- Chimera-users - RBVI Mailing Lists

Rendering TLS information in Chimera ?
by Steven Ludtke 24 Apr '12

24 Apr '12

Hi. A question about rendering B-factor information: Over the last decade, rather than simple anisotropic B-factors, it has become increasingly common to represent local "motion" using the translation-libration-screw (TLS) model, which provides for anisotropic representation of such motions. Is there a good way to represent this data in Chimera ? Here is an example. If you render the PDB structure 1OEL as atoms, and color the atoms by B-factor, you can immediately observe regions of high variability in the apical domain. This same data was later re-refined using a TLS model as PDB structure 1SS8. When you render this structure in Chimera in the same way, you see high B-factors only for a few specific sidechains. The overall large-scale variability is gone, presumably because the TLS parameters have absorbed it, and the "B-factor" is now only a residual B-factor. However, I can't see any obvious way of rendering the TLS information. Any tips ? ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu) Co-Director CIBR Center (www.bcm.edu/research/cibr) Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem) Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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remote session
by Hernando J Sosa 23 Apr '12

23 Apr '12

Hi I used to be able to run chimera remotely from a machine with an X- windows server (the one that comes with Cygwin in this case). But now I get the following error: Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 148 (GLX) Minor opcode of failed request: 181 () Serial number of failed request: 12779 Current serial number in output stream: 12784 I t does work fine if run directly from the computer where chimera is installed. Any idea what the problem could be? Thanks Server computer: Chimera v 1.5 (similar problem with 1.6) OS: Linux OpenSuse 11.3 64b Client computer: OS: Windows 7 64. Graphics: ATI Radeon HD 5450

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Displaying atoms within a distance
by Nikolay Igorovich Rodionov 21 Apr '12

21 Apr '12

Hi everyone, I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I've looked at the chimera manual and I am still confused on how these commands function. Thank you, Nikolay Rodionov

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Charge calculations PDB2PQR
by Nikolay Igorovich Rodionov 20 Apr '12

20 Apr '12

Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov

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Volume Viewer Mesh
by Terry Lang 19 Apr '12

19 Apr '12

Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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modeller interface
by Sadler, Evan 19 Apr '12

19 Apr '12

Hi, I'm trying to construct what I think should be a simple homology model and it's failing as below whether I use the web server or run modeller locally: Target seq: VWF_CK Template structures: 2TGI.pdb (#0)Run locally, the Modeller binary location: /Library/modeller-9.10/bin/mod9.10 Now, modeller is running locally... <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <function command at 0x17982770> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerDialog.py", line 579, in Apply veryFast=self.veryFastVar.get(), tempPath=self.pathTempOpt.get().strip(), **kw) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: <type 'exceptions.UnboundLocalError'>: local variable 'loopData' referenced before assignment UnboundLocalError: local variable 'loopData' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: See reply log for Python traceback. My version of Chimera is alpha version 1.7 build 36205, running under Mac 10.6.8. Do you have any advice? Thanks, Evan Sadler -- J. Evan Sadler, M.D., Ph.D. Chief, Division of Hematology Department of Medicine Washington University 660 S. Euclid Ave., Box 8125 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler(a)wustl.edu

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How to save high resolution image?
by Yogendra 19 Apr '12

19 Apr '12

Dear Sir, I am a new user of Chimera software. I am using this software for academic purposes (i.e. research publications). I am trying to save the image with more then 600 dpi but every time i am ending up with an image of 96 dpi. I am using the POV-Ray method for image improvement but everything is going to the drain when taking the final print of the document. Can you please help me ho can i save a high resolution image? I am briefly describing my protocol of image generation: 1) I am making a density map of particular PDB file. 2) loading in the Chimera and adjusting the volume by volume viewer option 3) Coloring it using described colors 4) Using Pov-Ray for increasing effects on plane 5) Increasing the pixels to about 5000 in the pixel option 6) finally trying to save an image with 600 or 1200 dpi. But at the end of this, i am just getting an image of 96 dpi every time. Can you please help me out to make an image of higher dpi (600, 1200 or more if possible). It will be very much helpful for me if can do it. I am stuck at this point.I am badly waiting for your reply whether i can do it or should i look for some another software. Regards Yogendra S Rathore Research Scholar ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

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Methanesulfinamide Stability and Synthesis
by Nancy 19 Apr '12

19 Apr '12

Hello All, I would greatly appreciate it if anyone has information on the stability of methanesulfinamide (SMILES: C[S](=O)N([H])[H]), as well as it's stability in water. Thank you.

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Command line "Render by attribute"
by rswett＠chem.wayne.edu 18 Apr '12

18 Apr '12

So, I"m wondering if there's a way to call "Render by Attribute" command line for movie making purposes. I have several Defined Attributes and i'd like to be able to recolor surfaces by the various attributes at different points in a movie. What would the format for that type of command be? Thanks for any help you guys have! ~Rebecca

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Check Marks in 2D Labels
by Paul Cernek 17 Apr '12

17 Apr '12

Hello, I'm having trouble inserting a check mark (Unicode page here: http://www.fileformat.info/info/unicode/char/2713/index.htm) into a 2D label, using the Chimera Daily Build from April 10 2012 on Windows Vista. I know that you can reference a special character via its Unicode escape sequence (in this case \u2713). Indeed, when I specify such text from the command line, or when I copy/paste the check mark into the text box of the 2D Labels window, it displays exactly what I want IN THE 2D LABELS WINDOW. However, in the main Chimera model display window the check mark is NOT properly depicted in the label. Instead, I get that empty square you get whenever a program encounters an unrecognized character. Other more conventional symbols (such as the Greek letter 'alpha') display normally. Why would the "2D Labels" window display the check mark properly, while the main display window does not? Any assistance in this matter is very much appreciated. Thanks, -Paul

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APBS maps
by Rebecca Swett 12 Apr '12

12 Apr '12

Hey guys, i'm working with some electrostatic potential maps and am interested in doing a difference map. Two nearly homologous proteins with nearly identical surface shapes, and radically different electrostatics. I"m thinking a difference map would illustrate the differences well, but in looking at the APBS output I have no idea how to do that manually. Does anyone here have an idea about how to do that in chimera?

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Re: [Chimera-users] [Dock-fans] Help with antechamber
by Trent E. Balius 10 Apr '12

10 Apr '12

Hi Brad, I am cc'ing this to the chimera list. I think that you should write a python script to run DOCK prep on the command line. See the following: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html For other example scripts see the following: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html You should not have to specify the AMBERHOME path. This is done internally to chimera. as an aside, It is unnecessary to run antichamber with sudo. I hope this helps, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/ -----Original Message----- From: Brad Ridder <clustro(a)gmail.com> To: dock-fans <dock-fans(a)docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber Hi Dockfans, My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University. We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI. Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens. Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running: sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/3GLRcharged.mol2 -fo mol2 Which returns the error: Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder. Here is what I have in my .bash_profile file in my home folder. export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6' I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect. I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem. I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files. What am I doing wrong that is preventing antechamber from executing correctly? -- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University _______________________________________________ Dock-fans mailing list Dock-fans(a)docking.org http://mailman.docking.org/mailman/listinfo/dock-fans

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vector of axis
by Gwo-Yu Chuang 09 Apr '12

09 Apr '12

Dear all, I am trying to figure of the principal inertia axis of a protein domain using Chimera. Is there any way to get the vector of the axis (the values), besides just showing it on the screen? Many thanks Yours Sincerely, Paul

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Morph with Cofactors
by Marco Jost 06 Apr '12

06 Apr '12

Hi, I am trying to morph two conformations of a protein that includes multiple cofactors. While the protein structure is morphed just fine, the cofactors are not included in the morph (or in the output PDB). I numbered the cofactors identically in both files and everything else should be consistent as well. Does anybody know how to include cofactors in the morphing and have them be written into the output PDB? Thanks! Marco Jost Ph. D. Student, Department of Chemistry Massachusetts Institute of Technology

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Re: [Chimera-users] [Open Babel] UCSF Dock mol2 files
by Scott Brozell 06 Apr '12

06 Apr '12

Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ? thanks, scott On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 > http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek(a)wojcikowski.pl > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff(a)geoffhutchison.net> napisał: > > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff

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Selecting submodels when they are density maps
by Javier Velazquez 05 Apr '12

05 Apr '12

Hi, I am interested in generating a map from a PDB with 2 chains, and color each chain differently. I can do it very easily using the graphical interface, but I couldn't figure out how to do it from the command line. Here are my commands: molmap #0:.A 7 molmap #0:.B 7 And now adding color is simple: volume #0 color red But this adds color to both maps. Is there a way to specify a submap, so I can add color separately. I am looking for something like this: volume #0:.A color red which I tried and didn't work. Thank you for your help. Javier

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Merge the protein sequences of two different chains
by Hsih-Te Yang 05 Apr '12

05 Apr '12

Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te

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Solvate models
by Nikolay Igorovich Rodionov 05 Apr '12

05 Apr '12

Hi all, I was wondering if some could explain to me the differences between the water models available under the solvate option. * POL3BOX - POL3 water model * SPCBOX - SPC/E water model * SPCFWBOX - SPC/Fw water model * QSPCFWBOX - qSPC/Fw water model * TIP3PBOX - TIP3P water model * TIP3PFBOX - TIP3P/F water model * TIP4PBOX - TIP4P water model * TIP4PEWBOX - TIP4P/Ew water model Thank you all in advance, Nikolay Rodionov

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Coloring distance labels
by George Tzotzos 04 Apr '12

04 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

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Coloring distance labels
by George Tzotzos 04 Apr '12

04 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

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color by RMSD
by Thomas Evangelidis 04 Apr '12

04 Apr '12

Dear UCSF Chimera users and developers, Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them? thanks in advance, Thomas

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Re: [Chimera-users] [Chimera] #10638: heme not included in morph trajectory
by Elaine Meng 04 Apr '12

04 Apr '12

Hi Francesco, There is some progress... in the newest daily build (Apr 4) I can run the commands below to successfully show a morph of 1hho and 2hhb that includes heme and iron. 1hho only has two chains, so it is necessary to delete C,D from 2hhb before morphing. To include heme and iron, it is necessary to delete all the other het residues that may be different between the structures. I hope this helps, Elaine Here between "----" are contents of Chimera command file, which you could save as plain text file named something.cmd and open in Chimera to execute the commands. Lines starting with # are just comments/explanation and don't do anything. ------------- open 2hhb open 1hho # # delete 2hhb chains C,D # delete #0:.c-d # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose the structures; I used "mm" with defaults but it could be # done with options, or MatchMaker GUI, or "match" command, # or manually with mouse # mm #0 #1 # # create morph trajectory which will be model #2 # morph start #0 frames 25 morph interpolate #1 frames 25 morph movie ~modeldisp #0,1 --------------------- Then I tried to get fancy and make a tetramer of 1hho so that the morph could be from tetramer to tetramer. However, then only the heme/iron from A and B were included, not from C and D. I don't know why, because they are all in the input structures!! Here is that script in case it might be useful: --------------------- open 2hhb open 1hho # # make 1hho tetramer; #1 is original, #2 additional copy # sym #1 # # combine #1,2 dimers into tetramer model #3, close #1,2 # combine #1,2 name 1hho-tetra newchainids true close true # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose #0 and #3 # mm #0 #3 # # create morph trajectory which will be model #1 # morph start #0 frames 25 morph interpolate #3 frames 25 morph movie ~modeldisp #0,3 ---------------------

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occupancy field
by Darjan Andrejc 03 Apr '12

03 Apr '12

Hey, Is it possible to change occupancy field to 1.0 in Chimera? I need a pdb file of my protein for docking and the file needs to have an occupancy field 1.0. Thanks for the help Darjan Andrejc, Mpharm PhD student, Department of Biotechnology National institute of Chemistry, Ljubljana, Slovenia

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Minimize with fixed atoms
by Hurt, Darrell (NIH/NIAID) [E] 02 Apr '12

02 Apr '12

Hi there, I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to <5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms. Am I in a local minima? Is that why nothing moves? The energy is very high (from the Reply Log): Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps Any ideas? I do have some hetero atoms... Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Re: [Chimera-users] morphing
by Elaine Meng 31 Mar '12

31 Mar '12

Hello Francesco! First make sure you are hiding the input conformations, so that you are seeing only the morph (for example, you could show Model Panel from Favorites menu, then uncheck the S(hown) boxes for everything except the morph results). I say that because if you see something not moving, it might be the original structure. As explained here, the morph should contain all of the atoms in the protein chain that are included in all of the input structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p…> Since your input structures are the same protein, if each one includes the sidechain atoms, the morph should contain all the same sidechains and they should move from one position to the other during the morph. They may not be displayed automatically, however. Try displaying all atoms (again better to hide the other structures first) to make sure of what is there. About the ion: even if the ion is in both structures, it may not be in the morph if you are using an older version of Chimera. However, there have been some fixes, and I believe if you are using Chimera 1.6 or newer, the ion should be included. The fix I'm thinking of was 6 months ago and is described here: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9886> If you try Chimera 1.6 and the suggestions above but you believe there is a bug, you could use Help... Report a Bug in the menu and describe how to reproduce the problem, attaching session file if necessary. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2012, at 5:24 AM, Francesco Malatesta wrote: > Hello from Rome! > I'm trying to morph 2 different conformations of the same protein. I get a very very nice movie, but I can't get amino acid side chains or heteroatoms (heme iron) to move also. > Is there any way to do this? > thank you for help > Francesco

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