry Tools / Volume Data / Volume Mean, SD, RMS. Tom Daniel Southworth wrote: > Tom: > > Hi. I'm a post-doc in David Agard's lab and I have a question about > the "fit model in map" function in chimera. I'm having some good > success fitting crystal structures into my low-resolution em maps > using this function once I get a global fit either by hand or using > situs. I'm wondering if there is any way to get a correlation value > out of the fits or how people typically report on their confidence of > the chimera fitting in publications? I know correlation values are > often different from program to program so perhaps the best measure is > to state the average map value? Any help would be great - thanks. > > Dan

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superimpose --matchmaker.
by Vinay Kumar 19 Dec '07

19 Dec '07

Hi all, There have been a few posts previously regarding superimposing of molecules. using matchmaker would work for a pdb file. I was curious if small molecules (ligands) could be matched. I did check out the documentation and the command match. But what i am not sure abt is, in wht format should the input file for a small molecule be?? could someone suggest!! regards, Vinay

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Question regarding multiple mutant in the same chimera session
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi, Is there a way to copy, in the same instance of chimera, a model X time? I'd like to generate different mutant of the same prot and have them stocked in the same session of chimera. Cheers, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

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rmsd cluster analysis
by Francesco Pietra 18 Dec '07

18 Dec '07

Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Problem with Chimera under Windows XP
by Peter Girard 18 Dec '07

18 Dec '07

I am running release 2304 of Chimera under Windows XP with service pack 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen for no apparent reason. With the structures I am currently working on, this has become frequent and often occurs after just a few seconds when I click anywhere in the Chimera window. I have found that if I use Model Panel, I can get the picture back by clicking the 'Shown' box to remove the tick mark, then clicking it again to re-insert the tick. But the picture soon disappears again. Occasionally, it doesn't disappear completely, but part of it collapses, or spurious long lines appear. I had the same problem with a previous release, 2184, and was disappointed that upgrading didn't fix it. I can find no mention of anything similar in the documentation or email archive. Can anyone suggest a possible cause? Peter Girard (University of Nottingham, UK)

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Regarding getSequence
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi again, I'd like to return the sequence of the protein I opened in chimera in the python shell. >From what I read through, I thought that chimera.getSequence could be used to do so. I was thinking in a simple script beginning with : import chimera s=chimera.getSequence(0,0) .. However the chimera.getSequence(0,0) comes back with: Traceback (most recent call last): File "<pyshell#50>", line 1, in ? chimera.getSequence(0, 0) File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences AttributeError: 'int' object has no attribute 'residues' and chimera.getSequence(0,A) with Traceback (most recent call last): File "<pyshell#48>", line 1, in ? chimera.getSequence(0,A) NameError: name 'A' is not defined Did I understand correctly the role of getSequence? if yes, what would be the correct syntax please? Thanks a lot! All the best, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

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Re: [Chimera-users] Chimera-users Digest, Vol 56, Issue 14
by Jonathan Hilmer 17 Dec '07

17 Dec '07

Ryan, Try this as a way to figure out what you can do with an object: dir(chimera.selection.currentResidues()[0]) In the above command I've indexed the list of selections to return just one object, and the dir() function will return a list of names defined by the currentResidues module. It should contain something like the following: ... 'addAtom', 'atomNames', 'atoms', 'atomsMap', 'bondedTo', 'count', 'findAtom', 'findRangeAtoms', 'getDefaultRibbonStyle', 'hasRibbon', 'id', 'isHelix', 'isHet', 'isSheet', 'isStrand', 'isTurn', 'kdHydrophobicity', 'label', 'labelColor', 'labelOffset', 'molecule', 'numAtoms', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'removeAtom', 'ribbonBinormals', 'ribbonCenters', 'ribbonColor', 'ribbonData', 'ribbonDisplay', 'ribbonDrawMode', 'ribbonFindStyle', 'ribbonFindStyleType', 'ribbonFindXSection', 'ribbonNormals', 'ribbonResidueClass', 'ribbonStyle', 'ribbonXSection', 'selLevel', 'type' If you try: chimera.selection.currentResidues()[0].type it will return a string with the 3-letter aa code, and the other options displayed by dir() will output useful things such as more strings, lists, or other objects that can be likewise explored. Try this combination: mySel = chimera.selection.currentResidues()[0] print "%s, %s" % (mySel.oslIdent(), mySel.type) On my test structure it returns '#0:127.A, ARG'. The second line is equivalent to 'print str(mySel.oslIdent() + ", " + mySel.type)', but the formatting I used in the above example helps to keep things clean if you have a complicated output that needs to have a specific format. There are some more advanced features of that approach detailed here: http://www.python.org/doc/1.5/tut/node45.html Jonathan > Date: Fri, 14 Dec 2007 19:55:39 -0500 > From: Ryan <pavlovicz.7(a)osu.edu> > Subject: Re: [Chimera-users] printing "zone" search > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <17bf4817f850.17f85017bf48(a)osu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. > > So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > > > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > > > #0:499 > > #0:496 > > ... > > What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, > > ryan

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Re: [Chimera-users] other/5067 (error adding hydrogens)
by Eric Pettersen 17 Dec '07

17 Dec '07

Hi Jean-Francois, I have seen this error reported, but only very rarely (maybe once a year at most). Is there any chance you can tell me how to reproduce it? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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setting pdb path for local mirror
by Moo Cow 17 Dec '07

17 Dec '07

Sorry for an easy question. Chimera has a hook to use a local mirror of the PDB (preferences-PDB) I am too thick to see what path to give it. If you have the PDB, you have the top level /blah/blah/pdb the structure directory /blah/blah/pdb/data/structures/all and the divided directory /blah/blah/pdb/data/structures/divided/pdb When a non-python reader looks at the code (__init__.py), it seems to be trying out the divided directory IDcode = IDcode.lower() subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" pdbDir = systemPDBdir() if pdbDir is not None: ..... but this does not look correct. The PDB divided path would want subpath IDcode[1:2] to get the subdirectory "pt" from a file like "5pti" Many thanks and sorry for a seemingly daft question. -- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174

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Loading .dx maps to chimera
by maya shcushan 17 Dec '07

17 Dec '07

Dear sir, I am trying to load a .dx file (electrostatic potential) onto a molecule in chimera. I successfully loaded the map onto a the molecule's surface. The problem is the potentials I get look differently than the original map. That is, the potentials appear different in the visualization tool of PMV, the program which generated the .dx file I tried to e-load on chimera. Thanks, Maya Schushan, Tel-Aviv university, Israel.

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crystallographic symmops and lattice translations in Chimera
by Boaz Shaanan 16 Dec '07

16 Dec '07

Hi, Since the question was raised before, I think I know the answer to my first question about lattice translations but let me verify: 1) Chimera can apply crystallographic symmetry operations to the model as they're listed in the pdb file but it won't apply lattice translations, or in other words, won't display molecules in neighbouring unit cells. Am I correct ? maybe you can surprize me me on this and prove me wrong ? 2) Is it possible to draw the unit cell boundaries after reading in the pdb or should I read in a dummy pdb with coordinates of the unit cell vertices ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Re: [Chimera-users] printing "zone" search
by Ryan 14 Dec '07

14 Dec '07

Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: print chimera.selection.currentResidues() i get a list like this: > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] but if i try: for x in chimera.selection.currentResidues(): print x i get output that is much closer to what i'm looking for: > #0:499 > #0:496 > ... What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, ryan

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Multi-scale models and BIOMT
by Ken Jang 14 Dec '07

14 Dec '07

Hello, I work at Boston University working mostly with pili and helical reconstructions. Recently we have been trying to fit our subunit structures into maps generated from EM data. Because what we work with are helical in nature, we use BIOMT symmetry since it is the easiest to generate using readily available data. We wanted to see just how close our subunits get and wanted to use the MSC or Color Zone commands, but we have run into a problem with the Multi-Scale Models command. Since we are using the same BIOMT data, we assumed that Multi-Scale Models would use the same origin and orientation. This appears to be the case if we don't move the subunit structure after opening it, but after we move the subunit, the generated models don't seem to be in any relavent orientation. I have attached two pictures, both from the same view, and one showing the placement of the subunits using the 'sym' command and the other showing the surface models using Multi-Scale models. Both cases were generated off the same selected subunit. Any advice or clarification on how to use Mult-Scale Models and BIOMT information would be greatly appreciated. Be seeing you- Ken Jang -and all places are alike to me

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Re: [Chimera-users] printing "zone" search
by Ryan 14 Dec '07

14 Dec '07

I am actually currently interested in doing something similar to Francesco's previous question about writing out a list of residue names within a certain zone of a ligand -- however i would like to do this from a Python script. I tried to find the zone selection command to use in a script, but could not. Would it be easiest to just use the runCommand('z<') function to select a zone? Also, when the zone is selected, are the selected residue names stored in a list? If so, how can i access this list to print out the residue names into an output file of my own? Thanks a lot, ryan

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edges
by Vincent Racaniello 14 Dec '07

14 Dec '07

When I display a protein as an edged ribbon, sometimes they have a black line on the edges, other times none. There seems to be no consistency in this behavior. The same also happens with surfaces. Is there a way to regulate this appearance?

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Morphing on small ligand
by Jean Didier Pie Marechal 13 Dec '07

13 Dec '07

Hi everyone, I have a " small" ligand with two substantially different conformations. Just for interest: could we use the morphing module to generate intermediate conformations between those two structures? Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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printing "zone" search
by Francesco Pietra 13 Dec '07

13 Dec '07

I am looking at the protein residues "responsible" for docking a single-residue ligand. select protein & :ligandname z<# works for various values of #. I would like to print the list of residues instead of having to detect them from the screen, which may lead to errors. Also, which section of the manual concerns RMSD? (I would like to calculate RMSD at various stages of DOCK6.1 and Amber9 MD for the above, i..e. how the ligand adapts and the protein follows it, or vice-versa). Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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Writing alignment and RMSD out
by shengzhiya＠nibs.ac.cn 10 Dec '07

10 Dec '07

Dear all, I would like to write both the sequence alignment and RMSD out after run “mmaker”, but I do NOT want to do this interactively because I have a batch of structures to deal with. I found Eric’s python script: structAlign.py, which is gui-only, but I do not know how to extract RMSD from the Reply Log in gui mode. Any help would be appreciated. Thanks a lot! Btw, may I know how to run structAlign.py? Is there any command like “chimera structAlign.py” and where should I put the input file structList? I can not run this script right now and here is the error message I got after run “chimera structAlign.py”: Traceback (most recent call last): File "/home/sheng/local/bin/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "/home/sheng/local/bin/chimera/from_mailinglist/structAlign.py", line 18, in ? pdb1, pdb2, output = line.strip().split() ValueError: need more than 2 values to unpack Error while processing structAlign.py: ValueError: need more than 2 values to unpack (see reply log for Python traceback info) Best wishes, Zhiya

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how to export the volume data which is stored in the memory?
by Zhiheng Yu 05 Dec '07

05 Dec '07

Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng

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Re: [Chimera-users] how to export the volume data which is stored in the memory?
by Tom Goddard 05 Dec '07

05 Dec '07

Hi Zhiheng, Here is a script to write out the maps in memory using Chimera 1.2199. You open this script with menu entry File / Open... from the main Chimera window. It will write the files to /tmp. Of course be sure to check those files before closing Chimera. Tom Zhiheng Yu wrote: > Hi Tom, > > I got the following information: > > Beta Version 1 build 2199 2006/01/24 > Platform: linux 2. Windowing system:x11. > > Apparently, it is an older version. > > Thank you very much for your generous help. I really appreciate it. > > Zhiheng > > Tom Goddard wrote: >> Hi Zhiheng, >> >> You must be using an older version of Chimera. Old versions read >> the original file even if the map was in memory when writing out the >> data. Maybe I can give you a script that will write the maps out >> from memory if you tell me what version of Chimera you are running >> (menu entry Help / About UCSF Chimera). >> >> Tom >> # # Write maps to files. For Chimera 1.2199. Only use in-memory copy. # Written for Zhiheng Yu to recover maps lost to failed disk. # from VolumeData import Array_Grid_Data from VolumeData.mrc.writemrc import write_mrc2000_grid_data from VolumeViewer import volume_dialog from os.path import join dir = '/tmp' # Location to write maps. d = volume_dialog() for v in d.data_regions: m = v.full_matrix(read_matrix = False) if not m is None: a = Array_Grid_Data(m, v.data.origin, v.data.step) path = join(dir, v.data.name) write_mrc2000_grid_data(a, path)

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(no subject)
by Julien Orts 04 Dec '07

04 Dec '07

Dear Chimera people, I would like to save a lot of pdb. I have for example 500 pdb. Each saved pdb file should contains 2 pdbs of these 500 pdbs. I can write a script for this but the command write does not work for more than two pdb. Is there any other way? thank you Julien

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question about the model panel
by jean-francois menetret 04 Dec '07

04 Dec '07

Is there is way to reorder the position of the models in the model panel ? (For example putting the mrc files on top and the pdb files at the bottom) 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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Re: [Chimera-users] Question regarding Chimera usage
by Tom Goddard 03 Dec '07

03 Dec '07

Hi Navya, If you have a 3-button mouse you move the atomic model with the middle button. If that is not working then you probably have the mouse modes assigned differently. You can look at and change what the mouse buttons do with menu entry Features / Preferences category Mouse. Usually button 2 is assigned to translate in x and y (second column of table). It may not be assigned to that operation if you have used other tools like volume path tracer or volume subregion selection that reassign mouse button 2. Tom swetha davuluri wrote: > Hi, > > Thanks for your reply. I am trying to move the atomic model using the > mouse. But I can only rotate the model but not transitionally shift it > i.e. I am not able to move the model either up/down and sideways. Not > sure how to do this. Please let me know. > > Thank you, > Navya. > > ----- Original Message ---- > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: swethadn(a)yahoo.com > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Sent: Friday, November 30, 2007 9:27:37 AM > Subject: Re: [Chimera-users] Question regarding Chimera usage > > Hi Navya, > > The first step is to move the atomic model using the mouse close to > the correct location in the EM map. The Fit Model in Map tool will not > move the atomic model if its initial position lies outside the map. > Here are instructions on how to do the fitting. > > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… > > Tom > > > > ------------------------------------------------------------------------ > Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See > how. <http://us.rd.yahoo.com/evt=51732/*http://overview.mail.yahoo.com/>

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Remove steric clashes
by Francesco Pietra 02 Dec '07

02 Dec '07

I would like to delete all water residues that are in steric clash with lipid residues. What I have is a single pdb file that includes both types of residues. Can't have the two as different models. Therefore I can't apply the zone tool that I know how to manage for two different models. The only alternative I can figure out is through the "Find Clashes,Contacts", writing a file for all WAT at a specified distance from the lipid residues and then manually deleting, or inventing a script for that (at <=0.6A there are 386 clashes). Hope to have missed an automatic tool from Chimera. If not, I suggest that as a most useful additional tool for cleaning systems. I dropped into the problem when at the first minimization, in view of MD, the system met segmentation fault after a few steps, with gradient decreasing by eight orders of magnitude along those few steps. Then I recognized not to have been careful enough before making the coordinate files for the MD suite. I should have not relied too much in the membrane builder and I had better spent time in checking for steric clashes. Thanks francesco pietra ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

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distance measurement
by sette＠uniroma2.it 30 Nov '07

30 Nov '07

Dear all, I would like to measure the distances between all atoms in a molecule, in particular between all hydrogens. I added the H but it seems to me that is possible to measure only the distance between two selected atoms and not between all atoms in a single command. How is possible to do? Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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morphing structures
by Elaine Meng 30 Nov '07

30 Nov '07

> Thank you for your help. I did superimpose the structure with pdv > viewer. I did save as a pdb file but when I open the morph > conformations tool and I add the pdb I am not able to create the > interpolation between the structure. > > Do you know why? > Hi Djemel, I would recommend just using Chimera to superimpose the structures. Starting with the two structures in two separate files, open them with File... Open in the Chimera menu, then superimpose them. There are lots of ways to superimpose them but probably this simple command (show command line with Favorites... Command Line) will work fine: matchmaker #0 #1 In Morph Conformations you have to specify more than one structure. There should be more than one line in the Conformations list. My guess (and it's only a guess) is that the way the other program wrote the file it was considered all one structure, not 2 separate structures. 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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