- Chimera-users - RBVI Mailing Lists

1.6.1 release out
by Eric Pettersen 14 Mar '12

14 Mar '12

Hi all, We have put out a 1.6.1 release which, along with some minor fixes, corrects these problems: - Graphics would be corrupted or chimera would crash on recent versions of Linux, e.g., Ubuntu 11.10 and Fedora 16 - Planes (of Axes/Planes/Centroids tool) failed to start - Inappropriate "file types" (e.g. PDB ID) included in the file-type list of the main File→Open dialog - Very old sessions (pre-2006) would not restore on 64-bit Windows Please download 1.6.1 if these problems are affecting you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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plz ans the ques
by rashmi gupta 12 Mar '12

12 Mar '12

Sir, I am working on insilico metabolomic and genomic study of edible cyanobacteria. What plan should i do to accomplish my goal. -- Rashmi research scholar School of Biomedical Engineering IT BHU

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resolution for volume fitting
by Bala subramanian 07 Mar '12

07 Mar '12

Friends, I am a newbie to fitting molecular structures on a volume map. I would appreciate if someone could suggest me some guidelines to choose an optimal resolution of the map before fitting. Thanks, Bala -- C. Balasubramanian

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Increasing the mesh thickness in Chimera Volume Viewer
by Pradeep Pallan 07 Mar '12

07 Mar '12

Hi, I wanted to know whether there is an option to increase the mesh thickness in Chimera? I have loaded the map in Volume Viewer, but do not know how to increase the thickness of the mesh. Thanks for your help, Pradeep -- -------------------------------------------------------------------

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Linux and Chimera 1.6
by Greg Couch 07 Mar '12

07 Mar '12

If you have are running a recent version of Linux, for example, Ubuntu 11.10 or Fedora 16, then you should wait for Chimera 1.6.1 before updating or use a daily build. -- Greg

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Re: [Chimera-users] [Dock-fans] Help with antechamber
by Scott Brozell 07 Mar '12

07 Mar '12

Hi, On Tue, Mar 06, 2012 at 08:04:51PM -0500, Brad Ridder wrote: > Thanks for the responses, but I am still stuck on antechamber. > > We are holding off on this python scripting; that was the plan before, but > I want to make sure I can get the individual components working properly > before I go to the effort of writing a python script to do dock prepping. > > I cannot get either the DOCK-supplied version of antechamber or the > CHIMERA-supplied version of antechamber to work correctly. ==== dock > First, I tried the DOCK distribution again. $AMBERHOME was not defined. I > used: > > *$DOCK_HOME/bin/antechamber -i $PDBFILES/3GLR.pdb -fi pdb -o > $DESKTOP/3GLRcharged.mol2 -fo mol2 -c bcc* > > This returns the error: > * > Total number of electrons: 0; net charge: 0 > > Running: $DOCK_HOME/bin/mopac.sh > Error: unable to find mopac charges in mopac.out > * It is possible that antechamber is working and that mopac really fails. Did you look in mopac.out ? Are you really trying to run antechamber on 3glr, which is a protein ? antechamber is not the way to assign charges to a protein. Read the AmberTools manual http://ambermd.org/doc11/AmberTools.pdf Here is one way to test your dock's antechamber: cd dock6/install/test/amber_score_181l make ../../../bin/antechamber -s 2 -i lig.1.mol2 -fi mol2 -o lig.1.gaff.mol2 -fo mol2 -nc 0 -c bcc This last command should emit: ... Running: $DOCK_HOME/bin/mopac.sh Running: .../dock6/bin/am1bcc -i ... ... > I then repeated this later with $AMBERHOME defined to $CHIMERA/bin/amber11, > which gives the new error message: > > *Total number of electrons: 0; net charge: 0 > > Running: $AMBERHOME/bin/divcon > sh: > /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/divcon: > not found > Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly, > exit* This approach - using dock's antechamber with amberhome defined to be inside chimera - is not a good one. However, you might get it to work: It is very likely that sqm, not divcon, is the qm program that should be invoked. So get help to look for the option to force sqm usage: antechamber -h ... -df am1-bcc flag, 2 - use sqm(default); 0 - use mopac ... is probably what you'll find; if so then add -df 2 to your antechamber command line. > Now, a few questions/reflections: > > 1. As per the first error message, why is mopac.out causing trouble? Is > this a file I am supposed to make? mopac.out is the output of the mopac qm program which antechamber invokes and then processes to make am1-bcc charges. > 2. As per the second error message, I have no idea what "divcon" is, or > what it is needed for. There is no divcon file that comes with the CHIMERA > amber11 directory, nor is there any divcon file in the AmberTools amber11 > directory I have on my Desktop. divcon is another qm program. ==== chimera > I then tried the version of antechamber with the CHIMERA distribution. > First I typed: > > *$CHIMERA/bin/amber11/bin/antechamber* > > And antechamber said "AMBERHOME is not set!" > > So, I set $AMBERHOME to be $CHIMERA/bin/amber11. Then I used > > *$CHIMERA/bin/amber11/bin/antechamber -i $PDBFILES/3GLR.pdb -fi pdb -o > $DESKTOP/3GLRcharged.mol2 -fo mol2 -c bcc* > > The Terminal then spams: > > *Warning: detected more than 10 Residue sequence numbers; > this may be a large multiple residue PDB file; > large multiple residue PDB files are not supported. > Continuing, but problems may be encountered.* > > And then finally stops with > > *Segmentation fault* This warning was absent in early versions of antechamber. And it likely right on target. mopac (above) probably failed because you are really trying to run antechamber on 3glr. antechamber is not the way to assign charges to a protein. > So, in short, I am utterly bamboozled. Obviously, antechamber can handle > "large multiple residue PDB files", since the Dock Prep tutorial used the > AM1-BCC charge model on the large 1ABE.pdb protein, and it worked fine. Why > is it not working for me? No, the receptor charges were assigned using residue matching. See step 1 of http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecule… and the chimera dockprep docs: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecontrib.html "Charges for standard residues ... are taken from Amber (details)." Read the force field chapter of the AmberTools manual and references therein for even more details. scott > On Wed, Feb 29, 2012 at 10:30 PM, Scott Brozell <sbrozell(a)rci.rutgers.edu>wrote: > > Here's another similar ligand prep script: > > http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html > > While it is a good pedagogical exercise to prep once manually, > > scripting is the only practical approach for lots of ligands. > > > > As far as running antechamber, be careful and be specific about which > > one you run: > > If you are manually running Dock's antechamber then define DOCK_HOME. > > Do not define AMBERHOME. > > See > > http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#Error%20from%20amberize_ligand > > ; > > > > If you are manually running Chimera's antechamber then DOCK_HOME > > is irrelevant but AMBERHOME may be relevant. > > ( I have not manually run Chimera's antechamber, so my advice may be > > wrong. ) > > > > Also note that Dock's antechamber is circa 2006 with some key subsequent > > bugfixes. Chimera's antechamber is much more recent. > > Dock's antechamber uses mopac for qm; > > Chimera's antechamber uses sqm for qm; > > (http://ambermd.org/#AmberTools) > > I have found mopac to be more robust than sqm. > > Your mileage may vary. > > > > scott > > > > On Wed, Feb 29, 2012 at 04:08:22PM -0800, Eric Pettersen wrote: > > > This previous posting to the dock-fans list seems to be more directly > > > pertinent: > > > > > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > > > > > On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote: > > > >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. > > > > > > > >-----Original Message----- > > > >From: Brad Ridder <clustro(a)gmail.com> > > > >To: dock-fans <dock-fans(a)docking.org> > > > > > > > >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?

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Surface charge density!
by IONEL , ALINA ELENA 05 Mar '12

05 Mar '12

Hi, My name is Alina Ionel and I am PhD student. I have a pseudoatomic model (in pdb format) for a capsid protein. I did a representation of the electrostatic potential in Chimera with the option “Coulombic Surface Coloring” for a hexamer, for example. The unit of this potential are in Kcal/mol*e and the surface is colored in a range of values -10 to 10 Kcal/mol*e. I want to know the surface charge density for this hexamer (in C/m2). I need the value. Can you help me, please? Thank you, Alina

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Atom distances
by Kyle Morris 05 Mar '12

05 Mar '12

Hi, Is there a way in chimera to search a PDB (or any structure file..) for a particular distance and report back in text or visually between what atoms this occurs, i.e. query whether a structure contains atoms spaced at between 5.5-5.6 Å and which ones? Thanks in advance for your help, appreciate it! Kyle

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how to show backbone carbonyl oxygen
by james09 pruza 03 Mar '12

03 Mar '12

Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James

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How to show the electron density of just selected residues? Thanks
by Pingyang Liu 02 Mar '12

02 Mar '12

Hi, How to show the electron density of just selected residues? Thanks I followed the Chimera tutorial, but still the electron density of the whole protein was displayed. Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online. Thanks a lot. Best, Andy --

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segmentation fault
by nauton lionel 02 Mar '12

02 Mar '12

Hello I send this Email, because I can't used chimera-1.6 for linux 64 bits ( 2-29-2012 version) it crash with this comment "segmentation fault", everytime I tried to load pdb or mol2 files. and I don't have this problem with chimera-1.6rc for linux-32 bits or chimera-1.6( 2-29-2012 version) and chimera-1.5.3 for linux 64bits works well on the same PC I used fedora 16... regards

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Chimera 1.6 officially released
by Eric Pettersen 02 Mar '12

02 Mar '12

Hello everybody, A new production release of UCSF Chimera (version 1.6) is available: <http://www.cgl.ucsf.edu/chimera/download.html> Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). This will be the last Chimera release supporting Mac PowerPC platforms and OS X 10.5 (Leopard). New features include a Rapid Access interface to frequently used data and tools, new ribbon spline options, improved transparency rendering, new fetch type: Uniprot protein sequence and annotations, and several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting, etc. More details are given below; see release notes for the full list: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html> Graphics, Depiction: * new spline options for ribbon closer to backbone atom positions * new initial model colors, pastel rather than saturated * improved transparency rendering (global single-layer on by default) * 3D labels drawn on top by default * fancy backgrounds: images from files, color gradients from Palette Editor * options for cleaner pocket/tunnel surface display (see "sop" command) Structure Analysis and Modeling: * AddH allows specifying less common states of Asp, Glu, Lys, Cys * FindHBond can label H-bonds with distances * Blast Protein shows more info for PDB hits (ligands, resolution, etc.) * Build Structure improvements for joining peptides, swapping substituents * tools to change chain IDs, renumber residues * minimization: - can be conjugate gradient (previously steepest descent only) - parts of structures can be ignored * distance and angle plotting for trajectories * Cage Builder tool for generating polyhedral cage models <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu… > * interface to MultiFit web service (simultaneous rigid fitting of multiple structures to density, developed by the Sali Lab, UCSF) * "fitmap" command: - global search with random initial placement - iterative sequential fitting - symmetric fitting * "measure" command options: - map symmetry - surface contact area - center of mass User Interface and I/O: * Rapid Access interface to frequently used data and tools shown at startup, can be hidden/shown at any time by clicking the lightning-bolt icon <http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html> * caching fetched data is turned on by default * scaling with mouse/touchpad scrolling can be turned off (Mouse prefs) * Model Panel: - group/ungroup function, such as for NMR ensembles - functions reorganized into favorites/all * new input types: SPHGEN spheres, Maestro/Glide docking output (ViewDock) * WebGL export (experimental feature) Sequence-related: * new fetch type UniProt: protein sequence and feature annotations * Multalign Viewer: - UniProt features can be mapped onto already open sequences - Region Browser improvements for handling feature annotation regions - calculation of region overall RMSD - interface to Modeller homology modeling allows including water, other HET Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] reading SMILES description into Chimera
by Elaine Meng 01 Mar '12

01 Mar '12

Hi Boaz, You can just use the command line, for example: open smiles:CC1=CC=C(C=C1)S(=O)(=O)[O-] I'm thinking it may be a mistake that SMILES shows up as a file type in the "Open File" dialog. The only other place I can think of is in Build Structure (under Tools... Structure Editing), where the Start Structure section includes a SMILES option. In that case you would just type or paste in the SMILES string in the indicated field. 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 1, 2012, at 7:08 AM, Boaz Shaanan wrote: > Hi, > > I'm trying to read a small molecule for which I have a SMILES description into Chimera. I selected 'smiles' from the input options but it's not clear to me how to proceed. Do I have to generate a text file with the smiles description in it? do I paste the smiles description in the file name line? or what? > > Thanks for your help. > > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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how to copy partial charges from a .mol2 file to another
by Thomas Evangelidis 29 Feb '12

29 Feb '12

Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? Thanks in advance. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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partial conservation coloring
by Eric Pettersen 28 Feb '12

28 Feb '12

Jill Voreis wrote: > I'm trying to use chimera to show conservation maps. Using pdb files > that I fetch from the database using the pdb id number and > alignments created in clustal that contain the sequence of the pdb > file, I select render by conservation. For some reason, the > conservation colors only go onto my model when it's in ribbon form. > When I try to show the surface representation or use spheres so that > I can use commans to show the SAS, the colors of my model do not > match the conservation model but rather are stuck on some sort of > coloring scheme related to the compounds that are there. The > majority of the map looks brown, like the default color before > rendering by conservation. If you could help me, I'd really > appreciate it! Hi Jill, There are a few possibilities here, though it's impossible to be certain what the problem without access to a concrete example. My best guess is that much of the surface region of your protein is poorly conserved and those areas have columns where the rows are more than 50% gap characters. For such columns no conservation score is assigned. That means that when you use Render By Attribute with default settings, those atoms / surface parts will retain their original colors. If in Render By Attribute you use the "No-value color" color well to assign a color to such regions (perhaps gray) you will be able to tell if this is what is happening. Two other possibilities are that you don't have the "Color atom" and "Color surfaces" check boxes checked [though I image you would have noticed this!] or that your protein has multiple chains and that only one is associated with the alignment and only that one is getting colored. If none of these are "it", if you can provide me with a specific example so I can reproduce the behavior then I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Not crossfade but coinciding bond command...
by Kevin D. Walker 28 Feb '12

28 Feb '12

I temporarily disabled a bond command and found this to be the cause of the selected bond problem I am having. I don't think crossfade has anything to do with it.

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Animate a Reacton Mechanism?
by Kevin D. Walker 28 Feb '12

28 Feb '12

I constructed a movie for the first part of a reaction mechanism (substrate docking). I would like the animated mechanism to continue as follows. The substrate donates a proton to a tyrosine residue of the enzyme, forming an intermediate. The intermediate rotates 180 (I have accomplished this part) and the proton rebounds to the intermediate forming a new product, which is released. I can animate the product release -- it's the reverse of substrate docking. The part of the animation I cannot envisage is how to smoothly show or morph the bond transitions (bond breaking and making) during the reaction progression. IAny advice on whether Chimera or other ancillary software can do this is appreciated.

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using CalcAttr from a Python script
by Roger L. Chang 27 Feb '12

27 Feb '12

Hi, 1) I need to get residue.areaSES for two separate selections (all polar amino acids and all nonpolar amino acids). I have successfully generated a list of residue.areaSES using the GUI simply by selecting the residues of interest and then using the attribute calculator typing "residue.areaSES" in the formula box of the Attribute Calculator, which outputs the list to the Reply Log. This is the data that I need, but I need to get it for >2000 PDB structures and would like to automate this analysis through a Python script. I am somewhat new to Python and Chimera and don't yet know all the ins and outs yet. I dug through the code and found a method "getResidueAttr" in the "ResidueDataWrapper" class from "CalcAttr". This seems to be what I need, but I don't know the proper syntax to call it from my Python script. Could someone please provide an example? 2) I would like to sum the residue.areaSES values once I have them. I tried "sum(residue.areaSES)" in the formula box of the Attribute Calculator in the GUI, but this returns the error "Formula evaluation error: expecting vector argument in function". I'm not sure again on the proper syntax to use "sum()" in the Attribute Calculator. If I knew how to generate/save the residue.areaSES data from the command line, I could just parse the saved file and sum the values in Python. How can Attribute Calculator formulas be used from the command line, and if they can't, how can I save the residue.areaSES data to file from a Python script? Thanks in advance, Roger -- Roger L. Chang Graduate Student Bioinformatics and Systems Biology Graduate Program University of California, San Diego

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Coloring molmap surfaces
by Tom Goddard 24 Feb '12

24 Feb '12

> Greetings Tom > > How can color the molmap surface of certain atoms/residues. > > Many Thanks, Vijay > Hi Vijay, Use the Color Zone dialog to color a molmap surface to match nearby atom colors (menu Tools / Volume Data / Color Zone). You select the atoms you want to use for color (e.g. menu Select / Select All) choose a distance range from those atoms to color in the Color Zone dialog and press the Color button. In Chimera 1.6 (release candidate available on the web) or daily builds there is a command version of color zone. For example scolor #0 zone @ca range 5 says to color molmap surface #0 to match C-alpha atom colors within a distance of 5 Angstroms. To avoid jagged edges in the coloring you should use the molmap gridSpacing option to specify a grid size about 1/5 to 1/10 the map resolution. The default value is 1/3 of map resolution making a fairly coarse surface mesh. Colors are only assigned to the mesh vertices, so a fine mesh is needed for smooth boundaries between different color regions. Tom

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batch peptide builder
by Xiao-Ping Zhang 23 Feb '12

23 Feb '12

Dear Chimera developers, I would like to generate some peptides from a protein sequence. The peptide builder in Chimera is a very nice application. I wonder if there is a stand alone script which I can use to generate series peptides from the command line. Thank you for your help. Xiao-Ping Zhang

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Drawing arrows without using .bild file
by Victor Muñoz 21 Feb '12

21 Feb '12

Dear all, I'm trying to make a script that draws an arrow on every atom and every frame during a trajectory using the MD movie. Right now, the script creates a .bild file to draw the arrows, but it is not a very good approach since it is creating a new file for every frame of the trajectory. I was wondering if there's a way to do the same thing without having to create the .bild file. I already checked the "shape" command but you can´t use it to draw an arrow. Maybe I should make a combination between a cylinder and a rectangle to draw an arrow? Is there any other easy way to do that? Thanks in advance. Kind regards, --

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bug
by Eifler, Jay Q. (UMKC-Student) 21 Feb '12

21 Feb '12

Whew, too much work to get you guys a message. The bug report form was lengthy. Anyway, can't join models in your latest 1.6 version but 1.5 whatever is fine. Should have never updated.

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(no subject)
by Valia Dimitrova 21 Feb '12

21 Feb '12

Hi, I am PhD student, and I am working with program Gaussian, I want ask you some questions. I want to make maps with electrostatic potential, I saw that with this program may be make very beautiful pictures. What type of files I have to have, so I can do these pictures? I have ".fchk" files and ".cube" files. May I use them to make this? I will be very appreciated if some one can help me. thank you in advance Valia Nikolova

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how to find
by Bishwajit Das 18 Feb '12

18 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* * --

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bug report
by Longfei Wang 16 Feb '12

16 Feb '12

Hi there, For nogui Chimera: Calls with script in nogui mode create the following traceback. terry@daisy[14]% chimera --nogui --script "coord_for_cluster_ATP_ bothChiFlip.py" Traceback (most recent call last): File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimeraInit.py", line 618, in init chimera.initializeGraphics() File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/__init__.py", line 2114, in initializeGraphics bgprefs.initialize() File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimera/bgprefs.py", line 211, in initialize onDisplay=_bgPrefDisp, onHide=_bgPrefHide) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 567, in register self._loadCategory(category, cat, inherit, convert) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 482, in _loadCategory cat.load(self._loadDict[name]) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 249, in load opt.set(value, asSaved=True, fromPref=True) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 64, in set self._callback(self) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimera/bgprefs.py", line 53, in _backgroundColorCB Midas.background(color=color, setMethod=False) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/Midas/__init__.py", line 966, in background method = chimera.viewer.Solid AttributeError: '_chimera.NoGuiViewer' object has no attribute 'Solid' Best Longfei -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115

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Re: [Chimera-users] radius of gyration
by Eric Pettersen 15 Feb '12

15 Feb '12

On Feb 14, 2012, at 6:07 PM, Daniel Gurnon wrote: > Hi Eric, > The radius of gyration interest stems from a little project I'm > starting with an undergrad. I'm interested in the radius of gyration > because I'm curious about how accurate our pictures of biomolecules > are, at least the ones that come from crystal structures. I'd like > to compare predictions of size-related behavior derived from the pdb > with measurements of size in solution, using gel filtration, SAXS, > or light scattering. That said, I don't know if I want center of > geometry or principal axis! Any advice? Hi Dan, I'm no expert, but it sounds like you want the radius of gyration from the center of geometry. Nonetheless, I'm cc'ing this to the chimera-users in case any others have thoughts. In an old posting to chimera-users, Elaine Meng provided a Fortran program to compute the radius of gyration: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003648.html I've attached a Python script that will print the center of geometry and radius of gyration from that center in Chimera's reply log. Run the script simply by opening it with File->Open. Depending on whether you feel nearby waters and ions will contribute to the measurements you are trying to model, you may or may not want to delete water and ions before running the script. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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radius of gyration
by Daniel Gurnon 14 Feb '12

14 Feb '12

Hi all, Can Chimera determine (or has a script been written to determine) the radius of gyration for a pdb structure? Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] possible Chimera bug?
by Ofeliia Mada 14 Feb '12

14 Feb '12

TkkyuluR X,=)RSISXSN:-P:(:=(=(=(=(=(:O(, G Sent from my Windows Phone esdcqppwevemeem

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fly command
by rswett＠chem.wayne.edu 14 Feb '12

14 Feb '12

Is anyone else having issues with the fly command lately? Seems like since RC 1.5ish flying to a savepos ignores the # of frames it's set to fly over. i.e. fly 50 in (where in is a saved position) does the fly in one frame, appearing the same as fly in or fly 1 in Additionally fly in 50 has the same effect. Has anyone else run into this? I have a few saved sessions i'd like to animate, and the older versions are having none of it. Suggestions? ~Rebecca

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Re: [Chimera-users] meaning of the ANISOU PDB parameters
by Eric Pettersen 13 Feb '12

13 Feb '12

On Feb 10, 2012, at 1:55 PM, Julian Chen wrote: > hi Eric, > > First of all, hello, I was in Stroud's lab for many years, until > 2003, when I left SF. Hi Julien! > I am in a rather interesting situation where we have been dealing > with neutron and X-ray refinement, and we have been able to do > anisotropic refinement on selected hydrogen atoms, from having high > resolution neutron data. I've been using Chimera. > > I am still somewhat confused as to the meaning of the six ANISOU > terms, I understand that the first three describe the three > orthogonal axes of the ellipsoid, and that the last three somehow > relate this to the coordinate space. The six terms actually describe a 3x3 matrix that is symmetric about the diagonal. The eigenvectors and eigenvalues of that matrix are the atomic displacement axes and the mean squares of the displacements respectively. The first thing to know is that the values shown in the ANISOU records are scaled by 10**4. The other thing to know is that the six numbers correspond to these positions in the matrix: 1,1 2,2 3,3 1,2 1,3 2,3. Since the eigenvalues are mean squares, one typically works with the square roots of the eigenvalues. > Specifically, I want to look at the ANISOU for the H/D atoms, and > want to try to correlate it to its bonded neighbor (the C or the N > or the O). If possible, I'd like to extract some vector for the > 'directionality' of the aniso atoms and relate them to one another. > I want to see if the vibrational motions of the hydrogen are > correlated to the vibrational motions of its bonded neighbor. Is > there anything in CHIMERA that could do something like this, or some > appropriate mathematical formula that could output the right sort of > information? The ellipsoids option in the program gives a > qualitative description, but I'd like to get something a bit more > quantitative in nature. Depending on how comfortable you are with programming in Python, you could either write your own external code based on the info above, or write something that runs in Chimera. The latter does have the advantage of you not having to write PDB-parsing code an so on. In Chimera, atoms with corresponding ANISOU records have an 'anisoU' attribute which is a 3x3 matrix (the matrix is often referred to as 'U' in the literature, hence ANISOU record). This code snippet (basically copied from the Chimera's Aniso module) will extract the eigenvectors/values for an atom and take the root of the values: from numpy.linalg import svd ignore, lengths, axes = svd(atom.anisoU) from numpy import sqrt lengths2 = sqrt(lengths) Let me know if you need more info or help with scripting. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Visualising AutoLigand affinity points
by George Tzotzos 09 Feb '12

09 Feb '12

Hi, I'm attaching a jpg image of ligand affinity map fill points generated by AutoLigand. My question is whether there's a way to depict these fill points as "disconnected" spheres. Actions/spheres generates something like I'd like to see but the size of the spheres is too large. Regards George

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pi-cation interaction
by Bishwajit Das 09 Feb '12

09 Feb '12

how to find cation pi-interaction in a docked molecule.......plz help me -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* *

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How to select
by Bishwajit Das 09 Feb '12

09 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* *

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Re: [Chimera-users] Rotamer copying- Specific Residues only
by Eric Pettersen 08 Feb '12

08 Feb '12

On Feb 8, 2012, at 8:27 AM, Ahir Pushpanath wrote: > Eric, although the script is highly useful for what I previously > asked, I have come to the realisation that simply copying all the > apo chi angles to the holo form may not be ideal for me in this > particular situation. I noted that of around 200 residues modelled, > around 90 of them are modelled different to the apo, the rest are > modelled similar to the apo form. Of these 90, only around half are > truly changed in the holo form(literature evidence from homolog), > therefore I do require a script that is able to accept an input of > which residues to copy the chi angles for, I think this will be > useful for other users who want to copy chi angles from apo-holo > forms and other applications, and probably could be included in > later build versions of chimera, under structure editing. > > Do you think you could help me with this? I am only learning python > now, so my scripting is not at a good level for these types of things. I've attached a modified script that will only copy the chi angles for residues that are selected in the lowered-numbered model. It's up to you to select them somehow. :-) > On another note, do you have any experience with using chimera to > model apo-holo transitions any other way without using Modeller? I don't. Maybe others on the list will have suggestions... ? > Also, does chimera have the ability to do docking of ligands, i.e. > given you know the apo crystal structure, can you tell it to dock a > ligand and change conformation of protein,(similar to autodock)? Currently Chimera cannot dock ligands. If our next 5 years of funding gets approved by the NIH, we have proposed interfacing Chimera to an Autodock Vina web service that would allow docking to be carried out directly from Chimera. Right now all you can do is prepare the input for / analyze the output of external docking programs in Chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to find hydrophobic interaction
by Bishwajit Das 08 Feb '12

08 Feb '12

how to find hydrophobic interaction in a docked protein structure......please help me.... -- BISHWAJIT DAS +91-9433237920 KOLKATA,West Bengal INDIA* *

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how to setup a default settings for a new pdb model?
by Xing Zhang 07 Feb '12

07 Feb '12

Hi, I have many different pdb models that need to be displayed at exactly the same settings, including color, background, stick scale and so on, so I want to set all these settings for the first model, and then apply these settings to a newly opened pdb model. Is there any way to save and load a default setting for a new pdb model? Thanks much. Xing

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Rotamer copying
by Ahir Pushpanath 07 Feb '12

07 Feb '12

Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively) Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog. However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right. Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues. Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you! Ahir

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associating multiple structures and sequences
by Uppal, Karan 07 Feb '12

07 Feb '12

Hi, I am writing a custom extension based on MultiAlign Viewer that highlights regions in a multiple sequence alignment based on numerical values stored in an external file. I modified the RegionBrowser.py script, and added a function that works just like "showSS". It works fine for one structure and sequence combination. However, I am trying to associate multiple copies of the same protein structure and its sequence. So, the structures are identical and so are the sequences in the sequence alignment, but each copy represents different information. My problem is that the sequences in the alignment viewer dialog box are highlighted in a random fashion. And, I want the sequences to be highlighted in an ordered fashion starting from first sequence to last sequence since we want to be able to map the highlighted regions back to the external file. Is there a way to control the order in which the sequences are highlighted in the alignment viewer dialog? Or is there a way to get the model # associated with a particular sequence and using the model # to highlight the alignment viewer? I would highly appreciate your help. Thank you, Karan Uppal Application Developer Emory University ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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minimization with nonstandard atoms
by Jon N. Rumbley 07 Feb '12

07 Feb '12

I was hoping to minimize a homology model containing two heme groups. To understand how I might do this I have been starting with the known structure 1a6m. As suggested in the documentation I begin with Dock Prep and calculate charges etc. To my surprise Chimera alpha version 1.6 (build 34702) actually assigned charges to the heme. The problem is with the minimization itself. Within Minimize Structure I turn off all of the Dock Prep steps and simply try to minimize the structure but get an error,"Element Fe (atom #0:154.A@FE) is not currently supported". I was assuming the charge calc was going to be the hard part but now I am stuck at this subsequent step. Is there something I can do to get the heme atoms recognized or is this simply not possible? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 Life Sciences 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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Manipulating representation during MD movie
by Jean Didier Pie Marechal 07 Feb '12

07 Feb '12

Hi guys, I have a MD movie I generated that I want to record. However, I would need to ask on the graphical representation at given frames (i.e. frame 60) so that the system changes (i.e. change the representation en stick or add a given label). Is there a way to do so directedly? Or should I go for a command file? In this case, how would I mix the MD movie with my own succession of events? All the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dilluns, Febrer 6, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 106, Issue 7 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.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. Rotamer copying (Ahir Pushpanath) > 2. Re: Rotamer copying (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 6 Feb 2012 18:51:22 +0000 > From: Ahir Pushpanath <ahir29(a)googlemail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Rotamer copying > Message-ID: > <CAMVKkxyEoXbnQUo7hxa+m2-u5wLCvMJn7DDY=hzZPJEbC_OvSw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello there, I have a question regarding MODELLER in Chimera and the > ability of chimera to adjust the model using some inbuilt features > quickly(i.e. automatically, instead of interactively) > > Firstly, I am trying to model the "holo" form of an enzyme with known > apo-form structure. I did this usinig the two independent domains > of the > apo form as a template (in a bid to get the domains accurate) and > for the > holo-form closure I used a very similar homologue that has been > solved in > the holo form. The results were good and I got a decent model that had > closed up like the homolog. > > However, I noticed that in the model a lot of the sidechains have > not been > modelled with the right rotamer. This is odd, as I gave it the two > independent domains as a template, so it had all the information it > neededto get that perfectly right. > > Either way, this means, I need to manually "copy" the rotamers from > the apo > form onto the "holo model", which is time consuming. I know from the > homolog that only two or three residues in the active site change > rotamerupon apo-holo conformational change. So, I just want an easy > way to edit > the rotamers in the holo-model to copy the rotamers of the apo-form > for all > residues. > > Is there an easy way to do this, is it possible to this with a > script? I > have no idea how to script, mind you! > > Ahir >

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how to find salt bridge
by Bishwajit Das 04 Feb '12

04 Feb '12

how to find salt bridge in a docked structure........plz help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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Coloring electrostatic potential
by George Tzotzos 03 Feb '12

03 Feb '12

Hi everybody, I'm using SiteHound for ligand binding identification sites. I'm comparing the highest affinity sites for two superimposable receptors. I'm attaching an example where the sites favourable to protein 1 are shown red, whereas those for protein two blue. I've opened in Chimera the file that contains the red and blue clusters (difference.pdb) as well as the corresponding potential file (potential.dx). I used the Volume Viewer to different affinity areas but had .... no luck. Any help would be greatly appreciated Best regards George

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export saved session
by Gabor PAPAI 02 Feb '12

02 Feb '12

Dear Chimera team, Is it possible to export a session with all of its files to a different location - for e.g. to a USB flash drive for portability reason? I'd like to open a session saved to a server on an offline computer (during travel). I know that I can do it manually just I'm searching for quick solution. Thank you in advance for the help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-88655748

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selection based on ring names
by Bala subramanian 02 Feb '12

02 Feb '12

Friends, I have two ligands with a common benzoxadiazole ring. I want to do the rmsd comparison only on the ring, but the names of the atoms forming the benzoxadiazole ring are different in both the ligands. Is there any way to use ring name as a string the compare the rmsd. ie. rmsd of benzoxadiazole of ligand 1 and benzoxadiazole ring of ligand 2 -- C. Balasubramanian

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stereo with zalman monitor
by Jose Miguel Mancheno 01 Feb '12

01 Feb '12

Dear colleagues, I am trying to see stereo images with chimera (candidate version 1.6 for mac) using a Zalman monitor ZM240W which works OK with COOT, which is connected to an iMac. As far as I know, I have to select (within the camera mode) the option: row stereo, right eye even (or odd). However, none of these options provided stereo images. If I select sequential stereo (or reverse sequential stereo) I see the image flickering, as expected, but this is not synchronized with the zalman glasses. Any suggestion about how to proceed to see in stereo mode? Thank you very much in advance. José Miguel --

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Selecting equivalent surfaces
by Ankush Aggarwal 01 Feb '12

01 Feb '12

Hi, I am opening up a viperDB file of a T=3 virus in Chimera. I want to select the 60 equivalent copies of a protein, so that I can change their color together. I am able to select selecting each of them separately. Is there a smarter way to do it? Also, after I rotate the view, is there a command to reset it to the default. Right now, I am "undoing" the move, but it can be a pain if I have moved the model a few times. Thanks, Ankush.

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Notebook
by Miguel Ortiz Lombardía 01 Feb '12

01 Feb '12

Dear all, Was the notebook feature implemented in Chimera? I found a message from some time ago but nothing else? Any plans to include a session notebook? I would ask for something really simple, just apt for text notes. Currently, I create text files with the same name than sessions but with .txt extension, however I think it would be useful to have this built-in in Chimera. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Re: [Chimera-users] HIV ligands
by Eric Pettersen 31 Jan '12

31 Jan '12

On Jan 30, 2012, at 5:27 PM, Forbes J. Burkowski wrote: > Hi: > > I think I have found a bug or least a small inconsistency... > > If you fetch 3NDW and do the menu invocation: > > Select... Residue... > > The list in the submenu offerings includes RIT. > > In a command line, I can use: > > sel :RIT > > to get the same selection. > > Now, repeat the above invocations for 2FDE. > > The Select... Residue... leads us to believe that the ligand can be > accessed as 385. But when I use: > > sel :385 > > I do not get a selection. > > This alternate strategy to do the selection is important for me > because I > am getting the same problem when I put this command into the > runCommand > string within a script. > > The same problem seems to exist for 3SM2 and 3SO9. Both have the > ligand > designated by a number so I have a suspicion that one must do > something > different in the sel command when a number is used to designate the > ligand > instead of a character triplet (such as RIT). > > Is this a bug or am I missing something in the syntax of the sel > command? Hi Forbes, Pedantically speaking, the single-colon (e.g ":532") syntax takes a residue sequence number afterward, whereas the lesser-known double- colon syntax (e.g. "::ala") takes the residue name. Now, as a convenience, if you type something that is not an integer after the single colon, then it assumes you mean the residue name and switches over to interpreting it like the double colon does. But in your case you have character strings that you always want interpreted as residues names regardless of whether they look like integers, so you should just use "::" all the time. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] how2 select named selections using command-line [chimera1.5.3]
by Eric Pettersen 31 Jan '12

31 Jan '12

On Jan 31, 2012, at 2:34 PM, frederick lee wrote: > thanks VERY much eric and elaine. > > last question: how do i find out about the alias definitions, if > any, stored > in a session from within chimera instead of looking inside the > python script > (of that stored session). Hi Fred, "alias" with no arguments will list all current aliases in the reply log. --Eric

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how2 select named selections using command-line [chimera1.5.3]
by frederick lee 31 Jan '12

31 Jan '12

dear chimera users, i can defined named selections and they work under the select menu. however, i canNOT use the command line to select them; e.g., i have 4 named selections 0a,0b,1a,1b dis 0a | 1a works sel 1a NOT working sel :1a NOT working (said selection cleared) i like to be able to select multiple named selections and further apply filters on them; e.g., "select 1a and 1b and atoms=side chain atoms" how do i accomplish this? as always thank you very much. fred

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