- Chimera-users - RBVI Mailing Lists

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 06 Mar '12

06 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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