- 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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Detecting residue from command line
by Francesco Pietra 30 Nov '07

30 Nov '07

Sorry for a question that was surely answered many times. How to detect on the screen (from command line) residues from their resSeq number?. I have two different sets of WAT: 522-9999 and 0-4759 and want to check where 0-521 are located in a protein-ligand-POPC membrane. Thanks francesco pietra ____________________________________________________________________________________ Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ

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morphing movie
by Elaine Meng 30 Nov '07

30 Nov '07

> Actually I would like to do some movie with chimera but I never used > before. I have two crystal structure of two different conformation of > the protein that I work with. I would like to see the trajectory from > conformation 1 to 2. I just downloaded the chimera but I don't know > how to start. > > Could you tell me how to make the movie? I would appreciate you help. > Is that possible to load molecule 1 and 2 and see how the trajectory > is ? Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: November 30, 2007 10:29:41 AM PST It sounds like you want to use the Morph Conformations tool (under Tools... Structure Comparison). If you have two structures, it will "make up" a series of in-between structures to create a trajectory. You have to match (superimpose) the two structures yourself first. There are different options of how to make the in-between structures and how many to make. The trajectory-viewing tool, MD Movie, is automatically started to show the trajectory. From MD Movie you can record the trajectory as a movie file (Quicktime or other formats) or just save it as a PDB file for later viewing in Chimera. Probably you will need to learn a little bit about using Chimera so that you can set the display (ribbons, background color, displaying important sidechains) how you want for the movie. Chimera comes with a User's Guide. You can open it directly or search it from the Chimera Help menu. Also clicking the Help buttons on dialogs will automatically open the corresponding man pages. I will give some links to our Web site, but most of the same pages are included with your download. Tutorial on matching structures and making nice images: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html Manual page for Morph Conformations: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html for MD Movie: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (see the "Recording a Movie" section) For basic Chimera use, there is "Getting Started" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html and a more detailed version of that at our web site (not in the User's Guide): http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html but if you get stuck or have trouble finding something, you can ask me about it. 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] Question regarding Chimera usage
by Tom Ferrin 30 Nov '07

30 Nov '07

------- Forwarded Message Date: Thu, 29 Nov 2007 20:06:54 -0800 From: swetha davuluri <swethadn(a)yahoo.com> To: tef(a)cgl.ucsf.edu Subject: Question regarding Chimera usage Dear Dr. Ferrin, I have a question Chimera usage. I am trying to fit a model to an EM map. I cou ld lock the map from moving but I am not able to transitionally shift the model . The translational shift box in "Fit Model in Map" is checked. Please let me k now how to transitionally move the model. Regards, Navya. _________________________________________________________________________ ___________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.ya hoo.com/ ------- End of Forwarded Message

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2D for 3D display
by Gang 'Gary' Ren 29 Nov '07

29 Nov '07

Hi, Chimera, I wonder how to create the 3D display by using the 2D image as below? http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png best regards Gary ---------------- Gang Ren, Ph.D. Phone: (415) 476-8284; Fax: (415) 514-2550 Email: gren(a)msg.ucsf.edu; Web: 3dem.ucsf.edu Department of Biochemistry & Biophysics 1700, 4th Street, Byers Hall (QB3), room 301C San Francisco, CA 94143-2532

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Re: [Chimera-users] Chimera-users Digest, Vol 55, Issue 29 (heightmaps)
by Jonathan Hilmer 29 Nov '07

29 Nov '07

I would also be interested to learn how to do heightmaps in Chimera, or if it would be possible to add such a feature. Right now we use ImageJ (which doesn't have enough functionality) and Blender (which has too much), while Chimera would be perfect. In response to Gabe's question, it's not terribly convenient but you could use the Zone tool to generate just the 'positive' region and save that as a unique file. The 'combine.py' could then be used to subtract out the positive from the original, leaving the zeroed parent density file. Jonathan > Message: 1 > Date: Wed, 28 Nov 2007 22:12:40 -0800 > From: "Gang 'Gary' Ren" <gren(a)msg.ucsf.edu> > Subject: [Chimera-users] 2D for 3D display > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <web-5552878(a)msg.ucsf.edu> > Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" > > Hi, Chimera, > > I wonder how to create the 3D display by using the 2D > image as below? > > > http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png > > best regards > > Gary > > ---------------- > Gang Ren, Ph.D. > Phone: (415) 476-8284; Fax: (415) 514-2550 > Email: gren(a)msg.ucsf.edu; Web: 3dem.ucsf.edu > > Department of Biochemistry & Biophysics > 1700, 4th Street, Byers Hall (QB3), room 301C > San Francisco, CA 94143-2532 > > > ------------------------------ > > Message: 2 > Date: Thu, 29 Nov 2007 10:23:49 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] reverse "zone" tool? > To: Gabriel Lander <glander(a)scripps.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <474F03B5.5060609(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Gabriel Lander wrote: > > Hi Tom, > > is it possible to somehow make the "zone" tool in the volume viewer do > > the reverse of what it does? I have a PDB docked into a density file > > and I want to remove the density surrounding it so that it's easier to > > focus on the rest of the structure. > > By the way, I thoroughly enjoyed your demo of the new Chimera features > > here at the cryo course, I'm sorry I didn't have a chance to chat very > > much afterwards, > > Cheers, > > -gabe > > > > > Hi Gabe, > > One trick would be to use the "Color Zone" tool to color the surface > near the fit model completely transparent (hence invisible). Use menu > entry Actions / Color / From Editor, click the Opacity button and set > opacity to zero. Your molecule will be invisible. Then use Tools / > Volume Data / Color Zone, select all atoms (Select / Select All) and > press the color zone dialog Color button. Then go back and change the > color of the molecule to something visible. > > Three drawbacks of this approach. First, it doesn't allow you to > save the map with the region near the molecule zeroed out -- it is only > coloring the surface. Second, having a partially transparent surface > makes the rendering slower. Third, Chimera only handles one transparent > model correctly. If you try to add a second transparent surface you > will see odd effects, like the invisible patch blocks the second > transparent surface. If these limitations are severe, I can give you a > bit of Python code that actually makes a copy of the map with the part > near the molecule erased. > > Tom > > > ------------------------------

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Re: [Chimera-users] reverse "zone" tool?
by Thomas Goddard 29 Nov '07

29 Nov '07

Gabriel Lander wrote: > Hi Tom, > is it possible to somehow make the "zone" tool in the volume viewer do > the reverse of what it does? I have a PDB docked into a density file > and I want to remove the density surrounding it so that it's easier to > focus on the rest of the structure. > By the way, I thoroughly enjoyed your demo of the new Chimera features > here at the cryo course, I'm sorry I didn't have a chance to chat very > much afterwards, > Cheers, > -gabe > Hi Gabe, One trick would be to use the "Color Zone" tool to color the surface near the fit model completely transparent (hence invisible). Use menu entry Actions / Color / From Editor, click the Opacity button and set opacity to zero. Your molecule will be invisible. Then use Tools / Volume Data / Color Zone, select all atoms (Select / Select All) and press the color zone dialog Color button. Then go back and change the color of the molecule to something visible. Three drawbacks of this approach. First, it doesn't allow you to save the map with the region near the molecule zeroed out -- it is only coloring the surface. Second, having a partially transparent surface makes the rendering slower. Third, Chimera only handles one transparent model correctly. If you try to add a second transparent surface you will see odd effects, like the invisible patch blocks the second transparent surface. If these limitations are severe, I can give you a bit of Python code that actually makes a copy of the map with the part near the molecule erased. Tom

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Server and Client machines with different OS
by Isabelle Vergely 28 Nov '07

28 Nov '07

Hello, I know that it is possible to open one or several pdb files on a linux machine using a system command line like "> chimera [options] [input1 input2 ...]". My question is: Is it possible to use this command on a linux server to display chimera on a Windows client machine? Thank you very much in advance for your help. Best Regards. Isabelle

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ppt and movies
by Markus Voehler 27 Nov '07

27 Nov '07

I have recorded a movie of a pdb in chimera with the following command: movie record supersample 3 . . movie stop movie encode bitrate 6000 mformat avi output ./pol_b_movie.avi I can import it into ppt (2004, V 11.3.5) on my Mac (OS X 10.4.11) and it plays fine in the editing mode, but when I go to the slideshow and start the movie, there is a blank screen for the duration of the movie. When it is done, it shows the standing slide again. Any idea what might be going on? Also, is there a better way to improve the resolution then setting the bitrate to 6000, 30 f/s? I have tried the supersample 3 option, but this does not seem to make much of a difference in the final movie. Any input is appreciated. Markus

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Re: [Chimera-users] [Fwd: Re: Chimera hide all models button]
by Eric Pettersen 27 Nov '07

27 Nov '07

I guess I do have some tips to offer here. You can use the "Configure..." button of the Model Panel to change what happens when you double click on a model. By default, double clicking shows the attributes of a model. You can have double click do any combination of button actions, so you could instead have double click both "show only" the model and "activate only" the model. With that configuration, if you wanted to show and activate two specific models you would click on one model and then control-double- click on the other one. If you want to show and activate all models you would click on the first model listed in the Model Panel and then shift-double-click the last model. --Eric On Nov 27, 2007, at 8:57 AM, Tom Goddard wrote: > Eduardo thinks we need better controls for showing just one or two > models and activating just one model when many are present. > > -------- Original Message -------- > Subject: Re: Chimera hide all models button > Date: Tue, 27 Nov 2007 08:34:07 -0700 > From: Eduardo Sanz-Garcia > To: Tom Goddard > > > Tom Goddard wrote: >> Hi Eduardo, >> >> Perhaps clicking on the "Shown" heading in the Model Panel could >> hide all models if all are shown, or show all if all are hidden. >> If some are hidden and some are shown maybe it would show all, >> then a second click would permit you to hide all. I don't really >> like this idea because very few people would know to try it. >> Usually clicking on list headings sorts using that column. > That is true. I didn't realize about this. >> Although sorting may seem not too useful for the "Shown" column I >> can imagine if you have 50 models open with just a few shown you >> might want to sort to bring those to the top. >> >> A slightly harder way to show just one model is to select its >> line in the Model Panel and press the "Show only" button in the >> right column of buttons. Unfortunately that button is way down on >> that scrolled list of buttons. You can hide many of those buttons >> using the "Configure..." button on the Model Panel and it will >> remember the hidden ones in your preferences file. But there is >> no way to reorder the buttons as far as I know. >> >> The oval next to the step size above volume histograms allows you >> to show/hide that map. Maybe I could enhance that so if you use >> the right mouse button instead of the left then it shows that map >> and hides all others. Cryptic but not unexpected behavior. > Yes, this is a little cryptic but a fast method. >> Still there are only 3 histograms shown by default. Perhaps if I >> added the scrollbar for the histograms as you suggest that would >> further improve switching display between individual maps. > I believe that the scrollbar is a very good idea! > > I believe that Chimera should improve the way to show or activate > all the models faster from the GUI. I spend a lot of time > activating two models, deactivating the rest, and showing only > these two models. The command line is fast but there are some, like > me, that always forget the commands. >> >> Let me know what ideas you think are best. It is quite difficult >> to make the user interface simple to use and powerful. Thanks for >> your ideas. >> >> Tom >> >> Eduardo Sanz Garcia wrote: >>> Do you mind if I share a very personal suggestion? >>> I always open 5 or more maps at the same time (chimera >>> directories*/*100.map) . I normally want to examine each >>> individually, and then compare them. I would like to undisplay >>> all of them at the same time. I know that this is possible from >>> the command line (~modeldisplay), but I always forget it. It >>> would be nice to have the same function from the GUI. I am >>> suggestion to be able to click in the black circle (bottom image) >>> and un/display all the models at once. >>> >>> Anyway, thanks for the volume viewer capabilities of chimera. >> >> >

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How do I
by Eduardo Sanz Garcia 26 Nov '07

26 Nov '07

I am using Chimera alpha version 1 build 2467 2007/10/31 I liked how each volume map opened has a different color. That's a great idea!! But I have a problem, I am displaying 4 volume maps at the same time. The volume viewer window only shows 3 histograms, therefore to modify the threshold of the fourth I have to close one of the volumes. Is there a way to modify the fourth histogram in the volume viewer window without close another? I also found a different behavior if you close the upper, middle and bottom histogram. Thanks.

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saving color palette
by William Jeffrey Triffo 26 Nov '07

26 Nov '07

is there a way I can save the color palette to a file? I realize it seems to be saved as a user setting somewhere because it always pops up again in the same configuration as the previous session, but I would like to be able to back it up intentionally if possible. Also, is it possible to save/load various palettes? thanks, -Jeff --

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Chimera vs Amber, which one digresses from the average pdb rules?
by Francesco Pietra 26 Nov '07

26 Nov '07

A lipid/water pdb file that was good for Leap (Amber9) to get top/crd, once passed through Chimera 2470 to remove residues is no more good for Leap. All TER were removed by Chimera, ATOM renamed HETATM, while CONECT records were added. As such, Leap said: In file [chirality.c], line 142 Atom named C217 from POP did not match Aborting I knew such type of message. There is no C217 atom. On previous (different) occasions, insertion of TER records put the house in order. I inserted all TERs between POPC residues and between WAT residues (thanks to Python!). Now Leap said: In file [atom.c], line 444 bond AtomProblem found Aborting As I did not know this type of message, I tried to investigate that line 444. Following vim's command :n,444 that line, indicated at bottom of terminal as "444,1", reads HETATM 441 O31 POPC 5 -44.082 -12.831 14.685 1.00 0.00 O A carbon atom (if "[atom.c]" means carbon, is at line 447,1, which reads HETATM 444 C32 POPC 5 -46.343 -12.925 15.140 1.00 0.00 C In the original (good for Leap) pdb those lines read: ATOM 441 O31 POPC 4 -37.722 -19.453 18.019 1.00 0.00 L11 O ATOM 444 C32 POPC 4 -39.844 -19.273 18.941 1.00 0.00 L11 C Chimera also changed atom names, such as in the final part of the POPC residue (Sybyl naming?, if so, there is an alternative in Chimera not to follow Sybyl rules?) HETATM 528 XH14 POPC 5 -47.646 -9.424 -0.112 1.00 0.00 H HETATM 529 YH14 POPC 5 -46.217 -10.553 -0.172 1.00 0.00 H HETATM 530 5C31 POPC 5 -47.890 -11.168 -1.419 1.00 0.00 C HETATM 531 XH15 POPC 5 -47.763 -12.309 -1.296 1.00 0.00 H HETATM 532 YH15 POPC 5 -48.986 -11.063 -1.417 1.00 0.00 H HETATM 533 6C31 POPC 5 -47.242 -10.566 -2.756 1.00 0.00 C HETATM 534 XH16 POPC 5 -46.135 -10.759 -2.831 1.00 0.00 H HETATM 535 YH16 POPC 5 -47.802 -11.112 -3.597 1.00 0.00 H HETATM 536 ZH16 POPC 5 -47.451 -9.454 -2.737 1.00 0.00 H TER which, in the original (good) pdb was: ATOM 528 H14X POPC 4 -38.665 -14.879 4.398 1.00 0.00 L11 H ATOM 529 H14Y POPC 4 -39.080 -16.603 3.952 1.00 0.00 L11 H ATOM 530 C315 POPC 4 -40.370 -15.221 2.996 1.00 0.00 L11 C ATOM 531 H15X POPC 4 -41.330 -15.752 3.099 1.00 0.00 L11 H ATOM 532 H15Y POPC 4 -40.694 -14.148 3.019 1.00 0.00 L11 H ATOM 533 C316 POPC 4 -39.787 -15.573 1.664 1.00 0.00 L11 C ATOM 534 H16X POPC 4 -39.553 -16.661 1.544 1.00 0.00 L11 H ATOM 535 H16Y POPC 4 -40.534 -15.211 0.948 1.00 0.00 L11 H ATOM 536 H16Z POPC 4 -38.782 -15.094 1.533 1.00 0.00 L11 H TER Although it is not clear to me yet where really Leap crashed (nor am I placing Leap as the standard; simply I have to get top/crd from it, if I want to carry out MD with Amber). Elaine already kindly clarified the ATOM/HETATM issue. I hope now to get help about the atom names , ie a table of conversion to get Leap working or a not-Sybyl choice in Chimera. Once again, I regret very much to pose so many problems of language. Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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<< Rendering proteins with Chimera >>
by Hatuey Hack 23 Nov '07

23 Nov '07

Hi all, As a Chimera new users, I notice that the proteins are rendering different depending on the program they where prepared. I used the preset to render them. I have a protein with all residues in different color and the other protein is rendered in a single color. My question is: this is a problem of Chimera or it is a problem with the protein file? Regards, Hatuey

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Aligning a protein into a membrane
by Francesco Pietra 22 Nov '07

22 Nov '07

Elaine: Relating to your instructions of last 19 Nov (I printed your mail, then unfortunately I deleted it) how to align a protein into a membrane (for both I have valid pdb and valid Amber parameters) I am probably made elusive mistakes at the stage of saving new pdbs. I aligned the protein into the membrane, then (with protein selected and membrane not active) I saved the new pdb, getting two files, "0" for the membrane and "1" for the protein. In Amber LEaP both these pdb file could be loaded and combined, however save top/crd failed because something was wrong with the membrane file. In fact, if the original pdb for the membrane is used, top/crd can be saved, though the protein is not accurately aligned. Clearly, my plan is to remove superimpositions among molecules for the "whole" obtained from Amber. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

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Re: [Chimera-users] ppt and movies
by Elaine Meng 22 Nov '07

22 Nov '07

Hi Markus, I can answer this one: > Why does the command movie record supersample 3 give virtually the > same file size then just movie record? Supersampling in Chimera initially saves a larger image for each frame but then samples it down to the requested size. This reduces "stairstepping" along edges without changing the pixel dimensions of the image that is ultimately saved for each frame. It increases calculation time rather than file size. Supersampling is also an option for saving individual images (File... Save Image) when you are not raytracing. You can see the difference provided by this feature independent of the movie-encoding process by comparing images saved with and without (1x1) supersampling. 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] chimera help - surface exposed sides
by Elaine Meng 22 Nov '07

22 Nov '07

On Nov 22, 2007, at 1:07 AM, Thomas C. Marlovits wrote: > Hi Elaine, > I am trying to find an easy way to determine solvent > accessible/surface exposed side chains but also buried side chains > from atomic structures. > The idea would be to: > - display the surface > - have a command that would highlight (color) surface exposed side > chains/amino acids > Optional: color the identified aa by physical property, etc > - show all the identified amino acids on a primary sequence > - write out the amino acids into a text file. > > Would be great if you can let me know, how to do this most efficiently. > Thanks, > -Thomas > ----------------------------------------------------------------------- > -------- > Thomas C. Marlovits, PhD, M.A.S. > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences (IMBA) > Hi Thomas, - First assign atoms (or residues) an attribute with values equal to their solvent-accessible surface areas (more details below). - Then you can use Select... By Attribute Value to select any subset of those based on some cutoff, for example all atoms with surface area > 0. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#select The selection can be written as a list of atoms (or residues) with Actions... Write List, and the Sequence tool will show the current selection on the protein sequence (it would also be shown on a multiple sequence alignment associated with the structure, if you have such an alignment). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html - Of course you could also color the selection, but now that numerical attributes are assigned, you can map values to colors that will gradually shade from one to another with "Render by Attribute" or the command "rangecolor" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html Now, back to how to get the attribute values assigned. Currently it is necessary to use the "Area/Volume from Web" tool (under Tools... Surface/Binding Analysis). It sends coordinates to the NIH StrucTools server. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html We are in the process of generating our own surface-calculation code that will provide these values within Chimera, but it is not done yet. The main inconvenience of this server approach is that you should first delete things like water and ligands if you don't want them lumped with the protein during the calculation. "Area/Volume from Web" has a few different options of what is calculated. You can use its MSMS method to calculate both molecular surface and solvent-accessible surface (this will generate two attributes) or the Gerstein method to calculate solvent-accessible surface. Atom attribute values will automatically be assigned by this tool. If you want them summed to residue attribute values, you must also use "Attribute Calculator". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html There are examples of using Area/Volume from Web, Attribute Calculator, and Render by Attribute in the Attributes tutorial, part 2: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ attributes.html#part2 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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Coloring a surface according to distance from a selection
by Paul.Pillot＠ac-nice.fr 21 Nov '07

21 Nov '07

Hello, I can color a surface according to the distance from a single point or a plane, but is it possible to do it according to the distance from a selection (eg an other chain or molecule) ? My aim is to show the contacts between an antibody and an antigen. I tried the tool intersurf for doing it, but the result is pretty crude (low definition of the surface compared to the usual surfaces available). Thanks in advance, Paul

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spaceball 5000
by Jean-Paul Armache 20 Nov '07

20 Nov '07

hello, i have a question regarding usage of a 3d manipulation device. i have a spaceball 5000 device, which i would like to use under linux (or windows). is there a way of using this device in chimera? best regards, Jean-Paul Armache AG Beckmann LMU Gene Center

3 2

move a structure into another one
by Francesco Pietra 18 Nov '07

18 Nov '07

I have installed chimera-1.2470 on Debian Linux i386. Thank you. I want to insert a protein into a lipid membrane in a precise opientation, then save the protein pdb in this configuration. I used VMD in the last few days to this redard. I wonder whether I can stick to Chimera for this purpose too. I tried by selecting "protein", though it was difficult to proceed. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

2 3

Puzzle with WAT
by Francesco Pietra 17 Nov '07

17 Nov '07

I am faced by a recurring puzzle with WAT (standard TIP3). In Amber9 xleap I loaded a pore protein_noH.pdb model getting top and crd files In both Chimera and VMD these showed that the WAT oxygen atom (natural, inside the pore) had been added of two hydrogens with intramolecular bonding between the two hydrogens. Otherwise, the geometry was correct for water. Correspondingly. in Chimera dockprep complained that one hydrogen of that WAT had incorrect valency, and refused to proceed. The protein.pdb created with ambpdb from such top and crd files showed the WAT correctly, without intramolecular H-H bonding. The geometry was exactly the same as for the above "wrong" WAT. With this protein.pdb, Chimera's dockprep was happy. That allowed docking with various (big) ligands, including amber re-score. I posted to dock-fans that the issue was solved, and how. Now I wanted to carry out Amber9 MD of that protein-ligand complex, inserting it into a lipid bilayer. I first tried the above protein.pdb alone into a membrane. A new venture for me. I posted separately a question how to create a hole around the protein. However, even when that is solved, I am faced again by the problem of viewing WAT into the pore as a triangle. Also, the many WAT mixed to the POPC of the membrane are also viewed as triangles. Actually, when that protein.pdb is loaded to xleap (as before leaprc.ff99SB and leaprc.gaff), the WAT into the pore is seen as a triangle. Thus, the protein.pdb, created with amdpdb is good for viewers and dockprep and docking, not back for LEaP. Although, it may seem as a loop, these are the facts (that so far I am unable to understand). I did not try yet if that allows MD, just because going on with such triangulated water seems unsafe. The protein.pdb ends as follows: TER ATOM 6885 O WAT 445 -0.036 0.094 -2.262 ATOM 6886 H1 WAT 445 0.921 0.094 -2.262 ATOM 6887 H2 WAT 445 -0.276 1.021 -2.262 TER END The membrane.pdb ends as follows: ATOM 50316 O WAT 3357 47.120 46.103 -26.069 1.00 0.00 W45 O ATOM 50317 H1 WAT 3357 46.727 45.819 -26.895 1.00 0.00 W45 H ATOM 50318 H2 WAT 3357 47.214 47.052 -26.153 1.00 0.00 W45 H END as a representative of the many WAT present. Thanks francesco pietra (the membrane was created with VMD and the file rearranged to be understood by Amber9) ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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1.2470 production release available
by Eric Pettersen 16 Nov '07

16 Nov '07

Hi all, The production release, version 1.2470, is out now. A list of changes from the previous production release (1.2422) can be found here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2470.html I think that page is pretty easy to scan through, but for those of us who are really time-challenged, the important changes, I think, are: 1) Incorporation of what were previously "experimental features", such as morphing between volume data sets 2) Volume Viewer improvements: a) Multi-data set interface b) Distinct initial map colors c) Resampling of rotated maps d) Improved large-file handling e) Single-plane display f) Scriptability 3) Display of dendrograms in Multalign Viewer 4) Use of rotamer libraries in swapping residue side chains with the ability to evaluate possible swaps based on clashing, fit into density maps, or hydrogen-bond formation Mac users with the new Leopard OS should note that it seems that 3- button mouse emulation is off by default in Leopard's X11. So, if you have a one-button mouse and want to be able to scale/translate using the mouse + alt/command, do the following: 1) click on the X11 icon (it should show up in the dock when you start Chimera) 2) open the X11 menu from the menubar at the top of the screen 3) choose the Preferences... entry 4) in the resulting dialog choose the Input tab 5) enable the Emulate three button mouse option --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Ramachandran Plots
by Quinton Dowling 16 Nov '07

16 Nov '07

Hi, I am interested in creating a ramachandran plot from an md trajectory. Particularly I would like to track the change in phi/psi angles over time for specific amino acids throughout the md in a fashion that is easily presentable. Is there a way to do this with Chimera? Or any way at all? Thanks a bunch. Quinton Dowling Research Computing Center The College of Idaho Caldwell ID 83605

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Re: [Chimera-users] Z-slice transparency
by Tom Goddard 15 Nov '07

15 Nov '07

I met Lu in San Diego and found out he was showing a volume slice and a second model which was also a volume using solid rendering style. The trouble is that Chimera cannot correctly display two transparent models -- at most one can be transparent. If two are transparent, the last one drawn (higher model id number) always appears on top of the other transparent models. This is a (serious) limitation of the Chimera graphics architecture. Technically Lu has the single plane set to be completely opaque, but all solid rendered volumes are rendered as if they have transparency even if the coloring is set for complete opacity. (The OpenGL z-buffer which records the depth of visible objects and prevents obscured surfaces from being shown is not used with "transparent" rendering). We tried using the TomoPlane Chimera extension from Karin Gross and Christoph Best and that draws truly opaque volume planes, but it is much slower. Tom Lu wrote: > Hi Tom, > > I tried everything that you mentioned, including adding multiple > points to the histogram, but I can still see stuff through the > Z-slice. Anyway, I noticed that you're going to be at the Scripps EM > workshop next week. If you have time at the workshop, I'd be happy to > show you the type of Amira movie that we'd ultimately like to make > using Chimera. > > Cheers, > -Lu

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mutation of residue
by hjoseph＠brandeis.edu 15 Nov '07

15 Nov '07

Hi everyone, I want to model my mutated residue into crystal structure and see its interactions. If anyone knows and easy way of doing it in Chimera please let me know. Thanks everyone, Helen Josephine

2 2

how to make a bond
by dominique matt 15 Nov '07

15 Nov '07

I want to draw a bond between two atoms which appear linked by a dotted line. This is often the case when one atom is a metal. How can I draw the bond ? Thank you for your help Kind regards Dominique MATT Strasbourg

3 2

Ribbackbone spec?
by Jean Didier Pie Marechal 14 Nov '07

14 Nov '07

2 2

Z-slice transparency
by Lu 13 Nov '07

13 Nov '07

Dear Chimera Crew, Is there a way to adjust the transparency of a Z-slice using the Volume Viewer's "planes" feature? Right now, it looks like the Z-slice has transparency and lets you see the isosurfaces/segmentations below it. We would like to turn off the Z-slice transparency so that it blocks everything that is behind it. Such a feature would allow us to use Chimera to make a movie that we've been using Amira for, i.e., a movie in which the isosurface (or segmentation) is "revealed" as the map's Z-slice drops down. If the effect that I'm describing isn't clear, I'd be happy to forward a link to such a movie. Thanks! -Lu -- Lu Gan Postdoc, Jensen Lab Caltech Broad Center, MC 114-96 1200 E. California Blvd. Pasadena, CA 91125 Tel: 626-395-8848 Fax: 626-395-5730

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Computer requirements
by Sandra Eriksson 13 Nov '07

13 Nov '07

Hi! I'm planning to buy a computer, and am checking on the requirements of my favourite programs. But, searching the Chimera home page, I found little information on the hardware neccessary to make the program run really smoothly. If you have suggestions for RAM, processor and graphics etc, I would be very grateful. Best, /Sandra

2 1

Question about the dotted bond
by Hyunmi Sun 13 Nov '07

13 Nov '07

Dear Whom it may concern Hello, I am currently using Chimera to access a pdb file. When I fetch the pdb file, one of the bonds between two ligands is illustrated as a dotted line in the wire representation. Why is this so? Thanks for the help! Sincerely, Hyunmi Sun

2 1

Output of volume rotation angles and shifts in Chimera
by Duncan Sousa 13 Nov '07

13 Nov '07

Hi, I use Chimera to manually align 3D electron microscopy structures. I'm hoping someone knows how to output the angles and shifts of rotated and shifted volumes. Since one can restore sessions, the angles and shifts must be saved somewhere right? Thanks, Duncan __________________________________ Duncan Sousa, Ph. D. Department Physiology & Biophysics Boston University School of Medicine 715 Albany Street Boston, MA 02118

2 1

Calculating the center of mass of a ligand
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I have another question: what would be the easiest way to calculate the center of mass of a given set of atoms? In particular, is there a python module that already has this function implemented? I am interested in particular to find the center of mass of a ligand bound to a protein. Thanks a lot, JD

2 1

IDLE for listing selected residues.
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I'd like to use chimera to generate the list of the oxygen atoms of the water molecules located at less than 5.0 A of a ligand. Selecting the water molecules have been the easiest part... select :HOH & :301.a zr < 5.0 with :301.a my ligand. Then in the IDLE, I tried a series of alternative to generate the list. I use the different tips that were posted in the digest recently and arrived to this: for i in range(1,len(chimera.selection.currentResidues()): print chimera.selection.currentResidues()[i] Right, this gives me the list of residues, unfortunately, that would be a LOOOT better for me is to have the Serial number of the oxygen atoms... currentSerialNum and currentSerialNumber do not see to be a correct selection type. If there is any way that can do this? Thanks a lot JD On Sat, 2007-11-10 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Z-slice transparency (Tom Goddard) > 2. production release candidate (Eric Pettersen) > 3. pipes and planks (Dougherty, Matthew T.) > 4. Re: pipes and planks (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 09 Nov 2007 12:47:12 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Z-slice transparency > To: Lu <lugan(a)caltech.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4734C750.5020803(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Lu, > > I think I know why the volume planes are slightly transparent for > you. You are using Chimera version 1.2422 and I changed the volume > solid rendering transparency behavior in the later Chimera version > 1.2434 (August 3, 2007). You can either get the most recent Chimera > from the daily builds web page: > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Or in older Chimera versions use volume menu entry Features / Brightness > and Transparency and change transparency to 0. You'll have to type this > in the entry field and press return because the slider does not go all > the way down to zero. This transparency value modulates the > transparencies given by the height of the brightness / transparency > yellow curve on the histogram. Newer Chimera changed the modulation > behavior to keep completely opaque voxels still completely opaque while > older Chimera did not. > > Tom > > > > ------------------------------ > > Message: 2 > Date: Fri, 9 Nov 2007 15:52:29 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [Chimera-users] production release candidate > To: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <7B31B33A-569C-4808-AD94-EBCD134DEC26(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > We have put a production release candidate up for download (http:// > www.cgl.ucsf.edu/chimera/download.html) It would help us out if > people would try it out and see if it all works okay. Major changes > from the 1.2422 release include: incorporation of what were > previously "experimental features", such as morphing between volume > data sets; major revamp of the Volume Viewer interface; display of > dendrograms in Multalign Viewer; use of rotamer libraries in swapping > residue side chains and the ability evaluate possible swaps based on > clashing, fit into density maps, or hydrogen-bond formation. A more > exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ > docs/relnotes/snapshot.html > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

2 1

RMSD
by Julien Orts 13 Nov '07

13 Nov '07

Dear all, First thanks a lot for the great software you provide us!!! I would like to compare structures after an MD simulation. There is a function called match which can be used to calculate the RMSD between selected atoms. The protocol is the following; I select atoms within 5 Angstrom to a reference atom in the structure 1: 300 atoms selected. I do the same for the structure 2 (reference atom is the same): 311 atoms selected The problem is then I can not use the match function since the atom number is different. I selected then residues (the one which are 5A away from the reference atom) instead of atoms but it is a bit fastidious plus it is not the same as a "zone selection" (some atoms are coming even if they are at 5.6A) I print out (from a pdb) the number of desired proton but the command sel @123 do not work because atom selection is done by name and not by number (if it is really the case then it would be nice to have this possibility as well ;-) The last solution would be really easy and quick to do if the selection on atoms can also be done by number. Is there any way to solve this? I need to use all the atoms, so the matchMaker give me an RMSD but it does not use all of the atoms in the calculation of the RMSD. Basically I need the intersection of the two sets (two structures) of selected atoms. In reality I have much more than 2 structures so the protocol should also be scriptable, but I guess everything is scriptable in Chimera (right?) thank in advance many greetings Julien

2 1

pipes and planks
by Dougherty, Matthew T. 09 Nov '07

09 Nov '07

I have about 80 pdb datasets, each corresponding to a single helix. I know I can do one at a time using the gui. What is the method for scripting? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

2 1

production release candidate
by Eric Pettersen 09 Nov '07

09 Nov '07

Hi all, We have put a production release candidate up for download (http:// www.cgl.ucsf.edu/chimera/download.html) It would help us out if people would try it out and see if it all works okay. Major changes from the 1.2422 release include: incorporation of what were previously "experimental features", such as morphing between volume data sets; major revamp of the Volume Viewer interface; display of dendrograms in Multalign Viewer; use of rotamer libraries in swapping residue side chains and the ability evaluate possible swaps based on clashing, fit into density maps, or hydrogen-bond formation. A more exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ docs/relnotes/snapshot.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Re: [Chimera-users] Z-slice transparency
by Tom Goddard 09 Nov '07

09 Nov '07

Hi Lu, I think I know why the volume planes are slightly transparent for you. You are using Chimera version 1.2422 and I changed the volume solid rendering transparency behavior in the later Chimera version 1.2434 (August 3, 2007). You can either get the most recent Chimera from the daily builds web page: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Or in older Chimera versions use volume menu entry Features / Brightness and Transparency and change transparency to 0. You'll have to type this in the entry field and press return because the slider does not go all the way down to zero. This transparency value modulates the transparencies given by the height of the brightness / transparency yellow curve on the histogram. Newer Chimera changed the modulation behavior to keep completely opaque voxels still completely opaque while older Chimera did not. Tom

1 0

(no subject)
by Ryan 07 Nov '07

07 Nov '07

I am trying to import Chimera in a python script but get the following error message: Traceback (most recent call last): File "./chimera_import.py", line 16, in <module> import chimera File "/usr/local/chimera/share/chimera/__init__.py", line 15, in <module> from _chimera import * ImportError: /usr/local/chimera/lib/_chimera.so: wrong ELF class: ELFCLASS32 Does anyone know what the problem is here? I can run Chimera without a problem in the GUI -- so i would assume that means the chimera class is being properly loaded in that instance. I have the 32 bit Linux version installed on my AMD64 system running SUSE. Thanks for your help, ryan

2 1

Fe in chimera antechamber
by snoze pa 07 Nov '07

07 Nov '07

Hi, I am new in this mailing list but found chimera more useful than any other software. I was building a protein that contain HEME. When I was calculating the charge using chimera interface, then it is asking for HEM[FE] and HEM[nonFE] formal charge. I know chimera is using MMTK and AMBER forcefield. If I will give the default value then it is assigning +2 charge to Fe, which is not a match based on AMBER forcefield. Meanwhile I try to change the Formal charge manually, but still it gives the same +2 for Fe. Anybody used chimera to prepare a protein having heme for dock or geometry build. My another question is: Is it possible in chimera to merge nonpolar hydrogen charges on the heavy atoms, the technique used in autodock. I will highly appreciate your help and suggestions in this matter. thanks in advance. s

2 8

Movies
by hsosa＠aecom.yu.edu 06 Nov '07

06 Nov '07

Hi, I've bee using the Movie recorder tool and noticed that the resulting movie seems in high speed motion. I recorded the movie while running the rock command. Settings: Output: AVI-MSPE-4v2 size: 760x482. constant bit rate 6000 (also tried 2000) Frames per second 33 (also tried 25). Any suggestions to get a movie playing at the same speed as when running the commands in chimera. Thanks Hernando

2 1

Angles
by hsosa＠aecom.yu.edu 06 Nov '07

06 Nov '07

Hi, I have a couple of questions: Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?. Is it possible to draw a box with the axes around a structure as it can be done with a volume ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

3 6

mac OS / Leopard
by William Jeffrey Triffo 06 Nov '07

06 Nov '07

anyone know if upgrading OS X to Leopard might effect Chimera (or have reason to think it might)? -Jeff

4 5

getting a density map for a protein
by Greg Pintilie 05 Nov '07

05 Nov '07

Some time ago when the 'Fit model into Map' feature was introduced there was a note that a tool to build a density map from a protein might be released at a later date. I haven't seen any evidence of this yet, has it been done? Otherwise, any pointers to other tools that do this? Thanks, Greg Pintilie

3 2

Re: [Chimera-users] Chimera AddH questions
by Eric Pettersen 31 Oct '07

31 Oct '07

On Oct 31, 2007, at 2:25 PM, Diep Quang Vinh wrote: > Dear Eric, > > Could you please do me an other favor? Could you please tell me how > to do your instructions automatic by command line? Since I will > deal with a hundreds of files like those and I have to add Hydrogen > atom to these file. Hi Vinh, There is no command-line equivalent for Build Structure, so you have to resort to Python here. Here's the Python code to change the currently selected atom the same way you did by hand: from BuildStructure import changeAtom from chimera import selection, Element changeAtom(selection.currentAtoms()[0], Element("C"), 3, 3, name="C") If you put the above into a script named addCH.py, then you can use these commands to add the hydrogen: sel :2.A@C open C:\<wherever you put the script>\addCH.py You might want to use the "alias" command for the above so you don't have to type so much. --Eric > ----- Original Message ----- From: "Eric Pettersen" > <pett(a)cgl.ucsf.edu> > To: "Diep Quang Vinh" <vdiep(a)purdue.edu> > Sent: Wednesday, October 31, 2007 4:01 PM > Subject: Re: Chimera AddH questions > > >> You're welcome. Glad I could help. >> >> --Eric >> >> On Oct 31, 2007, at 12:15 PM, Diep Quang Vinh wrote: >> >>> Dear Eric, >>> >>> Thank you very much for your help. It works right now. I >>> appriciate that so much. >>> >>> Thanks. >>> >>> Vinh >>> ----- Original Message ----- From: "Eric Pettersen" >>> <pett(a)cgl.ucsf.edu> >>> To: <vdiep(a)purdue.edu> >>> Cc: "chimera BB" <chimera-users(a)cgl.ucsf.edu> >>> Sent: Wednesday, October 31, 2007 2:32 PM >>> Subject: Chimera AddH questions >>> >>> >>>> On Oct 31, 2007, at 8:41 AM, chimera-bugs(a)cgl.ucsf.edu wrote: >>>> >>>>> The following bug report has been submitted: >>>>> Submitter Name: Vinh >>>>> Submitter Email: vdiep >>>>> Platform: windows >>>>> Chimera Version: 1 >>>>> Description >>>>> Hello, I would like to ask you some questions concern about >>>>> addh command. >>>>> >>>>> 1. I had an molecule which has 2-residues and one of them has >>>>> an termini -CO. This molecule is in fact was cut from a >>>>> bigger molecule and the original C have an bond with one H >>>>> atom. Now Can I by using addh command, recover the original >>>>> configuration? I mean there is only one Hydrogen added to >>>>> this Carbon. Since when I did it, chimera gave the an extra >>>>> Oxigen and not an Hydrogen. >>>> >>>> When Chimera looks at a peptide chain with an incomplete C >>>> terminus, it tries to deduce (by looking at SEQRES records) >>>> whether that residue is really the C terminus or is instead >>>> simply the last residue in a chain that is partially missing. >>>> I'm guessing that your structure file didn't have any SEQRES >>>> records, so Chimera guessed that the ending amino acid was >>>> really the C terminus and therefore made the C-O moiety into a >>>> carboxylate. >>>> >>>> If all you want to do is add a single hydrogen to that carbon, >>>> you should use the Build Structure tool to do that. Here's how: >>>> >>>> control-double click on the carbon >>>> choose "Modify Atom" from the menu that pops up >>>> In the Build Structure dialog that comes up, change the >>>> "Geometry" to "planar" and the "Name" back to "C" >>>> click on the "Change" button -- your hydrogen will be added >>>> >>>>> I try to add the hydrogen for example: >>>>> first : addh >>>>> then : addh spec :2.A@C >>>>> but both of them give me the same answer and on top of that it >>>>> adds one more H on the other nearby Nitrogen. >>>> >>>> The smallest thing addh can add hydrogens to is an entire >>>> model. If you specify something smaller, the entire model >>>> still gets protonated. This limitation is mentioned in the >>>> addh documentation. >>>> >>>> --Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> pett(a)cgl.ucsf.edu >>>> http://www.cgl.ucsf.edu >>>> >>> >> >

1 0

Distances problem
by hsosa＠aecom.yu.edu 31 Oct '07

31 Oct '07

Hi, I came across the following problem: When using the tool Tools -> Structure Analysis -> Distances to measure the distance between two atoms, a bug report window appears and all the chimera windows freeze. The error seems to happen when chimera is trying to draw the line between the atoms. The calculated distance appear in the distances window. I can't get the error message as all the windows are frozen. It says something about tcl ??? Any suggestions?. Thanks Hernando System Vaio PCG K37 laptop (Pentium 4 3.2 GHz, 1Gb RAM) running windows XP Home edition service pack 2 Graphics. ATI Radeon IGP 345M UCSF Chimera 2.4222 2007/06/21

2 1

chimera python shell
by Ondrej Marsalek 31 Oct '07

31 Oct '07

hi, i wanted to ask whether there are any plans to change the idle python shell in chimera for something else. i would be interested in something with completion and editable history, ideally ipython (http://ipython.scipy.org/moin/) i tried to add ipython to the python embedded in chimera but did not succeed. i will be grateful for any information or personal experience with this. regards, ondrej marsalek

2 1

Chimera AddH questions
by Eric Pettersen 31 Oct '07

31 Oct '07

On Oct 31, 2007, at 8:41 AM, chimera-bugs(a)cgl.ucsf.edu wrote: > The following bug report has been submitted: > Submitter Name: Vinh > Submitter Email: vdiep > Platform: windows > Chimera Version: 1 > Description > Hello, I would like to ask you some questions concern about addh > command. > > 1. I had an molecule which has 2-residues and one of them has an > termini -CO. This molecule is in fact was cut from a bigger > molecule and the original C have an bond with one H atom. Now Can I > by using addh command, recover the original configuration? I mean > there is only one Hydrogen added to this Carbon. Since when I did > it, chimera gave the an extra Oxigen and not an Hydrogen. When Chimera looks at a peptide chain with an incomplete C terminus, it tries to deduce (by looking at SEQRES records) whether that residue is really the C terminus or is instead simply the last residue in a chain that is partially missing. I'm guessing that your structure file didn't have any SEQRES records, so Chimera guessed that the ending amino acid was really the C terminus and therefore made the C-O moiety into a carboxylate. If all you want to do is add a single hydrogen to that carbon, you should use the Build Structure tool to do that. Here's how: control-double click on the carbon choose "Modify Atom" from the menu that pops up In the Build Structure dialog that comes up, change the "Geometry" to "planar" and the "Name" back to "C" click on the "Change" button -- your hydrogen will be added > I try to add the hydrogen for example: > first : addh > then : addh spec :2.A@C > but both of them give me the same answer and on top of that it adds > one more H on the other nearby Nitrogen. The smallest thing addh can add hydrogens to is an entire model. If you specify something smaller, the entire model still gets protonated. This limitation is mentioned in the addh documentation. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

Re: [Chimera-users] Selector Construction Panel
by Eric Pettersen 30 Oct '07

30 Oct '07

Hi Virginia, The Selector Construction panel could probably stand some interface improvements for sure. "Existing Selection" has nothing to do with what's selected in the Chimera window as you construct the selector. "Existing Selection" grabs whatever is selected in the Chimera window when the selector is used (either by choosing the selector from Chimera's Select menu, of invoking it from the Select region of the construction panel) -- so it can be a different selection every time it is used. Anyway, you can ignore that because it doesn't really help you with your problem. There is no easy way to select all lysines within 8 angstroms of another lysine in Chimera, so you were on the right track with trying to construct a selector, but it requires actually putting some custom Python code in your selector since you need to loop over lysine residues individually in order to get what you want. So open the Selector Construction panel, pick "Show workbench selector contents" in the Panels menu, and paste in: from chimera import specifier sel.merge(selection.REPLACE, specifier.evalSpec(":LYS")) nearRes = [] sel2 = selection.ItemizedSelection() for r in sel.residues(): sel2.clear() sel2.add(r) sel2.merge(selection.REPLACE, specifier.zone(sel2, specifier.ATOM, None, 8.0, models)) selRes = [sr for sr in sel2.residues() if sr.type == "LYS"] selRes.remove(r) nearRes.extend(selRes) sel.clear() sel.add(nearRes) Since the remailer for this list may break long lines, I've also attached the above as a file. If you are using the X11 version of Chimera for the Mac, pasting in the text is tricky -- if you're using that let me know and I can send instructions about how to get the pasting to work. --Eric On Oct 30, 2007, at 10:50 AM, Virginia Pett wrote: > Eric, > Yes, my ultimate goal is more complicated than the examples that I > gave. I would like to find all the Lys residues in the structure > that are less than 8 Å apart from each other. After several hours > of frustration with the Selector Construction Panel, I decided to > try a simpler question in order to test whether I was using the > Workbench correctly and to test whether any information was being > saved. > > I may not have understood your reply correctly. Here is what I > tried just now. I selected all atoms NZ (@NZ). THEN I invoked the > Selector Construction Panel. (In my previous experiments, the > Construction Panel had been invoked before I made the selection in > the main window.) Then I proceeded as before, in the Selector > Construction Panel: Workbench, Load from current. The Status panel > shows workbench content: Existing Selection. Then Workbench, > Save, as All NZ atoms, for example. However, as before, when I go > back to the main window, Select, Clear Selection and then Select > All NZ atoms, there is nothing selected. > > Virginia > > > > > On 10/25/07 7:56 PM, "Eric Pettersen" <pett(a)cgl.ucsf.edu> wrote: > >> Hi Virginia, >> Perhaps you could describe what your ultimate goal here is -- >> there may be an easier way to achieve it than by constructing a >> custom selector. >> But in regards to your problem, for the purposes of selector >> construction the "Existing Selection" isn't what is selected at >> that instant -- it's what's selected at the time the selector is >> invoked from Chimera's Select menu. This allows you to build >> selectors that intersect the peptide backbone with the current >> selection for example. >> If you want to make a selector that simply holds what's currently >> selected, use the Name Selection... entry in Chimera's Select >> menu. That creates a selector under Named Selections in the >> Select menu, and will also be remembered in saved sessions. >> >> --Eric >> >> >> Eric Pettersen >> >> >> UCSF Computer Graphics Lab >> >> >> pett(a)cgl.ucsfedu >> >> >> http://www.cgl.ucsf.edu >> >> >> >> On Oct 25, 2007, at 2:22 PM, Virginia Pett wrote: >> >>> Hello, >>> There is a difficulty with the Selector Construction Panel. I >>> make a selection in the main window, such as chain A or atom >>> @NZ. The Inspect Selection panel shows that I have made a >>> selection. Then in the Selector Construction Panel: Workbench, >>> Load from current. The Status panel shows workbench content: >>> Existing Selection. Then Workbench, Save, as chain A, for >>> example. However, when I go back to the main window, Select, >>> Clear Selection and then Select, chain A, there is nothing selected. >>> >>> I downloaded the latest version of Chimera for Mac OS X a few >>> days ago (chimera-1.2422-osx_x11.dmg). I’m running it on a >>> PowerBook G4 with Mac OS X (10.4.10). >>> Virginia >>> _____________________________________________________ >>> >>> Virginia B. Pett >>> Professor of Chemistry >>> Department of Chemistry, The College of Wooster >>> 943 College Mall, Wooster, OH 44691 >>> Telephone: 330-263-2114 >>> Fax: 330-263-2386 >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://wwwcgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> > > > _____________________________________________________ > > Virginia B. Pett > Professor of Chemistry > Department of Chemistry, The College of Wooster > 943 College Mall, Wooster, OH 44691 > Telephone: 330-263-2114 > Fax: 330-263-2386 >

1 0

request regarding atomspec balloon
by Jean Didier Pie Marechal 26 Oct '07

26 Oct '07

Hi Everyone, long time no...written... I observed that the "show atomspec balloon" does appear when I point an atom with the cursor. I have the preferences well set but I can't have it working. I use the last build (25 october) and I work on windows XP. 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

2 1

Cartoon: Helix appearance
by kroneml＠hotmail.de 26 Oct '07

26 Oct '07

Hello, I observed that Chimera (like almost all other protein viewers) aligns the ribbon of a helix in a way that the ribbon is parallel in every twist (the ribbon virtually forms a cylinder). My question is: is this correct, strictly speaking? I thought that the ribbon should lie in the plane defined by two successive C-alpha atoms and the associated O atom? (Mike Carson defines it that way in his "Ribbons", following the instructions of Richardson's "The anatomy and taxonomy of protein structure"). If you draw it that way, the ribbon forming the helix will tilt slightly outwards. Is the alignment of the helix ribbon in Chimera done simply because it looks better this way or is there another reason? I did some research on this topic via google and even asked a certified biologist (scientific assistant), but the internet had not much to say about it and the biologist only told me that cartoon drawings don't have to be very accurate, since they are only a tool to get a general idea of the protein's structure. Best regards, Michael Krone

2 2

Selector Construction Panel
by Virginia Pett 25 Oct '07

25 Oct '07

Hello, There is a difficulty with the Selector Construction Panel. I make a selection in the main window, such as chain A or atom @NZ. The Inspect Selection panel shows that I have made a selection. Then in the Selector Construction Panel: Workbench, Load from current. The Status panel shows workbench content: Existing Selection. Then Workbench, Save, as chain A, for example. However, when I go back to the main window, Select, Clear Selection and then Select, chain A, there is nothing selected. I downloaded the latest version of Chimera for Mac OS X a few days ago (chimera-1.2422-osx_x11.dmg). I¹m running it on a PowerBook G4 with Mac OS X (10.4.10). Virginia _____________________________________________________ Virginia B. Pett Professor of Chemistry Department of Chemistry, The College of Wooster 943 College Mall, Wooster, OH 44691 Telephone: 330-263-2114 Fax: 330-263-2386

2 1

post minimization energy report?
by Alec Zander 25 Oct '07

25 Oct '07

Hello! New to the software and this list. Looks great! I minimized a structure, and I'm seeing the changes afterwards. However, I also want to see an output file with a detailed energy report on the stability and what terms contributed how much, like at the end of a CHARMM run (which is what I've used almost exclusively till now). Any pointers? Thanks, Alec

2 1

Atom does not have a type
by Francesco Pietra 24 Oct '07

24 Oct '07

Thanks to Eric Pettersen I have fixed problems of long bonds and mis-assignement by prepare_amber.pl (from HIS to HIE, while it is HID). Two types of problems remain because I was either unable to correct or did wrongly. The error log from attempted fixing problems: WARNING: The unperturbed charge of the unit: 24.000000 is not zero. FATAL: Atom .R<GLH 443>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 402>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 386>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 375>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 373>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 334>.A<H 14> does not have a type. FATAL: Atom .R<GLH 332>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 291>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 275>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 264>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 262>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 223>.A<H 14> does not have a type. FATAL: Atom .R<GLH 221>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 180>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 164>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 153>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 151>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 128>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 112>.A<H 14> does not have a type. FATAL: Atom .R<GLH 110>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 69>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 53>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 42>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 40>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 17>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 1>.A<H 14> does not have a type. UNABLE : I don't know how to rename the hydrogen on serine nitrogen. In my protein.pdb, the section around residues 333/334: ATOM 5155 O THR X 333 15.694 -15.150 25.132 0.00 0.00 O TER 5156 THR X 333 ATOM 5157 N SER X 334 -16.176 22.312 10.940 0.00 0.00 N ATOM 5158 H SER X 334 -15.301 22.760 10.966 0.00 0.00 H ATOM 5159 CA SER X 334 -16.224 20.932 11.429 0.00 0.00 C ATOM 5160 HA SER X 334 -17.198 20.770 11.905 0.00 0.00 H ATOM 5161 CB SER X 334 -15.868 19.959 10.306 0.00 0.00 C ATOM 5162 HB2 SER X 334 -15.761 18.918 10.709 0.00 0.00 H ATOM 5163 HB3 SER X 334 -14.903 20.280 9.956 0.00 0.00 H ATOM 5164 OG SER X 334 -16.906 19.973 9.300 0.00 0.00 O ATOM 5165 HG SER X 334 -16.948 20.844 8.983 0.00 0.00 H ATOM 5166 C SER X 334 -15.185 20.856 12.533 0.00 0.00 C ATOM 5167 O SER X 334 -14.212 21.643 12.566 0.00 0.00 O Actually, I only inserted "TER" (where it is now) between residue 333 and 334 to get rid of a long bond between the two; numbering and THR X 333 came out automatically. Also, automatically the pdb file now begins with a series of HELIX. BADLY DONE: to correct for the carboxyl hydrogen being on the wrong oxygen of ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the section ATOM 6851 CD GLU X 443 -10.347 20.009 21.724 0.00 0.00 ATOM 6852 OE1 GLU X 443 -10.341 20.227 23.079 0.00 0.00 ATOM 6853 OE2 GLU X 443 -10.192 20.919 20.907 0.00 0.00 ATOM 6854 HE1 GLU X 443 -10.239 21.145 23.232 0.00 0.00 was rewritten by exchanging two lines, which automatically were renumbered ATOM 6854 CD GLH X 443 -10.347 20.009 21.724 0.00 0.00 C ATOM 6855 OE1 GLH X 443 -10.341 20.227 23.079 0.00 0.00 O ATOM 6856 OE2 GLH X 443 -10.192 20.919 20.907 0.00 0.00 O ATOM 6857 HE1 GLH X 443 -10.239 21.145 23.232 0.00 0.00 H ATOM 6858 C GLH X 443 -13.205 16.911 22.895 0.00 0.00 C and the issue on prepare_amber.pl was not resolved. It is obvious that I am carrying out such adjustments for the first time. I got the impression that from now on, what I do increases the mess. Must say that with my imperfect pdb I could carry outt all DOCK tutorials, except the amber_score. Thanks francesco pietra __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [Chimera-users] Atom does not have a type
by Francesco Pietra 24 Oct '07

24 Oct '07

Elaine: Yes, I need the mol2 file for the scoring grid, though I also wanted what I thought to be a fixed pdb, may be for amber_scoring, or Amber MD. While I'll try to do better on the basis of your observations, I am attaching the log file, should it help the diagnosis. I was quite surprised by the query on total charges, suspecting that it arose from some fault doing from my side. Is it a documentation of the pdb format adopted by Chimera? In an attempt to discover non adherence to the pdb format (if that does not emerge from attached the error log), that would help me. Antechamber found no problems with the ligands, though big and complicated. Thanks francesco ----- Original Message ---- From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Francesco Pietra <chiendarret(a)yahoo.com> Cc: chimera BB <chimera-users(a)cgl.ucsf.edu> Sent: Wednesday, October 24, 2007 6:19:26 PM Subject: Re: [Chimera-users] Atom does not have a type Hi Francesco, I don't know the details of your structure, but here are a few thoughts. There must still be atom name errors or missing atoms, because you are getting nonintegral charges. > > On saving mol2, 1 model(s) had non-integral charge. I loaded this > mol2 file to > Chimera and saved as pdb. - Do not save Mol2 format and then read it in and write out again as PDB if you want PDB format. If you save Mol2 with SYBYL atom names, for example, you will have the wrong names when you change it into PDB format. Maybe that is part of the problem. The reason Dock Prep has the option to save Mol2 is that you may need this format to calculate the scoring grid for DOCK. If you want PDB format, just save PDB format after using Dock Prep (File.... Save PDB). > (I was unable to command the > visualization in Chimera of a particular residue, say THR 444. > Command :THR:444 > returned all THR. - to specify just residue 444, don't say THR... for example display :444 means display residue 444 display :444.x means display residue 444 in chain X only display :thr means display all THR display :thr:444 means display all THR and also residue 444 > (6) Running Dock-Prep (all selected, except "Delete non-complexed > ions"; also > consider H-bonds; residue name HID specified. > A query was presented (in SYBYL naming) that I did not find where > to get help > about; therefore, I accepted the charge settings as it was presented: > > ASH + ALA + ASN +0 > > ASH + ALA + PRO +0 > > ASH + GLY + MET +0 > > GLH + ARG + LEU (w/HE2-1) +1 > > GLH + ARG + LEU (wo/HE2-1) +0 > > GLH + ARG + THR (w/1H-3) (wo/OXT-3) +1 > > GLH + ARG + THR (w/OXT-3) (wo/1H-3) +0 - I don't understand what you mean here by SYBYL naming or these charges. Shouldn't GLH, LEU, and THR always be 0 (except at the termini, as you said) and ARG always be +1? Also, it should not be asking you about the charges for standard residues. There must be some naming or formatting error that causes the program to think these are nonstandard residues. For the residues with nonintegral charges, there should be messages about which atoms are not recognized, or if there are no such messages, they must be missing some of their atoms. 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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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About Chimera subscribe
by Francesco Pietra 22 Oct '07

22 Oct '07

Elaine: While using Chimera (to which I was already subscribed on a personal basis) I was asked to subscribe as 15-days trial had elapsed. I though I had to do to be able to continue using Chimera. Then I received two messages, one to confirm, the other one warning as reported below. This mail simply because I suspect there is a bug in the subscribing service. Regards francesco pietra WARNING MESSAGE: An attempt was made to subscribe your address to the mailing list chimera-users(a)cgl.ucsf.edu. You are already subscribed to this mailing list. Note that the list membership is not public, so it is possible that a bad person was trying to probe the list for its membership. This would be a privacy violation if we let them do this, but we didn't. If you submitted the subscription request and forgot that you were already subscribed to the list, then you can ignore this message. If you suspect that an attempt is being made to covertly discover whether you are a member of this list, and you are worried about your privacy, then feel free to send a message to the list administrator at chimera-users-owner(a)cgl.ucsf.edu. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [Chimera-users] Chimera-users Digest, Vol 54, Issue 16
by Jonathan Hilmer 18 Oct '07

18 Oct '07

Regarding Chimera movies in PowerPoint: I'm not sure exactly what the end result is like on a Mac, but using a standard Windows setup, PowerPoint will degrade the quality of any movie that you just drop into it. I haven't investigated exactly why this occurs, but it is noticeable. I was able to restore the full quality by embedding a Windows Media Player object into the PowerPoint file, with VB code that loads the movie of interest by default. This might not be an option for a Mac, but perhaps someone else might find it useful: I can give details on the method if anyone would like. As a useful secondary effect, by using an absolute pointer to the movie file rather than an embedded (and relative) link to the directory and file as PowerPoint usually stores, you can place movies in a central repository via http server: this makes it possible to have smaller, more mobile PowerPoint files that don't require a full copy of every included embedded movie. Regarding the quality of output from Chimera, it is possible to composite movies from individual frames. It's not a simple method, but it does remove all limitations on resolution, sampling, etc, and simplifies post-processing as well. One example of a Chimera-produced movie that might not have been possible another way can be found on our server (11MB, mpeg-4): ftp://guest@dratz2.chemistry.montana.edu/capsid_visuals/movies/non-capsid/20060401_both_02.zip Jonathan > Hi > > We have just installed Chimera on a MacPro running OS X 10.4. I would > like to be able to record simple movies of rotating peptides for use in > PowerPoint ( 2003) presentations. > > I have been able to record and insert the avi format into PowerPoint > and the movie does play correctly. But I am noticing a considerable > loss in resolution as compared to the original molecule in Chimera. > > Is there some adjustment I should be making in Movie Recorder to improve > the image resolution? > > Should I be running POV-Ray on these files? > > Thanks for any suggestions. > > > Gene > > (Eugene Coats)

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Model loops with modeller-chimera error
by Gatsogiannis, Christos 18 Oct '07

18 Oct '07

i'm getting this error when i try to run the "model loops"-tool: Error processing trigger "check for changes": TypeError: coercing to Unicode: need string or buffer, Popen found (see reply log for Python traceback info) and the progress-monitor stays by 0% - My chimera version is 1.2422 and my modeller version is 9v2 Thanks in advance Christos ################################################# Gatsogiannis Christos Dipl. Biol. Johannes Gutenberg University Mainz Institut of Zoology cryoEM-Lab +49-6131-39-23091 gatsogia(a)uni-mainz.de #################################################

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Questions on recording movies for use in PowerPoint
by Coats, Eugene 18 Oct '07

18 Oct '07

Hi We have just installed Chimera on a MacPro running OS X 10.4. I would like to be able to record simple movies of rotating peptides for use in PowerPoint ( 2003) presentations. I have been able to record and insert the avi format into PowerPoint and the movie does play correctly. But I am noticing a considerable loss in resolution as compared to the original molecule in Chimera. Is there some adjustment I should be making in Movie Recorder to improve the image resolution? Should I be running POV-Ray on these files? Thanks for any suggestions. Gene (Eugene Coats)

2 2

Non-standard atom names
by Francesco Pietra 18 Oct '07

18 Oct '07

Problems with atom names in preparing a protein for docking. The protein (K ion channel) was obtained as monomer from Protein Data Bank and then as tetramer from Protein Quaternary Structure database through Chimera Fetch ID. The tetramer was stripped to leave --Two helices --Selectivity filter --Pore helix Prepare with Chimera 1.2422 (I had previously carried out successfully the tutorial) along defaults Tools .. Strct edit .. Dockprep All selected except "Delete non-complexed ions" Add hydrogens (also consider H-bonds) To write mol2 use untrasnformed coordinates; use Sybyl type H naming; write current selection to @SETS, Save reported: Correct charges are unknown for 15 non-standard atom names in otherwise standard residues (charges 0.0 assigned to these atoms. 1 model had non integral total charge. Looking at the mol2 file, I could only identify nine type of atoms assiggen 0.0000 charge: H, HD1, HD2, HE1, HE2, HG1, HG2, HH1, HH2 such as (for a small initial portion): 2 H .... 1 SER1 50 HD1 ... 4 LEU4 95 HD1 .... 7 LEU7 97 HD2 ... 7 LEU7 135 HG2 ... 10 THR10 150 HD1 ..... 11 LEU11 168 HE2 .... 12 GLN12 226 HH1 ... 16 ARG16 259 HD2 ... 18 LEU18 279 HD1 ... 20 LEU20 281 HD2 .. 20 LEU20 294 HD1 ... 21 LEU21 296 HD2 ... 21 LEU21 306 HG2 ... 22 ILE22 308 HG1 ... 22 ILE22 310 HD1 ... 22 ILE22 365 HD2 ... 25 LEU25 397 HG1 ... 27 ILE27 430 HG1 .. 30 ILE30 445 HD1 ... 31 LEU31 578 HE1 ... 40 GLU40 601 HD1 ... 42 ASP42 718 HG2 ... 51 ILE51 847 HG1 ... 59 VAL59 861 HG2 ... 60 VAL60 900 HG2 ... 63 THR63 926 HG2 ... 65 VAL65 974 HD1 ... 69 ASP69 1037 HG2 ... 73 ILE73 1039 HG1 ... 73 ILE73 1041 HD1 ... 73 ILE73 1063 HG1 ... 75 VAL75 Being new to these procedures, could you please indicate how to fix the issue? Thanks francesco pietra ____________________________________________________________________________________ Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/

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Lipid bilayer
by Francesco Pietra 12 Oct '07

12 Oct '07

How far (and how close to reality) can we go in building a lipid bilayer with Chimera for use with Amber and Dock? If possible, where to drop in Chimera? I mean a lipid bilayer for a model of ion channel, i.e. ca 30A thick. Thanks francesco pietra ____________________________________________________________________________________ Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545433

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Re: [Chimera-users] multalignviewer/4650 (associations dialog problem)
by Eric Pettersen 12 Oct '07

12 Oct '07

Hi Roberta, The bug you ran into is that the associations dialog wasn't handling non-polymer models correctly (some of your models had had all the protein removed, leaving just ligand). I've just put in enough of a fix so that your session can be used. If you get tomorrow's test build (following the "Test Builds" link off www.cgl.ucsf.edu/chimera) that will have the fix in it. It's not yet a complete fix because it only handles the case where you open the associations dialog _after_ the protein deletion has occurred (which is okay for you). I need to put in more work to make it handle the case where the deletion occurs after the associations dialog is open. When that fix is done you will get an automated mail about it as I change the bug report from "open" to "internal-fix" -- and then it will be available in the next test build. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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molecular modelization softwares
by DESPLAT Nelly 11 Oct '07

11 Oct '07

Dear sir or madam, I am currently studying at the Université Paul Sabatier of Toulouse (France), in a Bioinformatics program (master degree) and I have a report to write, concerning molecular modelization softwares. Could it possible to obtain additional informations about your software Chimera? I would like to know its price, the price of an additionial module, and also how its maintenance work. I thank you ahead of time for your help. Sincerely. Nelly DESPLAT _____________________________________________________________________________ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail

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Visualizing an ion channel
by Francesco Pietra 11 Oct '07

11 Oct '07

Hi Elaine: Perhaps trivial, though new for me: How to assemble reliably the essentials (to get the teepee) of the four alpha subunits of an ion channel when the Protein Data Bank gives the pdb file for one on the subunits? For example 2A79, a mammalian Kv1.2 ion channel. Thanks francesco pietra ____________________________________________________________________________________ Check out the hottest 2008 models today at Yahoo! Autos. http://autos.yahoo.com/new_cars.html

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Chimera POVRAY and Vista?
by Frank Neese 09 Oct '07

09 Oct '07

Dear Chimera team, First of all congratulations for a really nice program and thank you very much for making it available to the community! I like it a lot. I was nevertheless running into a problem when trying to create povray pictures on a windows vista PC. Is there anything i can do about it? With my best regards, sincerely yours, Frank Neese The output is below: running "C:\Program Files\Chimera\bin\povray.exe" "d:\HomeD\Research\Bonn\COLLAB - Gross\image.ini" "+Id:\HomeD\Research\Bonn\COLLAB - Gross\image.pov" "+Od:\HomeD\Research\Bonn\COLLAB - Gross\image.png" "+V" povray: cannot open the user configuration file C:\Users\neese\AppData\Roaming/.povray/3.6/povray.conf: No such file or directory povray: I/O restrictions are disabled. povray: cannot open an INI file, creating a temporary file 'C:\Users\Public\Desktop/pov36.ini'. povray: cannot write to C:\Users\Public\Desktop/pov36.ini: Permission denied Persistence of Vision(tm) Ray Tracer Version 3.6.1 (cl /nologo /Zc:forScope /Op- /GRX /EHc- /GF /G7 /MD /Zl /O2i) This is an unofficial version compiled by: UCSF Chimera <chimera(a)cgl.ucsf.edu> The POV-Ray Team(tm) is not responsible for supporting this version. POV-Ray is based on DKBTrace 2.12 by David K. Buck & Aaron A. Collins Copyright 1991-2003 Persistence of Vision Team Copyright 2003-2004 Persistence of Vision Raytracer Pty. Ltd. Primary POV-Ray 3.5/3.6 Developers: (Alphabetically) Chris Cason Thorsten Froehlich Nathan Kopp Ron Parker Contributing Authors: (Alphabetically) Steve Anger Eric Barish Dieter Bayer Steve A. Bennett David K. Buck Nicolas Calimet Aaron A. Collins Chris Dailey Steve Demlow Andreas Dilger Alexander Enzmann Dan Farmer Mark Gordon Christoph Hormann Mike Hough Chris Huff Kari Kivisalo Lutz Kretzschmar Jochen Lippert Pascal Massimino Jim McElhiney Douglas Muir Juha Nieminen Bill Pulver Eduard Schwan Wlodzimierz Skiba Robert Skinner Yvo Smellenbergh Zsolt Szalavari Scott Taylor Massimo Valentini Timothy Wegner Drew Wells Chris Young Other contributors are listed in the documentation. Support libraries used by POV-Ray: ZLib 1.2.3, Copyright 1995-1998 Jean-loup Gailly and Mark Adler LibPNG 1.2.16, Copyright 1998-2002 Glenn Randers-Pehrson LibJPEG 6b, Copyright 1998 Thomas G. Lane LibTIFF 3.8.0, Copyright 1988-1997 Sam Leffler, 1991-1997 SGI Redirecting Options All Streams to console..........On Debug Stream to console.........On Fatal Stream to console.........On Render Stream to console........On Statistics Stream to console....On Warning Stream to console.......On Parsing Options Input file: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov (compatible to version 3.61) Remove bounds........On Split unions.........On Library paths: C:\Program Files\Chimera\share\fonts Output Options Image resolution 512 by 384 (rows 1 to 384, columns 1 to 512). Output file: d:\HomeD\Research\Bonn\COLLAB - Gross/image.png, 24 bpp PNG Graphic display......On (gamma: 2.2) Mosaic preview.......Off CPU usage histogram..Off Continued trace......Off Tracing Options Quality: 9 Bounding boxes.......On Bounding threshold: 1 Light Buffer.........On Vista Buffer.........On Draw Vista Buffer....Off Antialiasing.........On (Method 1, Threshold 0.300, Depth 3, Jitter 1.00) Clock value: 0.000 (Animation off) 0:00:00 Parsing File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Possible Parse Error: Could not find file 'transforms.inc' File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 File Context (5 lines): #include "transforms.inc" global_settings { charset utf8 max_trace_level 10 } Parse Error: Cannot open include file transforms.inc. File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Parse Warning: Check that the file is in a directory specifed with a +L switch or 'Library_Path=' .INI item. Standard include files are in the include directory or folder. Please read your documentation carefully. Total Scene Processing Times Parse Time: 0 hours 0 minutes 0 seconds (0 seconds) Photon Time: 0 hours 0 minutes 0 seconds (0 seconds) Render Time: 0 hours 0 minutes 0 seconds (0 seconds) Total Time: 0 hours 0 minutes 0 seconds (0 seconds)

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Re: [Chimera-users] surface/4623 (Chimera surfacing failure)
by Eric Pettersen 09 Oct '07

09 Oct '07

Hi Jeff, Chimera doesn't communicate depth-cuing/fog info to POV-Ray yet. I will open a bug report about it with you included on the recipient list. What you may want to do in the interim to get a better looking image is to reposition the lights in the scene to reduce the shadows. You use Tools->Viewing->Lights to bring up the interface for position the key (bright) and fill (dim) lights. I've attached two images where I've done that. In both the key light is just slightly overhead and centered. The fill light in one is coming from slightly below and centered, and in the other the fill light is off (you have to go to the "advanced" section of the lighting interface to turn off lights). --Eric

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Re: [Chimera-users] dock-prep problem with Zn and K ions
by Eric Pettersen 08 Oct '07

08 Oct '07

Hi Joe, If you care about the protonation of the SHH ligand in that structure then I would actually recommend you use one of the new test builds (follow the "Test Builds" link off the Chimera home page). There have been improvements since the 1.2422 release in protonating atoms involved in coordination complexes, and in protonating ring nitrogens in non-standard residues (though the latter isn't directly relevant in your case). --Eric On Oct 8, 2007, at 12:17 PM, zzj wrote: > Hi Eric, > Sorry for the mess. The old Chimera version is 1.2259. > I just downloaded the latest version (1.2422). It works perfectly fine > the same PDB. Guess I'll stick to this version. > thanks a lot. > -Joe > > On 10/8/07, zzj <zzjsail(a)gmail.com> wrote: >> Hi Eric, >> thanks for your reply. I am using PDB 2PQO. The Chimera version is >> beta version 1 build 2259 2006/07/11 >> platform: darwin >> windowing system: aqua >> I am working on a Mac OS X 10.4.10 (G5). It seems Chimera works fine >> other than the problem I mentioned. >> -Joe >> >> On 10/8/07, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> I can run Dock Prep on a PDB file containing zinc (1zip) without >>> the problem >>> you're getting. Can you tell me what PDB you're using, and what >>> version of >>> Chimera? >>> >>> --Eric >>> >>> >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu >>> >>> http://www.cgl.ucsf.edu >>> >>> On Oct 8, 2007, at 10:54 AM, zzj wrote: >>> >>> Hi there, >>> I am preparing dock6 files in Chimera using the Dockprep option. The >>> Zn and K ions in the PDB files are giving me problems at the >>> point of >>> adding hydrogen. Everthing works fine if I remove these ion atoms. >>> Here is the Chimera Error message: >>> AttributeError: addHinfoDialog instance has no attribute >>> "cancerlCB". >>> I can select and highlight these ions without problem. I tried to >>> give >>> different names for the ions. Nothing worked. >>> Any suggestion is highly appreciated! >>> -Joe >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>

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dock-prep problem with Zn and K ions
by zzj 08 Oct '07

08 Oct '07

Hi there, I am preparing dock6 files in Chimera using the Dockprep option. The Zn and K ions in the PDB files are giving me problems at the point of adding hydrogen. Everthing works fine if I remove these ion atoms. Here is the Chimera Error message: AttributeError: addHinfoDialog instance has no attribute "cancerlCB". I can select and highlight these ions without problem. I tried to give different names for the ions. Nothing worked. Any suggestion is highly appreciated! -Joe

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End graphical representation from Dock tutorials
by Francesco Pietra 08 Oct '07

08 Oct '07

I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The relevant files used for, and got from, the flexible-ligand docking tutorial are attached. I believe I used defaults. The out file attached is the one of the four out files (from mpirun -np 4 ....) that seems to me to be relevant. How to view graphically the best scored ligand from flex_scored.mole2 in the protein? Just combine flex_scored.mole2 with the ligand-deprived receptor? This in view of my project of looking for docking between a family of lypophilic natural products (conformationally studied in vacuum with Amber9 simulated annealing) and a complex, large protein. I.e., by carrying out a process of the type illustrated by the docking tutorial for each pocket of the protein. I know there is interaction between the two (though a mere disassembling of the lipid bilayer can't be rigorously ruled out yet) but no idea where. Thanks francesco pietra ____________________________________________________________________________________ Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658

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Protein RMSD
by Elaine Meng 05 Oct '07

05 Oct '07

Hi John and everybody, I forgot to mention the following additional ways to calculate RMSD in Chimera if you are working with a conformational ensemble (different conformations/configurations of the same set of atoms): - if the ensemble is opened as a trajectory in MD Movie, you can calculate an all-by-all RMSD map http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (go to the "RMSD Analysis" section) ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 - if the ensemble is present as multiple MODELs within a single PDB file opened the normal way in Chimera, you could use the EnsembleMatch tool http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembletut.html I don't know if these pertain to the original question, but I mention them for completeness. 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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Generating Spheres tutorial
by Francesco Pietra 05 Oct '07

05 Oct '07

I am running Chimera 1.2422 on a Linux desktop and DOCK6.1 and DMS on a scp-linked Linux parallel machine. Following the "Generating Spheres" tutorial of dock, I verified that DMS works correctly. Though, I am unable with Chimera to visualize properly the rec.ms and sphere_cluster.pdb (the files I have generated are identical to those downloaded). With rec.ms I am unable to visualize the small molecule inside the protein. With sphgen_cluster.pdb I can only see disconnected pieces, thogh placed as expected from the tutorial. Clearly, I need to pass to a Chimera tutorial. Which one(s) for the case in point? I apologize for the pedestrian questions. Though, coming from organic chemistry and ab initio calculations, I am finding Amber9, DOCK6.1, DMS, and Chimera no minor burden. Quite interesting, however. Thanks francesco pietra ____________________________________________________________________________________ Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC

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Re: [Chimera-users] How to "Align" two atoms
by Thomas Goddard 04 Oct '07

04 Oct '07

Hi Matt, Many Chimera commands are defined in chimera/share/Midas/__init__.py They are sometimes a pain to call from Python. Here is some code for the align command. Tom from chimera import openModels, selection m = openModels.list()[0] sel = selection.ItemizedSelection() sel.add(m.atoms[0:2]) from Midas import align align(sel) Matthew Baker wrote: > I'm writing a module. I've created a model and added it to the open > models. How can I reproduce the command-line function > > align #1:1 #1:2 > > The variable names for my two atoms are newModel.atoms[0] and > newModel.atoms[1]. > > Thanks, > Matt >

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Fit map in map
by src9697 04 Oct '07

04 Oct '07

Hello, I was just searching the archieves and I understand now that my last question was alittle dumb (i.e. the x,y,z rotation angles are not helpful). In this case does the "Rotation angle" and the " Axis" define a single rotation that transforms the "Fit map" to the "with in" map. Can I draw the axis using a .bild file (i.e .arrow with start and end coords given by axis and axis point). if I want to compare several maps to one reference, is it possible to define a single axis for them all? such that i can compare them all just by the magnitude of the rotation? does this make sense? thanks in advance sean

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Fit map in map
by src9697 04 Oct '07

04 Oct '07

Hello, I was wondering if it is possible to use the output (translation matrix, axis, ect.) from the "Fit map in map" command to obtain the angles of rotation around the x, y and z axis given an arbitrary origin (i.e. the center of the map). thanks sean

1 0

Protein RMSD
by Beale, John 03 Oct '07

03 Oct '07

Is there any feature in Chimera that will allow the calculation of the RMSD between a protein and a reference structure? Thanks! John Beale

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updating hydrogen bonds in an MD movie
by E. Merkley 03 Oct '07

03 Oct '07

Hi Chimera crew, I am using chimera to visualize an MD trajectory. I want to look at the fluctuations of hydrogen bonding patterns in a helix over the course of the trajectory. Is there a way to use Find HBonds on each frame and display the updated pseudobonds as I view the movie in Chimera? Also, may I take this occasion to point out that requiring consecutive frames to have consecutive numbers in the file names is inconvenient. For instance, my simulation is 41 ns long, and the structures are stored (in our in-house format) every 1 ps. So rather then write out 41000 .pdb files, I'll write them out every 10 or 100 ps. To use chimera to view a movie, I have to rename the files using a perl script. Incidentally, I've been using Chimera for 3 years now and love it. -Eric Merkley Graduate student Biochemistry Department University of Washington

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chimera instalation
by Paola Beassoni 03 Oct '07

03 Oct '07

Dear all, i have downloaded chimera 1.2422 for linux and i don know hoe to install it. I have OpenSUSE but i am really new in linux. I have the file "chimera-1.2422-linux.exe" but i don know how to run it. My shell doen recognizes the command "run". So, please if anyone can help me i would really appreciate it. Best Regards Paola -- Paola Beassoni - PhD Dpto. Biologia Molecular - FCEFQyN Universidad Nacional de Rio Cuarto Río Cuarto - Argentina 00-54-358-4676422 00-54-358-4676232 (Fax)

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chimera for Amber9
by Francesco Pietra 02 Oct '07

02 Oct '07

Having installed DOCK6.1/DMS (debian Linux parallel amd64) and Chimera 1.2422 (scp-linked desktop Debian Linux i386), may I ask: 1) Can I use Chimera for Amber9 in place of VMD, which I currently use? 2) Being superficially familiar with VMD, I was looking in Chimera for *.prmtop and *.inpcrd file types, as well as rst file, etc.. I suppose I was unable to turn Chimera to use with Amber9. That said, I was very much impressed by Chimera at the first touch. Thanks francesco pietra ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469

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Setting camera viewpoint
by Thomas Goddard 01 Oct '07

01 Oct '07

Hi Matt, There is no Chimera command to set the camera. But there are commands to orient and position the displayed models precisely (turn, move, scale, cofr, clip, savepos, reset). The Chimera world keeps the camera fixed and moves the models. If you want to use Euler angles there is a plugin to do that called Transform Molecule Coordinates available at: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom Matthew Baker wrote: > Tom, > > Is there a way of specifying a camera position and a viewing angle from > the command line in chimera. I want to make a few snapshots of a > molecule (actually, several different PDBs) with very specific view angles. > > Thanks > > Matt

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Frozen chimera
by hsosa＠aecom.yu.edu 28 Sep '07

28 Sep '07

I have the following problem: When rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash, the blue screen appear and a whole reboot is needed. The problem most likely is graphic card related. I did reported it before and was suggested to change the driver. I did but it did not solve the problem. My system currently is as follow: Chimera 1.2422 Windows XP service pack-2 Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.0027.05 ForceWare version: 78.01 Before I had: ForceWare version 91.36 So both of these video driver had problems. I wonder if anybody has experienced something similar and found the right driver. Thanks Hernando

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reconstructing x-ray structure
by Nevin Gerek 27 Sep '07

27 Sep '07

Hello, I am wondering if there is an option in Chimera to reconstruct exact place for binding peptide. I do have x-ray structures and binding peptide was incorporated as a C-terminal extension. When I used these structures, I do not get protein-peptide contact information in our model. Is there any way to reconstruct x-ray structure data with the right peptide binding information? Any help would be appreciated. Thanks. Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek(a)asu.edu

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sgi core dump
by bala 27 Sep '07

27 Sep '07

Dear chimerians, Goodday. I installed the latest-chimera for sgi irix. Installation was completed successfully. But when i give chimera, it throws the following core.. Kindly write me how to get rid of the same. ce/BPT/RangeErr/DivZero/Ovflow trap (core dumped) thanks, Bala

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Docking of PDB data
by Alexander Solodukhin 19 Sep '07

19 Sep '07

Dear Listers, I have got the CCP4 3d map of PKC created from tilted series of 2d crystals grown on lipid monolayers. Unit cell: a=b=53A, alpha=beta=90 deg and gamma=120 deg. X-rays 3d structures of three fragments: C1b, C2 of the regulatory domain and catalytic domain are available from PDB data bank. When I try to dock PDB files or their maps created with SPIDER or SITUS programs by the use of 'fit models in maps' or 'fit maps in maps' in CHIMERA, programs place this fragments into one only place around the point that looks like a 'center of gravity' of CCP4 model. If I cut off the part of model where this point is, anyway program places these fragments into the same point out of the selected subregion. How can I fix this problem? I understand that I have to assign the same origin of coordinates for my model and fragments, but I do not know how to do this. Alexander Solodukhin, Ph.D. Department of Anesthesiology University of Virginia Health System P.O.Box 800710 Charlottesville VA 22906-0710

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Molecular surface crash
by Thomas Goddard 13 Sep '07

13 Sep '07

Hi Markus, I computed a molecular surface for the PDB file you gave me by changing the probe radius from 1.4 A to 1.399 A. I set the new probe radius using the "New Surface" category of the Preferences dialog (menu Favorites / Preferences). The "New Surface" category was added in Chimera 1.2430 (July 23, 2007) so you'll need the newest Chimera snapshot on Linux http://www.cgl.ucsf.edu/chimera/download.html#snapshots or a weekly Chimera build (very latest code) on other platforms (Mac, Windows) http://www.cgl.ucsf.edu/chimera/alpha-downloads.html New Chimera surface calculation code is still 6 months away. Tom Markus Voehler wrote: > Tom > > I have switched from my SGI to a RHEL 5 machine and see the same > behavior now on that computer as I have seen on the Mac. Some pdb files > do not seem to allow me to show the surface plot. This leaves me with no > option to display the surface for some pdb's. In the past I was just > doing this work on the SGI, which worked fine. I have tried your > suggestion about increasing the vdv radius again on the Linux box, but > it did not help either on this computer. Has there been any resolution > to the mentioned report 1295? > > I have deposited the pdb online, in case you want to reproduce the > problem on your cpu. The link is: > > [deleted] > > Any help is appreciated. > > Markus >

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When structures and density maps don't align
by Walter R.P. Novak 10 Sep '07

10 Sep '07

Hi All, Amongst my colleagues (to whom I constantly evangelize Chimera) there is often an issue opening pdb and map files together. Specifically, sometimes the maps and pdb coordinates are not superimposed (often drastically). I have been able to reproduce the issue so let me explain what works and what doesn't. What works: If you take a pdb file and an mtz into Phaser (from the ccp4 suite) then refmac for rigid body refinement and convert the output mtz to a map using mapman it works. The pdb and map superimpose perfectly. What doesn't work: If you take a pdb file (of known correct solution but not transformed to the correct coordinates) and throw it into refmac (ccp4) and do some rigid body refinement and then convert the resulting mtz into a ccp4 map, the map is perfectly good (the statistics are identical to using the phaser placed model), but when opened in Chimera they do not superimpose. Both of the methods above appear valid as far as structure determination (R and Rfree are identical, etc) and I know coot will align the model and map and I believe pymol will too, though I don't use pymol personally so I cannot vouch for that. Is the correct transformation information hidden in a file somewhere so that Chimera can align the two files automatically. Often people skip the phaser step and drop the model right into refinement and then manually aligning in Chimera becomes difficult. Best, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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Benchmark scores
by Thomas Goddard 10 Sep '07

10 Sep '07

Hi Gabor, Your Quadro FX 1500 benchmark scores are about the same as the fastest system we have seen. I'll add them to our benchmark web page today. http://www.cgl.ucsf.edu/chimera/benchmarks.html Thanks for sending the numbers. Tom Gabor Papai wrote: > Hi! > > The benchmark scores of my PC are: > > CPU Information > Processor (CPU): Intel(R) Core(TM)2 CPU 6600 @ 2.40GHz > Speed: 2 401,96 MHz > Memory Information > Total memory (RAM): 2,0 GB > Total Swap: 4,0 GB > > OS Information > OS: Linux 2.6.20-1.2952.fc6 i686 > System: Fedora Core release 6 (Zod) > > Display Info > Vendor: nVidia Corporation > Model: Quadro FX 1500 > Memory: 256 MB > > Benchmark scores > surface 839 mesh 809 contour 179 solid 435 recolor 161 > > Test was done: 07 Sept. 2007 > Chimera 2422 > > I don't know whether these scores are good or not, I'm not familiar with > them. > Bye, > Gabor >

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seelction around map
by Dhiraj Srivastava 07 Sep '07

07 Sep '07

Hi all Is there any way that we can select atoms or residues within some distance of a ccp4 map in chimera? i know tha we can select map within some distance of any selected atoms but can we do opposite and if yes then how? thank you Dhiraj -- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153

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MRC map values -128 to 127
by Tom Goddard 07 Sep '07

07 Sep '07

> Hi, > > I have some mrc files on a 64 bit linux machine (linux version > 2.6.9-42.0.8.ELsmp, x86_64) and the chimera on that machine displays the > volume data fine with a range from 3 to 255 and a histogram centered > around 120 and the 3D structure shows up very well with a threshold of > 108. But after I transfer these data to a mac os x 10.4.10 and use the > chimera on the mac, the data range becomes -128-127 with the histogram > splitted into two halves close to each end of the data range. What's > worse, I can not get a good threshold to show my 3D structure. Can you > please tell me what is possibly wrong and how to fix this? > > Thank you very much. > > Zhiheng Hi Zhiheng, The trouble with displaying your MRC files with Chimera is that the files contain unsigned 8-bit data values (0-255 range) and that format is not supported by the MRC standard. Only signed 8-bit data values (-128 to 127) is supported by MRC. So why does it work on your 64-bit linux Chimera and not the Mac Chimera? I believe that is because your Linux Chimera is an old version of Chimera. About one year ago (September 19, 2006, Chimera version 1.2290) I changed Chimera to follow the MRC standard and use signed 8-bit whereas earlier versions incorrectly assumed unsigned 8-bit values. Your Mac version of Chimera is probably newer and your Linux version older. The MRC file header gives no indication that the values should be unsigned 8-bit as that value type is not supported. But some software programs ignore that, use unsigned 8-bit values and set the MRC header field to indicate signed 8-bit. They rely on software to ignore the MRC standard. I added a way to work around this problem in newer versions of Chimera (Nov 29, 2006, version 1.2315). You open then MRC map then use the keyboard shortcut "u8" to reinterpret it as unsigned 8-bit. Then you will need to save the map with the volume dialog menu entry File / Save map as... if you want to avoid using u8 every time you open the map. Saving a map which is unsigned 8-bit will automatically use the signed 16-bit MRC mode. You probably should not overwrite your original file but instead make a new file. To use this u8 shortcut you first have to turn on shortcuts with Chimera menu entry Tools / General Controls / Accelerators On. Then you can type u8 in the main Chimera window. It operates on the map currently shown in the volume dialog so you can switch maps and apply it to other maps as well. You may also be interested in shortcut "Im" which inverts the map, mapping the range value v to (255-v). Tom

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Display axes for global frame of reference?
by Andrew D. Fant 07 Sep '07

07 Sep '07

Hello All, I'm considering using Chimera as my general purpose modeling graphics front-end and have run into a snag. I have a protein that I need to globally translate and rotate to move several residues to be oriented along the x, y, and z axes. In InsightII, there is an option to display the global coordinate system in the main graphics window, so that it's easy to manipulate a structure to a given orientation. Is there a way to display the global axes like that in Chimera, and is it possible to write out the transformed coordinates of a PDB file without a lot of difficulty? Thanks, Andy

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Chimera electrostatic potential
by Kate Hardie 07 Sep '07

07 Sep '07

Hi, I've been unable to figure out how to colour the electrostatic surface of a protein red/white/blue. I'm assuming that you have to some how assign electrostatic potential before colouring but how is this done? I'm using a Mac and I've tried to use apbs with pymol but it will not recognise my pqr file generated on the pdb2pqr server or generate it itself. Thanks, Kate

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Re: [Chimera-users] problem while readin .phi file
by Thomas Goddard 06 Sep '07

06 Sep '07

Hi Ula, I do not use DelPhi so I don't know what the "maximum number of radius records" means. But I don't think Amber can produce a DelPhi format electrostatics file, and your *.phi file probably does not open in Chimera because it is not the expected DelPhi format. An alternative to DelPhi for computing electrostatics is APBS. It is free and not too hard to use and Chimera will display its output. Tom Urszula Uciechowska wrote: > Hi Tom, > > I was trying to use DelPhi program but i am getting the error: > > maximum # of radius records exceeded > increase nrmax > FORTRAN STOP Do you know maybe how to get rid of it? > so i used amber to get phi file. > > Ula

2 1

benchmark scores
by Waterman, DG (David) 06 Sep '07

06 Sep '07

Hi, My info: Graphics - NVIDIA Quadro NVS 285 Processors - 2 Intel Pentium 4 Clock (MHz) - 3400 OS Type - Windows Surface - 261 Mesh - 116 Contour - 144 Solid - 110 Recolor - 95 Notes - Test Date - 04 sept 2007 Chimera Version - 2422 Machine - Dell Precision WorkStation 380 Graphics Memory (Mb) - 64 Main Memory (Mb) - 1024 OS Version - XP Professional, 5.1.2600 Service Pack 2 Build 2600 Driver Version - 7.1.8.4 Host name Dr. Dave's computer The machine isn't that bad, I guess it is let down by a poor graphics card. Cheers, D David Waterman Post-Doctoral Research Associate Macromolecular Crystallography +44(0)1235 778722 Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom <DIV><FONT size="1" color="gray">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom </FONT></DIV>

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soliciting chain-trace opinions
by Eric Pettersen 05 Sep '07

05 Sep '07

Hi all, Right now, if you do the "chain trace" action (or type "chain @ca") Chimera shows carbon alphas and any inter-residue connectivity of those residues, including disulfide linkages. I'd like to know if users generally like this behavior or would instead prefer a "strict" backbone-only trace, so I can determine whether to change the behavior, offer both alternatives, or leave things alone. This is only really relevant to the "trace" depiction since although the "full" and "minimal" backbone depictions also show disulfides, that can be turned off by turning off auto-chaining via the Model Panel, Selection Inspector, or "setattr" command*. So what do people think? --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu * in the setattr command you would be setting "autochain" to false.

1 0

selection of some chain but not some particular residue
by Dhiraj Srivastava 05 Sep '07

05 Sep '07

Hi All I am new to Chimera and i have hard time finding commands like how to select some chain and exclude 1 or 2 residue in that chain? also i have a protein with 2 chain. how can i make different model for different chain or different portion of same chain so i can perform some action like clipping on these model independentaly? can any one please help me for these problems? Thank you -- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153

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(no subject)
by Wang, Xuelin 05 Sep '07

05 Sep '07

Dear Chimera's users: I have a problem to make an Amber MD movie using Chimera. I am sure I used the right Amber top file and mdcrd file, since I can use VMD to display them. In my trajectory file, I already striped water and counter-ions. Only box information was left with trajectory. However, when I display trajectory, all trajectories were out of shape. I saw the similar thing when I used VMD to display the trajectory without including PBC option. I doubt that there is something wrong with box information. But I don't know how to fix it. Any ideas? Thanks Xuelin

2 1

problem while readin .phi file
by Urszula Uciechowska 05 Sep '07

05 Sep '07

Dear chimera users, I am trying to open my .phi file in chimera, but i am getting this message on the reply log: pbsa.phi: Record size at end of record 538976288 != size at head of record 20 it is becouse my file is too big? Thanks in advance! Ula -- MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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Vista compatibility
by Forbes J. Burkowski 30 Aug '07

30 Aug '07

Hi: Does anyone have any information about Chimera running on the Vista OS (specifically the 64-bit version)? Thanks in advance. Forbes Burkowski

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chimera on AMD workstation-> followup
by Vinay Kumar 30 Aug '07

30 Aug '07

Hello Tom and other list members, Your suggestion proved right. Chimera is installed and working well. Thankyou. Vinay On 8/10/07, Thomas Goddard <goddard(a)cgl.ucsf.edu> wrote: > > Hi Vinay, > > The chimera-1.2422-linux_x86_64.exe distribution is for 64-bit > versions of Linux. If you are using a 32-bit linux (even with a 64-bit > processor) then you need chimera-1.2422-linux.exe instead. > > If that is not the problem, could you be more specific about what > goes wrong when you try to install? What is the error message? > > Tom >

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(no subject)
by guiqing＠mailer.sb.fsu.edu 27 Aug '07

27 Aug '07

If I manually move and rotate the object in Chimera, how could I know the exact displacements along x, y, z and the rotation angle? Anyone has any suggestion? Thank you! Guiqing ----------------------------------------------------------------

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input file to make movie
by shivesh kumar 27 Aug '07

27 Aug '07

Dear all I am using chimera very first time.I want to know how to make the input files from .pdb file to make a movie.Thanx in advance for the suggestions. Shivesh Kumar

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Installing Chimera
by John Beale 27 Aug '07

27 Aug '07

I have a LINUX computer on which I have been running Chimera for a couple of years. On this system installing Chimera was very straightforward- just click on the executable. I just took delivery on a new Linux system and I have been trying to install Chimera. I downloaded the file from your site (an *.exe file). When I click on the executable my system tells me that the file had been downloaded as an MS/DOS file and I should open the file some other way. The executable would not run. I have no idea what to do with this. Can you suggest a solution? It is strange because it was so easy to install on my previous system. (I am using RedHat Enterprise LINUX). Thank You! John Beale jbeale(a)stlcop.edu

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benchmark results 1.2422-linux_x86_64
by Damir Perisa 23 Aug '07

23 Aug '07

hi there, i just set up my new laptop with archlinux 64bit and since i'm going to use everything 64bit on this machine (no 32bit libraries), i tried first time chimera 64bit. details on machine: Thinkpad x61t (Tablet Laptop) Linux Apollon 2.6.22-ARCH #1 SMP PREEMPT Wed Aug 15 22:51:57 CEST 2007 x86_64 Intel(R) Core(TM)2 Duo CPU L7500 @ 1.60GHz GenuineIntel GNU/Linux graphics: Intel integrated graphics 965GM VideoRam: 262144 KB (xorg version 1.3.0 xf86-video-intel version 2.1.1) ram total: [damir@Apollon ~]$ free total used free shared buffers cached Mem: 1002364 570780 431584 0 9524 142080 -/+ buffers/cache: 419176 583188 Swap: 979924 372324 607600 benchmarks: surface 130 mesh 129 contour 158 solid 128 recolor 129 Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 762.0 677.0 150.0 150.0 736.0 109.0 7634.0 1YTI (798): 981.0 554.0 50.0 48.0 702.0 36.0 2305.0 2GBP (2575): 877.0 375.0 17.0 17.0 609.0 16.0 713.0 1GOT (6449): 601.0 213.0 6.0 6.0 468.0 9.0 216.0 2HMG (12189): 254.0 134.0 3.0 3.0 291.0 6.0 87.0 2PDA (18894): 165.0 91.0 2.0 2.0 191.0 4.0 51.0 1YNJ (24369): 132.0 67.0 5.0 10.0 217.0 3.0 40.0 1F4H (33805): 97.0 53.0 1.0 1.0 128.0 2.0 28.0 quite low scores, no? ... in addition i'm observing that only 50% of cpu is used (means only one core). chimera is not multi-threaded? greetings, Damir

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A problem
by EFFICIENT ECON AND ENVIR FRIENDLY PRD OF KEY INTER OFMJ ANTI 22 Aug '07

22 Aug '07

Dear Sir/Madam, I am very interested in your UCSF Chimera. Unfortunately I don't know how to use it to open my PDB files derived from molecular modelling. Could you help me? Your reply will be greatly appreciated. Best wishes, Qi Zhang ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk

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copy and paste a model
by William Jeffrey Triffo 22 Aug '07

22 Aug '07

is there a way to 'copy and paste' an entire model? for example, I have a volume data map with some surface and volume renderings that I would like to display in a few different orientations (same map, maybe rotated by 45 deg) side by side in the same scene/window. -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Fitting informations
by Magali Cottevieille 21 Aug '07

21 Aug '07

Hi, Could you tell me where I can find informations of the fitting procedure of Chimera (Fit model in map)? I would particularly like to know if it is in real or Fourier space. Thank you, Magali.

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stereo view
by Rutledge, Robert (NIH/NCI) [V] 21 Aug '07

21 Aug '07

I have been trying to get chimera to work with stereo. I now have an NVidia Quadro FX 1500 card, and I start Chimera with the --stereo option. The program starts fine, but produces the following error: "can not open camera mode". Stereo will not work when I try to select it from the camera tab. My computer has 3 monitors; two are connected to the Quadro card. The first monitor (the one active during boot) is connected to an NVidia 7800GTX. Do I need to swap my cards so that the Quadro becomes the first card or is there another solution? Thanks, Robert Rutledge

2 1

New benchmark
by David Konerding 21 Aug '07

21 Aug '07

Hello, here is a new benchmark HP xw9400 2 dual core Opteron 2220 8GB RAM Quadro FX3500 256MB nvidia driver 100.14.11 Chimera version 2422 Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 15318.0 12309.0 1401.0 1313.0 15107.0 3208.0 6848.0 1YTI (798): 8422.0 7090.0 469.0 453.0 11649.0 900.0 2585.0 2GBP (2575): 448.0 2287.0 122.0 127.0 1443.0 289.0 536.0 1GOT (6449): 172.0 559.0 39.0 43.0 590.0 87.0 186.0 2HMG (12189): 173.0 254.0 26.0 27.0 246.0 52.0 78.0 2PDA (18894): 96.0 172.0 18.0 14.0 208.0 33.0 40.0 1YNJ (24369): 75.0 128.0 14.0 13.0 184.0 24.0 30.0 1F4H (33805): 46.0 114.0 9.0 8.0 72.0 25.0 21.0 surface 842 mesh 846 contour 153 solid 477 recolor 153 Dave

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VRML output
by Andrew Carter 17 Aug '07

17 Aug '07

I have been testing the vrml output from chimera (for loading into cinema 4d) and I can get a ribbon representation to work ok. However when I try a surface rendering it looses all the color. Am I dong something wrong. Also with the surface rendering is there a way to change how course the vrml output is? Many thanks Andrew

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potential bug in saving sessions using IMOD import
by William Jeffrey Triffo 17 Aug '07

17 Aug '07

not sure if this has already been reported, but if I save a session in which I have imported IMOD models (surface meshes + contours), and then reload the session, only the contours appear - the surface meshes do not. this is using build 2416, May 30 2007 release. -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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NRAMM workshop
by Thomas Goddard 16 Aug '07

16 Aug '07

Hi Scooter, Bridget Carragher suggests I give a demo of Chimera at the NRAMM (National resource for automated molecular microscopy) workshop on November 14. I think I will do that. Do you have special interest in talking with Bridget and Clint Potter about our proposed collaboration to use Chimera as a viewer of their EM database? Tom Bridget Carragher wrote: > Hi Tom, > We are hoping that we might be able to persuade you to come to our > upcoming workshop: "Workshop on advanced topics in EM structure > determination" which will be held during November 10-16, 2007 at NRAMM. > We will have a number of afternoon demonstrations of various relevant > software and we would be delighted if you would agree to give a half > hour presentation of the most relevant aspects of Chimera to the cryoE > community during the afternoon of Wednesday November 14. We will of > course, cover your airfare, as well as accommodation and all meals while > you are here and we'd encourage you to stay for as much of the workshop > as you can manage. I'm attaching a draft agenda of the workshop so you > can get an idea of the basic outlay - all except the highlighted talks > are conformed. > Best regards, > Bridget and Clint > > > ------------------------------------------------------------------------ > > > ---------------------------------------------------------------------------------------------------------------------------------- > Bridget Carragher, Associate Professor > Automated Molecular Imaging Group, Department of Cell Biology > The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, > La Jolla, CA 92037 > tel: (858) 784-9070; fax: (858) 784-9090; bcarr(a)scripps.edu; > http://ami.scripps.edu > National Resource for Automated Molecular Microscopy: > http://nramm.scripps.edu > ---------------------------------------------------------------------------------------------------------------------------------- > > > >

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Re: [Chimera-users] sym command in Chimera
by Thomas Goddard 16 Aug '07

16 Aug '07

Hi Nevin, The sym command places molecule copies relative to the coordinate frame of a density map. If you do not have a density map open it will not work. The solution is to open a density map, any map will do even if it is not related to your system -- it is just providing a coordinate frame. Here's a density map (potassium ion channel electron microscope data) if you don't have one. ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1094/map/emd_1094.map.gz You'll need to uncompress it (for example, with gunzip, or on the Mac it will offer to uncompress automatically when you download it) before opening it in Chimera. Once it is open in Chimera and you use the sym command you can undisplay it with Favorites / Model Panel. You also use Model Panel to freeze the map (uncheck the "active" button) in order to make motions of the molecule generate new positions for the molecule copies. Here is why a map is needed to define a coordinate frame. You might think the positioning matrices could just be applied in the global coordinate frame. But when you rotate the Chimera models with the mouse to get a different view point, that moves all the models around in the global frame, and that would cause all the monomers to assume a new arrangement if the matrices were applied to the rotated reference model. So in order to be able to see you models from different view points without changing their relative positions the symmetries are applied relative to the coordinate frame of a density map. (Could be relative to any other model but the command was created for people fitting molecules into density maps.) If you rotate the density map and molecules together then the matrices still keep the same relative positions of the molecules. Tom Z. Nevin Gerek wrote: > > Hello, > I am having another problem with sym command. When I test on some > proteins including the example (1i84) provided in the website, I get > 'No opened volume or reference model specified" error. > I used sym and then sym #0 but they give same error. Do I need to copy > another feature for this command? Is there anyway I can fox this problem? > > Thanks again, > > > Z. Nevin Gerek, Ph.D. > Postdoctoral Fellow > ----------------------------------------------------- > The Center for Biological Physics > Arizona State University > PO Box 871504 > Tempe, AZ 85287-1504 > Phone: (480) 727-8897 > nevin.gerek(a)asu.edu <mailto:nevin.gerek@asu.edu>

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Manually assigning secondary structure to residues
by Oren Shalev 16 Aug '07

16 Aug '07

Dear Chimera team and users, I'm modeling chains with gaps using in-house software. When opening in Chimera a model in which a secondary structure element is broken or flanked by the start/end of a gap, the secondary structure of the residue adjacent to the gap is assigned to be 'coil'. I guess this is expected, since one needs to know both Phi and Psi angles to determine the secondary structure of a given residue, yet I always have knowledge that the residue adjacent to the gap does indeed belong to a secondary structure element. My question is this: is there a way to assign the secondary structure of a given residue to either 'helix' or 'strand'? I'm interested in this for imaging purposes, so potential negative consequences on other aspects of Chimera's operation (perhaps on analysis tools?) don't matter to me. Thank you, Oren

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sym command in Chimera
by Z. Nevin Gerek 15 Aug '07

15 Aug '07

Dear Chimera team, I am trying to use sym command to generate symmetry related copy of a protein. I followed this link: http://www.cgl.ucsf.edu/chimera/experimental/symmetrycopies/ symcopies.html The version I am using is 1.2422. When I write sym, I get this error: "unrecognized command: "sym" Then I found this link http://www.cgl.ucsf.edu/pipermail/chimera- users/2005-September/000464.html and put necessary files to Chimera.app/Contents/Resources/share folder. Then I restart Chimera, I get same error. Is there another way to use sym command in Chimera? Thanks for your help, Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek(a)asu.edu On Aug 11, 2007, at 12:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. transposing a pdb structure ("copy & paste") (Ben Keshet) > 2. Re: transposing a pdb structure ("copy & paste") (Elaine Meng) > 3. Re: transposing a pdb structure ("copy & paste") (Eric > Pettersen) > 4. Re: chimera on AMD workstation (Vinay Kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Aug 2007 15:53:33 -0400 > From: "Ben Keshet" <keshet1(a)umbc.edu> > Subject: [Chimera-users] transposing a pdb structure ("copy & paste") > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: <000001c7db88$238da8b0$29ad5582@umbc80a173302c> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera fans and team, > > I have a pdb file of a fragment of an amyloid fibril constructed of > 8 layers > (8 parallel strands of beta sheet). I would like to overcome the end > effects when modeling it, so I would like extend the existing > structure by > duplicating it at its end. > > Does Chimera has a tool do the following: duplicate existing pdb > molecule > coordinates, position the duplicated molecule at a desired > location, and > then align it reasonably with respect to the original molecule? > > Thank you very much for your time and help. > > Ben > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Aug 2007 16:04:20 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] transposing a pdb structure ("copy & > paste") > To: "Ben Keshet" <keshet1(a)umbc.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8f3e5fad823ed51cc9da3fa7677864cc(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Dear Ben, > Chimera doesn't have the ability to figure out for you the proper > position of one copy relative to another. You could open multiple > copies, perform manual positioning, and then write out all the > coordinates, but I imagine it might be difficult to get the right > position of one copy relative to another, even manually/interactively. > > To manually position a structure relative to another, you could > interactively rotate/translate and/or use the "move" (translation) and > "turn" (rotation) commands. You can freeze/unfreeze a copy using the > Active checkbox in the Model Panel (in the Favorites menu by default), > the command "select," or the little checkboxes under the Command Line > (also under Favorites). > > If you did manage to position copy 2 relative to copy 1 to your > liking, > you could write the transformation matrices out (see "matrixget" > command). From those you could calculate the transformation of 2 > relative to 1 and also generate appropriate matrices that would then > position 3, 4, ... correctly (see "matrixset" command). I admit I > don't know how to do those calculations. Anyone? > > Yet another snag depends on how you will be using these coordinates. > Does it require all the PDB files to be merged into one? If so, can > they be in a multi-MODEL form, or in a single model? Chimera can > output separate PDB files or a single multi-MODEL PDB file. If you > need all the coordinates to be in one model, however, you would > have to > edit the PDB output from Chimera so there are not atoms with duplicate > atom numbers and chain IDs. However, it all depends on what the > *next* > program you will be using requires and expects. If you will just be > using Chimera, however, no further editing would be required (in fact, > you could just save a session rather than writing out coordinates). > > Maybe someone else will have a smarter and less discouraging set of > suggestions! Best, > Elaine > > On Aug 10, 2007, at 12:53 PM, Ben Keshet wrote: > >> Dear Chimera fans and team, >> >> I have a pdb file of a fragment of an amyloid fibril constructed of 8 >> layers >> (8 parallel strands of beta sheet). I would like to overcome the end >> effects when modeling it, so I would like extend the existing >> structure by >> duplicating it at its end. >> >> Does Chimera has a tool do the following: duplicate existing pdb >> molecule >> coordinates, position the duplicated molecule at a desired location, >> and >> then align it reasonably with respect to the original molecule? >> >> Thank you very much for your time and help. >> >> Ben > > > > ------------------------------ > > Message: 3 > Date: Fri, 10 Aug 2007 16:53:36 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] transposing a pdb structure ("copy & > paste") > To: Ben Keshet <keshet1(a)umbc.edu> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <E5C1411A-58C1-49A8-8899-24816E53E043(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Aug 10, 2007, at 4:04 PM, Elaine Meng wrote: > >> To manually position a structure relative to another, you could >> interactively rotate/translate and/or use the "move" (translation) >> and >> "turn" (rotation) commands. You can freeze/unfreeze a copy using the >> Active checkbox in the Model Panel (in the Favorites menu by >> default), >> the command "select," or the little checkboxes under the Command Line >> (also under Favorites). >> >> If you did manage to position copy 2 relative to copy 1 to your >> liking, >> you could write the transformation matrices out (see "matrixget" >> command). From those you could calculate the transformation of 2 >> relative to 1 and also generate appropriate matrices that would then >> position 3, 4, ... correctly (see "matrixset" command). I admit I >> don't know how to do those calculations. Anyone? > > It's a little tricky. Basically, you want to get copy 1's matrix to > be the identity matrix while keeping copy 2 in the same relative > position. Here's one way to do it (and maybe someone can suggest > something better): > > 1) open yet another copy (copy 3) as a reference > 2) use "matrixset" to set copy 3's matrix to be the identity matrix > 3) use the "match" command with the 'active' keyword to match copy 1 > onto the reference (copy 3) while also moving copy 2 appropriately > 4) use "matrixget" to get copy 2's new transformation matrix > > I would imagine that copy 2's matrix is essentially all translation > components (i.e. the upper 3x3 is all zeroes or near-zeroes) so all > you need to do to place additional copies to multiply the translation > components by 2, 3, etc. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > pett(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu > > >

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Request
by Rajendra P. OJHA 14 Aug '07

14 Aug '07

Dear Sir, After installation on a AMD opetron machine(64 bit) it gives the following error message Pease rectify the problem and oblige. Thanks Ojha ************************** Message ********************** ./chimera-1.2422-linux_x86_64.exe UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/rpo/CHIMERA' inflating: chimera_install_KUOeVj/installer inflating: chimera_install_KUOeVj/chimera.exe ./installer: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by ./ installer) result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_KUOeVj' Installation is done; press return. ____________________________________________________________________________________ Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. http://autos.yahoo.com/carfinder/

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stereo display
by Rutledge, Robert (NIH/NCI) [V] 14 Aug '07

14 Aug '07

I am trying to get stereo working with Chimera. I use the --stereo switch when I start up the program. This results in the following error: "unable to find hardware stereo support (Togl: couldn't choose stereo pixel format)". The graphics card connected to the CRT monitor is NVIDIA 7900GS. I run Chimera under Windows XP media center edition. I have a cheap pair of shutter glasses (edimensional), which work properly when tested by the test application on the graphics card. Do I need another graphics card or glasses, or is something else the problem? Robert Rutledge

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modeling non-standard amino acids
by Dan Wendt 14 Aug '07

14 Aug '07

Hello, My name is Daniel Wendt and I work for Biomarin Pharmaceuticals in Novato, Ca. I'm trying to use Chimera's modeling software to predict structural changes that are imparted on my 22 amino acid peptide by the insertion of two non-standard changes to the peptide bond. In one case, I am adding a methyl group to the backbone amide bond. In another case, I'm removing a carbonyl from the backbone amide bond. This peptide then needs to be cyclized by the formation of a intra-disulfide bond. I do have x-ray crystal structure data of my cyclized peptide bound to one of its receptors. Do you know how one goes about doing this? Do you have any references that might help? Thank you in advance! Daniel Wendt Senior Scientist BioMarin Pharmaceutical Novato, Ca 94949 (415) 506-6131 This message is intended only for the confidential use of the intended recipient(s). If you have received this communication in error, please notify the sender by reply e-mail, and delete the original message and any attachments. Any unauthorized disclosure, copying, or distribution of this message (including the attachments), or the taking of any action based on it, is strictly prohibited.

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mrc maps
by Gorelik, Tatiana 13 Aug '07

13 Aug '07

Dear Chimera-team, Can I load several .mrc maps at a time and rotate them one against another? Thanks, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail:gorelik@uni-mainz.de ************************************

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macintosh/stereographics/boot camp
by Dougherty, Matthew T. 11 Aug '07

11 Aug '07

There are some difficulties deep in the apple graphics driver implementation that prevent X11 and openInventor and openGL stereographics. I can report that mac-bootcamp-windows running with a quadro fx 4500 (card supplied by apple, other cards have the wrong firmware); does correctly do stereographics under XP windows correctly with no noted problems. ========================================================================= Matthew Dougherty *** 713-433-3849 National Center for Macromolecular Imaging ========================================================================= =========================================================================

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chimera on AMD workstation
by Vinay Kumar 10 Aug '07

10 Aug '07

Hello all, recently we bought a AMD workstation. I tried to install chimera_linux x86_64 on it. But it did not install. went through installation instructions. still did not work. i would like you to give me some suggestions and some variations that i could try to install chimera. Thank you Elaine, for your post on spheres. shall inform when my adventures have a result. regards, Vinay

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Teaching with Chimera
by Fabian Glaser 09 Aug '07

09 Aug '07

Dear Chimera team, I'd like to use both chimera and chimera tutorials for a new "Structural Bioinformatics practical course" I am preparing here at the Technion in Israel. I will of course acknowledge appropriately. Is there any legal limitation for using chimera for this purpose? Thanks for creating such a fantastic tool Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)tx.technion.ac.il Tel: +972-4-829-3701 Cell: +972-52-2357731

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writing translation/rotation
by Thomas C. Marlovits 08 Aug '07

08 Aug '07

Hi, am looking for an analysis tool in Chimera that would write out - let's say a matrix for translation/rotation of a pdb-file in respect to another one. Usage: would like to align chain A and chain B present in a pdb-file and want to know which translation/rotation matrix has to be applied in order to convert the non-aligned pdb-coordinates of chain B to the 'new" aligned pdb-coordinates. Thanx for your help, -Thomas ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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how to select spheres for docking?
by Vinay Kumar 06 Aug '07

06 Aug '07

Hello all, I have a few queries to ask. hoping you all will reply. i use DOCK6.0, the dms program under DOCK, can create and execute a total of 9999 spheres. I would want to know, how do i selectively select spheres using chimera? Is it possible to select certain residues and generate the molecular surface for it? and use it for docking?? My previous problem with chimera got resolved. Thank you Greg. I had to change the OS from RHL9.0 to fedora core. with regards, Vinay ps- please ignore if off-topic. i have posted the same query on dock mailing list. still awaiting a reply there.

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Re: [Chimera-users] odd glare when volume rendering
by Tom Goddard 03 Aug '07

03 Aug '07

Hi Jeff, Aha! Now I see Chimera is working as expected and I can reproduce the glare on my computer. If you have depth cueing set to "No color", which is the default, *and* you use a light background color, then Chimera interprets "no color" as white. With a dark background color, I use black, "no color" for depth cueing is interpreted as black. So all I had to do was set by background color to a light shade to see the glare. So this is bad behavior. The white depth cue color does not work with volume rendering -- it is way too powerful -- all the far planes in the data become slightly white, and this ends up making a very white brick. Oddly, I have already fixed the problem, accidently! My current development version of Chimera (not on the web) has a new blending mode for volumes. I made the change to address a serious problem you raised earlier that the brightness in volume rendering changes a lot when you change step size. The new mode fixes that and will be the default in the next snapshot. Coincidentally the new blending mode also makes white fog work as expected without an overly powerful effect. I have also added better handling of large EM tomography maps -- file loads report progress and can be canceled, default initial display can show a single z plane, the z plane slider is built into volume viewer, hdf5 format map files can be written which contain subsampled versions of the map allowing rapid display of the data at any scale. I'm testing all this on an 2048^3 map. A snapshot should be out in a month or so, though if you really want bleeding edge stuff I could probably give you an earlier version for mac os. Tom William Jeffrey Triffo wrote: > hello, > > I am getting an odd glare when I use solid rendering in VolumeViewer - > it is orientation dependent, which makes me think it has to do with > lighting? I am using build 2416; is it possible to forward a screenshot > to the list? > > thanks, > >

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odd glare when volume rendering
by William Jeffrey Triffo 02 Aug '07

02 Aug '07

hello, I am getting an odd glare when I use solid rendering in VolumeViewer - it is orientation dependent, which makes me think it has to do with lighting? I am using build 2416; is it possible to forward a screenshot to the list? thanks, -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Problem with Gasteiger charges of a formally charged ligand
by cdeligka＠purdue.edu 02 Aug '07

02 Aug '07

Dear all, I tried to calculate the Gasteiger charges of peroxynitrite anion using Chimera (I tried the version that was recently released as well as some previous ones). This is my PDB file: HEADER HETATM 1 O 2 2 1.225 0.000 1.819 HETATM 2 N 2 2 0.138 0.000 1.281 HETATM 3 O 2 2 0.138 0.000 -0.086 HETATM 4 O 2 2 1.359 0.000 -0.746 The formal charge of this molecule is -1. For some reason Chimera generates the Gasteiger charges for the molecule but these charges correspond to a formal charge of zero and not -1. If I try the other method AM1-BCC the charges that are calculated do correspond to a formal charge of -1. In my calculations I do need the Gasteiger charges and so I cannot use the ones that are calculated by AM1-BCC. If you have any suggestions please let me know. Are you aware of any other software that might be able to do this calculation? Thank you all, Christos

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Moving individual markers
by J. Evan Sadler 02 Aug '07

02 Aug '07

Is it possible to move single markers from the command line, instead of using the mouse under the Volume Path Tracer tool? If so, it would greatly simplify certain model constructions. Evan Sadler

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Chimera on Linux
by Beale, John 30 Jul '07

30 Jul '07

I have been using Chimera on a Linux-equipped laptop for a long time. All that I had to do to get the software working was to download the appropriate version of Chimera and click on the executable. I am trying to install Chimera on a new Linux workstation. I downloaded the program for Linux, but when I try to run the executable I get a message that says that the software downloaded is for MS-DOS and not Linux, and I am unable to install Chimera. Has anyone run into this problem, and is there a fix for it? John Beale

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CSB 2007 Molecular Visualization tutorial
by Conrad Huang 30 Jul '07

30 Jul '07

Scooter Morris and Conrad Huang will be giving an introductory molecular visualization tutorial using Chimera on August 13 at CSB 2007 (the Conference on Computational Systems Bioinformatics) in San Diego. Interested folks can visit http://www.lifesciencessociety.org/CSB2007/index07.html for more information on CSB 2007. The tutorial abstract is attached below. An Introduction to Molecular Visualization Tutorial at the Computational Systems Bioinformatics (CSB) conference (AM2) University of California, San Diego August 13, 2007 Abstract Projects such as Structural Genomics are providing increasing numbers of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools. Attendees will learn the basics of molecular visualization and will be provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own data to the visualization. Outline: 1. Introduction to Molecular Visualization 2. Available Tools 3. Using UCSF Chimera 4. Scenarios of use 5. Extending Chimera

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Fwd: CCL: hydroxide for dock
by Elaine Meng 25 Jul '07

25 Jul '07

Begin forwarded message: > From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner- > chemistry(a)ccl.net> > Date: July 25, 2007 7:50:36 AM PDT > Subject: CCL: hydroxide for dock > Reply-To: "CCL Subscribers" <chemistry(a)ccl.net> > > Hi, everyone, > I'm preparing structures with Chimera for docking with Dock6. There > is a Zn-coordinating hydroxide that I want to keep in the > structure. When I prepare dock files, Chimera always treat it as a > water. Is there any way to define it as a hydroxide in Chimera? > Thanks, > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan_+_mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ Dear Yubo, I could answer more precisely if I could see the file, but without seeing it, I recommend: (a) looking at the residue name of the hydroxide in the text of the file. Is it WAT or HOH? If so, you could edit it to a different name, say XOH or HOM. (b) then, run Dock Prep in Chimera including hydrogen addition and all the steps before that (but don't assign charges or write the Mol2 file). (c) check the structure; if hydrogen is added where you didn't want it, simply delete it. For example, Ctrl-click to select an atom and use "Actions... Atoms/Bonds... delete" in the menu to delete it. The protonation states are intended to be reasonable at physiological pH, but if a group is expected to have a perturbed pKa (for example, in an active site or near an ion), it is a good idea to check it and manually add/delete hydrogens as needed. ( more details in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html ) (d) run Dock Prep again with only the steps AFTER hydrogen addition (charge assignment and Mol2 file output) turned on. If it asks for the net charge of XOH (or whatever you named it), indicate -1. (e) that procedure will use Antechamber to calculate the partial charges on the hydroxide O and H. If, however, you already know the charges you want to use for these atoms, you can edit the charge values in the output Mol2 file. In that case you wouldn't even have to go through all these steps, but could simply also delete the extra hydrogen from the Mol2 file, if you can figure out which line it is! I just realized this last point, so it wasn't in my original reply. 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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Windows Vista
by Jason M Walraven 23 Jul '07

23 Jul '07

I just installed the latest version of Chimera on my Windows Vista operating system (home basic). Everything seems to work perfectly, except that the colors appear to be messed up. The colors appear darker than on my previous computer (with Windows XP). Has anyone else had this problem? All colors in all other programs are normal on my computer except for in Chimera. I assume it is a compatibility issue, but I don't know enough about it to say that for sure. jw

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Re: [Chimera-users] Reading a data set from a text file
by Thomas Goddard 17 Jul '07

17 Jul '07

Hi Kyaw, I see what you've done and see that you have a set of (x,y,z) coordinates. But I'm not sure what you want or what these coordinates represent. To make a surface out of a set of points you need to know which points are next to each other. In Chimera you need a set of points, and a set of triangles, each triangle defined by 3 integer indices into the set of points that give the triangle vertices. If you can define the set of triangles I can tell you how to make the surface. Tom Kyaw Zeyar Myint wrote: > Hello Tom, > I apologize for not being able to respond to you earlier. The > set of view vectors that I want to make surface out of it are in (x, y, > z) coordinates. > > So far, I've done a quick and 'rough' way of using these vectors for > display. What I did in chimera was that I wrote a mini plugin which > makes a .bild > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> file with a > set of cylinders, given a set of vectors. > Each cylinder is centered at origin (0,0,0) and drawn according > to the vector (which is from my set of view vectors). So if the V(x,y,z) > has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by: > /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 / in .bild file. > Then .bild file is fed into chimera and then a set of cylinders > is displayed. In a sense, each cylinder represents each view vector in > the set. But this is just a quick solution. > If you can share some ideas of how to better do this, please let > me know. I'd really appreciate your help. > > Thanks a lot! > Kyaw > (P.S: I've attached .bild file which you can display in chimera and see > what inside using a text editor.) > > ------------------------------------------------------------------------ > > > On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote: > >> Hi Kyaw, >> >> I'm not sure I understand what type of data you want to display in >> Chimera. Is it a list of density values, or is it a list of x, y, and >> z coordinates? If it is density values in text rather than binary, >> you could reformat it into XPLOR format >> >> http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html >> >> which can be read into Chimera. >> >> Tom >

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presets criteria
by Roberta King 17 Jul '07

17 Jul '07

Hello, I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket? This is a useful shortcut, but I would like to understand the specific criteria. Thank you very much, Roberta ******************************** Roberta S. King, Ph.D. Associate Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 16 Jul '07

16 Jul '07

Hi Pasquale, You can definitely open multiple PDB files and move them independently. By default everything will move together, which might even be what you want. However, if you don't want them to move together, you can freeze any structure in place ("deactivate" it), move the other(s), and then "activate" the first structure again if you want it to be movable. There are several ways to control activation/deactivation; probably the easiest is to open the Model Panel (Favorites... Model Panel). Then just uncheck/check the box in the Active column to freeze/ unfreeze a model. We use the word model to mean the contents of a structure file (PDB, Mol2, etc.), so if you read in two separate PDB files, there would be two models listed in the Model Panel. Alternative ways of controlling activation/deactivation are with the little checkboxes under the Command Line and using the command "select". You would still be able to minimize multiple models as a single system by choosing all of them in the "Minimize Structure" dialog. 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 Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote: > well in order to make the dimer i used two separate pdb files and > imported them both into the same gaussian gjf file. then i imported > that file as a mol2 file into chimera, so unless i can manipulate > separate pdb files in chimera then that would be great but i cannot > figure out how to move separate pieces of my dimer. > > On 7/15/07, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Pasquale, > I had one long-shot possibility for getting the correct atom and > residue names - did you start with a PDB file before the guassian > calculations? If so, that file may have had the correct atom and > residue names. If that starting file had all the same atoms > (including hydrogens) and the order of the atoms is exactly the same > in that gaussian output, you could simply replace (probably with a > script) the coordinates in each line of the starting PDB file with > those from the gaussian output. That would only work if the order is > exactly the same, however. > > Otherwise it would be extremely tedious to figure out which > coordinates go with which atom/res/number. > Best, > Elaine

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ValueError: More than 2 coplanar positions specified!
by Mike Gretes 13 Jul '07

13 Jul '07

Hello, When trying to calculate hydrogen bonding between two molecules, I get the error: "ValueError: More than 2 coplanar positions specified!" I have successfully calculated h-bonding between two other similar molecules, so I'm not sure what the problem is (I have no alternate conformations or anything weird in the PDB files I don't think... is there anything that usually triggers this error?) thanks! mike ___________________ Michael Gretes PhD Candidate (Structural Biology) Senior Graduate Trainee, Michael Smith Foundation for Health Research NCJ Strynadka Laboratory Dept. of Biochemistry, University of British Columbia Life Sciences Center, 2350 Health Sciences Mall Vancouver, BC Canada V6T 1Z3 phone 604 822 7729 fax 604 822 5227 ____________________

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Forward of moderated message
by mailman-bounces＠cgl.ucsf.edu 13 Jul '07

13 Jul '07

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 11 Jul '07

11 Jul '07

Hi Pasquale, As Eric figured out, your mol2 file does not contain substructure information. For the structure to be read by Chimera as a series of residues, there would need to be residue information in each line in the @<TRIPOS>ATOM section and then a corresponding @<TRIPOS>SUBSTRUCTURE section at the bottom. You would have to edit that information into your file. Otherwise, the structure appears as one big residue. Mol2 format description: http://www.tripos.com/mol2/mol2_format8.html ATOM section - need substructure ID and name (residue number and name) for each atom http://www.tripos.com/mol2/mol2_format33.html#1370 SUBSTRUCTURE section - more information on those substructures (residues) To get an example mol2 file, open a PDB file of a protein in Chimera, add hydrogens if you want those in your example, and then write it out as Mol2 (File... Save Mol2...) 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 On Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote: > Hi Pasquale, > If your structure all got put into a single residue named UNK, > that typically means that your file was missing the @SUBSTRUCTURE > section (http://www.tripos.com/mol2/mol2_format33.html#1370) > There is an entry in our bug database (#3518) for better handling > of files with missing @SUBSTRUCTURE sections. I will add your name > to that report so you'll know when it gets fixed. For now, you > will have to edit your file and add an @SUBSTRUCTURE section "by > hand". > > --Eric >> >> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote: >> >>> Hey Elaine, >>> My structure is currently being labeled as one big residue >>> (UNK) and when I minimize it it says it does not recognize the >>> residue, so it seems like the calculation program is using >>> residue parameters and not those for specific atoms. Also, my >>> structure contains a Zn(II) metal center and I was wondering if >>> the parm files would detect it as such if it actually used the >>> atom types. I attached my mol2 file so you can check it out. Thanks >>> -Pasquale Iacono

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memory usage
by jean-francois menetret 11 Jul '07

11 Jul '07

It seems that Chimera is not releasing memory easily on our linux PC. Is this a know problem for Chimera ? 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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Chimera and Debian
by Arkadiusz Czader 11 Jul '07

11 Jul '07

Hi, I have a problem running 32 bit linux version of Chimera on Debian64. When I run it, it complains about some libraries. Below I pasted what I get when I type chimera in a terminal window arek@teton:~$ chimera Traceback (most recent call last): File "/home/arek/progs/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "/home/arek/progs/chimera/share/chimeraInit.py", line 231, in init import chimera File "/home/arek/progs/chimera/lib/python2.4/site-packages/PIL/__init__.py", l ine 15, in ? ImportError: libGL.so.1: cannot open shared object file: No such file or directory The library libGL.so.1 is only in /usr/lib. Should it be in a different place? Any help appreciated. cheers, Arek ____________________________________________________ | | __ __ | | Arkadiusz Czader | | | _| | __ | | Department of Chemistry | | | | | | | | | | University of Houston | | | | | | | | | | Houston, TX 77204-5003 | | | | |_|_| | | | Phone: (713)-743-5101 | \ \_| ___ | | | E-mail: aczader(a)uh.edu | \___| |/ | | | | | | | | | | | | |__| |__| | |____________________________|_______________________| ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/

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Re: [Chimera-users] pdb-l: Selecting phytols in Chimera?
by Eric Pettersen 09 Jul '07

09 Jul '07

On Jul 9, 2007, at 6:39 AM, Morgan Ryan wrote: > Is it possible to write a selection string that will select all the > phytol substituents in a model? I'm looking at photosystem II. I > would like to select all the phytol side chains of the many > chlorophyll molecules and hide them, so that only the porphyrin-like > chlorin ring structures are visible. Can that be done? Thanks! Morgan Hi Morgan, I think the only direct way is to use the command line (Favorites- >Command Line). This command should do it: ~disp :cla@c=; disp :cla@c?a,c?b,c?c,c?d It undisplays all the carbons in the chlorophyll (:cla@c=) and then redisplays the carbons involved in the porphyrin ring (all of which have 3-letter names that end in A-D). You might want to consider posing Chimera-specific questions to the Chimera users mailing list (chimera-users(a)cgl.ucsf.edu) since there will be more people able to answer there. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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clobbered chimera, can't start from fresh install (help)
by William Jeffrey Triffo 09 Jul '07

09 Jul '07

hello, I changed some of the preferences for the IDLE shell, which produced errors that would not allow IDLE to run (tried to remap a couple of keys). This problem persisted when restarting Chimera. so, I deleted that install (Mac OS X) and re-installed the most recent release, but still produced the errors, and cannot launch IDLE. I went ahead and deleted the files in ~/.chimera, but the errors still occur. Are there any other user-specific files that I can delete that might be causing the problem? I am assuming this is the case, because even a fresh install has the same problem. I submitted a bug report about the IDLE preferences issue I experienced, but am hoping a simple fix might allow me to launch IDLE again. thanks, -Jeff

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occupancy calculation
by bala 09 Jul '07

09 Jul '07

Hello, 1) I want to calculate the occupancy of water around few base pairs in a RNA duplex. I had one query while i was going through the "calculate atomic occupancy" documentation. "For example, cations or water hydrogens may tend to occupy space around a negatively charged solute group" In the options give for this particular calculation, nowhere there is an option to select whether i am interested in WATER or ION occupany. How then chimera calculates the occupancy. 2)I presume that chimera calculates the occupany of say water as follows, if i select a residue, it puts the residue in a grid and calculated the density of water molecule in the grid points in frame. Is this the way it calculates the occupancy. I am not getting how i should differentiate occupancy and density. thanks, Bala

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chimera question
by 明明 08 Jul '07

08 Jul '07

Dear sir: I download the software UCSF chimera(version: chimera-0.2422-win32.exe). the I setup it in my computer(Windows XP). I want to use it to open my pdb file and the VIPERdb file. But I always could not open them. It always says that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see reply log for python traceback info). Then I want to ask for you help. How can I open the pdb file and VIPERdb file correctly? please read the appendix Thank you. Qiting Harbin veterinary research institute --------------------------------- Mp3疯狂搜-新歌热歌高速下

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chimera question
by 明明 08 Jul '07

08 Jul '07

Dear sir: I download the software UCSF chimera(version: chimera-0.2422-win32.exe). the I setup it in my computer(Windows XP). I want to use it to open my pdb file and the VIPERdb file. But I always could not open them. It always says that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see reply log for python traceback info). Then I want to ask for you help. How can I open the pdb file and VIPERdb file correctly? please read the appendix Thank you. Qiting Harbin veterinary research institute --------------------------------- Mp3疯狂搜-新歌热歌高速下

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Custom presets
by Eric Ganz 06 Jul '07

06 Jul '07

Is there a way to create new presets for molecule views? We want to apply the attributes of one molecule to subsequent molecules. Is there an easy way to do this? Our second question is how to set half-bond mode off for our views.

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Re: [Chimera-users] Using mol2 files
by Eric Pettersen 06 Jul '07

06 Jul '07

Hi Pasquale, If your structure all got put into a single residue named UNK, that typically means that your file was missing the @SUBSTRUCTURE section (http://www.tripos.com/mol2/mol2_format33.html#1370) There is an entry in our bug database (#3518) for better handling of files with missing @SUBSTRUCTURE sections. I will add your name to that report so you'll know when it gets fixed. For now, you will have to edit your file and add an @SUBSTRUCTURE section "by hand". --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Using mol2 files
by Pasquale Iacono 03 Jul '07

03 Jul '07

Hi I imported a .mol2 file from Gaussian to Chimera because I want to run an amber minimization with a better parameter set. However, the mol2 files are not like pdb files and do not come with atom types for amber calculations. Is there anyway to (auto?)assign amber atom types to the atoms in my file so your program can run a calculation? Thank you. -Pasquale Iacono, B.S. Ithaca.College

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POVray shininess
by Tom Goddard 03 Jul '07

03 Jul '07

Edward Egelman wrote: > Hi, > The new POV rendering is very nice, but suffers from one problem > that I do not see how to fix. Is there any way to control the surface > properties (reflectivity, "shininess", etc.)? I only see the standard > brightness and transparency for the "save as" feature. > Regards, > Ed Hi Ed, You can control the shininess of surfaces in Chimera using menu entry Tools / Viewing Controls / Shininess. The shininess you set is exported to POVray when you save a raytraced image. The POVray appearance doesn't exactly match the Chimera graphics window appearance so you may need some trial-and-error experimentation to get the desired shininess in the POVray output. Tom

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seg faults
by Tom Goddard 03 Jul '07

03 Jul '07

Edward Egelman wrote: > Hi, > I have a question about very complicated chimera sessions (20 or so > large PDB files, 10 or so large brix volumes). We will sometimes get a > segmentation fault and the session will close. This is on a 32-bit > linux machine with 2GB memory (our only system with stereo display). > If we move to a 64-bit machine with more memory, will we be less > likely to crash? Or is this due to some internal memory limitations in > chimera itself? A second question is whether you have any experience > (or know of others who have) using fast nvidia stereo boards (such as > the Quadro FX3500) to accelerate display operations in chimera. > Regards, > Ed > -- Hi Ed, There are only two Chimera crash situations that I understand and are frequently reported. Computing molecular surfaces of PDB models (menu entry Actions / Surface / show) crashes for many large PDB models. If the surface calculation gives an error but does not crash it has usually corrupted memory and Chimera will crash later. The solvent excluded surface code comes from Michel Sanner and is very complex (~20000 lines of C code). We have been working on a replacement for it for over a year but it is not yet ready. The second type of crash is caused by graphics driver bugs. These are common, more so on higher-end graphics cards where Chimera takes advantage of OpenGL features that are used by few applications, also more common on laptops. Here are some of the graphics driver problems observed in Chimera. http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards I have never had Chimera crash when I am working with large PDB models and maps (using Mac systems with 1-2 Gb memory), but that is probably because I only work with a few models and maps at a time, and for short sessions. It could be that memory allocation failures cause crashes in these situations. I am doubtful that using the 64-bit Linux Chimera will help. Using the 32-bit Linux Chimera on a 64-bit machine almost certainly will not help because the 32-bit address space can only access 4 Gb of memory and segments of that address space are already used by shared libraries and program stack -- so you probably only have 2 Gb of usable space. With 2 Gbytes of physical memory you probably have at least 4 Gb of virtual memory, so the 32-bit address space is the main limitation. Chimera catches memory allocation failures for large allocations (e.g. opening a new map) and those do not cause a crash. It is only when a small allocation that is not checked fails that a crash might happen. The difference in speed rendering surfaces between say a Quadro FX 3400 and an ATI Radeon Pro 9800 (in my 3 year old desktop computer) is about a factor of 4. That is about the speed up to expect between a card that is a couple years old and the latest graphics card. Benchmark scores using Chimera for different cards are on the web http://www.cgl.ucsf.edu/chimera/benchmarks.html although there are few numbers for the latest cards. For volume surfaces look at the Surface column of the table. The score is the grid size of a triangulated cube that can be rendered at 10 frames per second. Since the number of triangles increases as the square of the size you should look at the *square* of the ratio of scores between cards to gauge the increase in speed expected for a fixed size volume. Tom

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Fixing MSMS crash
by Thomas Goddard 02 Jul '07

02 Jul '07

P. Qian sent me a PDB model that caused Chimera to crash when calculating an MSMS surface (menu Actions / Surface / show). He got it not to crash by shifting the coordinates of all atoms (by moving and saving the PDB with "use untransformed coordinates" turned off, and reloading that file). This is a little nicer than changing atom radii as we've advised in the past. Not sure how often a simple shift (or rotation) avoids the crash though. Tom

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Origin question with maps
by Eduardo Sanz-Garcia 29 Jun '07

29 Jun '07

I found that the origin of /mrc/ maps is read correctly and can be used to place one map in respect of another. For example: 1.mrc (origin: 10,0,0) is going to be shifted 10 pixels with respect of map 0.mrc (origin: 0,0,0). I can not reproduce the same behavior with CCP4 format (.map) . The origin is not read correctly. Thank you.

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conjoined unit cells
by Bartosz Siemiński 29 Jun '07

29 Jun '07

Hi all, I was working with Chimera for some time, beeing convinced I don't need no help, until I'd got to this. Is there a possibility of conjoining several (let's say four, nine or sixteen) unit cells? I use the el. density map (converted to cpp4, so it could be loaded by Chimera) for structural alignment and such an operation would be very usefull. Thanks in advance, Bartek ____________________________________________________________________________ Czy już jesteś w Yahoo!? Masz dosyć spamu? Poczta Yahoo! dysponuje najlepszą ochroną przed spamem http://pl.mail.yahoo.com

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mrc maps
by Gorelik, Tatiana 29 Jun '07

29 Jun '07

Hi, I image an .mrc map in Chimera. The surface map is displayed using a selected range. As a result I see blobs. I want to be able to select such a blob and get back its 3d information - coordinates, etc... Would it be possible to implement this feature? Greetings, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail:gorelik@uni-mainz.de ************************************

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