- Chimera-dev - RBVI Mailing Lists

thank you so much
by Corey Fugate 26 Oct '09

26 Oct '09

I started using Chimera a few weeks ago. It is wonderful, I love it.

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select opt
by Victor MuÃ±oz 23 Sep '09

23 Sep '09

Dear Mr/Miss: I'd like to know if there's a way to select the select mode "append" using the command line instead of the visual interface. Thanks for your help. Your sincerelly, Victor Muñoz

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About Backbone Dependent Library
by ylei＠ecs.umass.edu 17 Sep '09

17 Sep '09

Hi all I am currently working on a project, which needs to rebuild the statistics using modified protein structures, say, some other set of proteins. There is one quick question about interpreting the BBDep Library. What's the exact definition of the fourth column "N" in the library file format? I thought for each residue within some (phi,psi) angle pair bin, it is the total number of sidechains found in all of the 850 proteins. However, I checked ASN and GLN these two types of amino acids using "Chimera" to return the (phi,psi) dihedral angles for each ASN and GLN residue among 850 proteins with tens of exceptions which have no dihedral angles returned from Chimera(I just ignore them). Then, I count the number of sidechains for each (phi,psi) bin(10*10 degree). It turned out that this number is not consistent with the "N" value in BBDep. e.g. For ASN at bin (phi=-70,psi=-40), Chimera returns 372 sidechains in total from those 850 proteins, while BBDep says 2348. The difference is so large and very common over almost all the bins. I thought probably there might be some stupid errors in my understanding of the "N" value, but could you point that out for me? Or, did Dunbrack guys use another set of proteins other than those 850 ones? Best regards and thanks, Yang Lei Electrical & Computer Engineering University of Massachusetts, Amherst

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suggestion for feature addition to chimera
by Rocco Varela 09 Sep '09

09 Sep '09

Hello, I have a small suggestion for an additional feature for Chimera that I think would be useful. I often look at structures of multiple small molecules, some artificial and some real, and I noticed something interesting with the way Chimera writes mol2 files. Here is Scenario 1: 1) I open a mol2 file that contains multiple molecules flagged as "separate" MOLECULEs. 2) I save the loaded file as mol2 and select "a single file [combined @ MOLECULE section]" for the "Save multiple models in" option. 3) After saving and reloading this new mol2 file that now has a single MOLECULE section, all the "names" of the previous molecules have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the SUBSTRUCTURE section "UNK0" is used. It would useful if Chimera could name the components of the new single molecule with the proper names. I could easily write a script to fix this after the fact but I thought it might be a useful option for other people too? Scenario 2: 1) Same as 1 above. 2) Now I want to save all the MOLECULEs in the file as separate mol2 files but with the proper "names" that are listed in the original file loaded. Currently the only option is to provide a common name and to append the "model number". It would be nice if we were allowed to NOT provide a common name and allow it to name all the files according to the molecule "names" not model numbers. Thanks for your time :-) Rocco

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problems with xformCoord and coord
by Elisabeth Ortega 09 Sep '09

09 Sep '09

Dear All, I'm doing a script change the coordinates x,y,z for one molecule to move it using xformCoord coordinate system but my script doesn't work very well. My function looks like: atom.setCoord(a.coord()-0.1*(vector(x,y,z))) How can I write it in xformCoord? a.setCoord doesn't return to me xformCoord even if I write all the variables using xformCoord. In other words, I'm asking about the "translation" of the function atom.setCoord() in xformCoord coordinates. Thank You -- Elisabeth Ortega Carrasco Universitat Autónoma de Barcelona (Spain) eortega(a)klingon.uab.es

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Suggestion: define selection name for startup chimera
by Jean Didier Pie Marechal 09 Sep '09

09 Sep '09

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suggestiion 2: altLoc attribute for residues
by Jean Didier Pie Marechal 08 Sep '09

08 Sep '09

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timeline for python2.6 in Chimera on OS X?
by Mark Moll 08 Sep '09

08 Sep '09

On OS X 10.6 (Snow Leopard) the default python version is 2.6. Python 2.5 is also available, but is kind of hacky. Part of the problem is that python2.5 doesn't compile as a framework. Another (possibly related) problem is that Tk depends on Carbon (at least the "native" version does) and Carbon no longer exists in 10.6. See http://bugs.python.org/issue6802 for details. I'm relying both on MacPorts and Chimera for dependencies, so I need them to be in sync (for example, boost.python built against python2.6 won't work with Chimera's python2.5). I could try to hack around the python2.5 problems on 10.6, but it'd be nice if I could drop in python2.6 in Chimera and everything would "just work." This is unlikely going to be the case, so I was wondering if the Chimera team already has a switch to python2.6 planned in its development roadmap. -- Mark

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OT: off-screen app on OSX
by Randy Heiland 04 Sep '09

04 Sep '09

Hi folks, Off-topic, but would one of you have any insight as to why a new vis app I built/ran on OSX appears partly off-screen (off the top). I was thinking that maybe I've seen this same behavior at times with Chimera, but can't recall the circumstances. Fwiw, the app is from vtkedge.org. I'm exchanging emails with one of the developers who has admitted that they haven't done testing on OSX yet. thanks, Randy

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Re: [chimera-dev] [Chimera-users] Ignored settings
by Eric Pettersen 24 Aug '09

24 Aug '09

Hi Mark, I don't know how you're opening these molecules but if you're using the "open" command then providing the "noprefs" keyword will prevent smart display. Also, if you are using openModels.open() or openModels.add() then there is a 'noprefs' keyword that you could specify as False. The 'noprefs' keyword for the open command has been around for awhile, but that keyword is new for the openModels functions, so if your plugin needs to work with a variety of Chimera versions either you will need to introspect the openModels function (using Python's inspect module, probably the getargspec function) or check chimera.version. I actually recommend the inspect approach since the format of chimera.version has changed over time, so inspect is more bulletproof. Using that setAttr command for stickScale works for me. You are aware that stickScale defaults to 1, right? There will be some minimal speed advantage to using direct Python calls to runCommand (elimination of some of the text parsing), but I would only expect the difference to be noticeable if we are talking about thousands of calls to the functions. I guess I'm referring to the type of code you sent, where the Midas-module equivalent function is called (so only the parsing is eliminated). There certainly could be more savings in some cases where the generic Midas-module code is replaced by special-purpose code. --Eric On Aug 24, 2009, at 11:42 AM, Mark Moll wrote: > Eric, > > I'm observing some odd behavior with a recent daily build (build > 28565) that may be related to this. I am working on a plugin that > creates new models. *After* the chimera models have been created, > the plugin runs a number of Midas commands in the python code: > > Midas.undisplay('element.H') > Midas.represent('stick','#') > Midas.represent('bs','@ca') > Midas.color('byhetero','#') > Midas.setAttr('m','stickScale',1,'#') > Midas.setAttr('m','ballScale',.35,'#') > > This doesn't seem to have the desired effect. Turning off "smart > initial display" works a little better, but the stickScale command > still has no effect... > > (BTW, is there any speed advantage to using python commands rather > than runCommand statements?) > -- > Mark > > >

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Crash on Ubuntu
by Svetlana Lockwood 12 Aug '09

12 Aug '09

I am just wondering if anybody has used successfully Chimera on Ubuntu. I downloaded and installed it ok, launch - ok, but then while opening (or fetching) a file - oops! Chimera disapears (program closes). Any ideas why or how to fix this? Meanwhile I'm using it on a PC - and scripting on there is not a fun. Cheers,

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Rotation of a single submolecule in a mol2
by christopher lau 08 Aug '09

08 Aug '09

Hi, I am currently working on a project to modify the ViewDock program to work on a Tiled Wall Display. I am reluctant to require the user to download the daily build to allow use of molecule specific rotations in my TDW ViewDock program. I was wondering if there was a way from the Command Line to rotate a single molecule, say #0.1, without rotating all the molecules in model #0. If it is possible to inactivate all the submodels except for #0.1, I can use the rotation commands (roll, rock, turn) to rotate a single submolecule. I know that I can split the submolecules into individual molecules and apply the rotations in this manner, but that would make the data handling very difficult. I was having problems learning how to deactivate models using the select command with the current stable version of chimera. I was wondering if anyone had any insight on this problem. I would prefer to not require the daily build and would not want to use the split command line command to separate the submolecules into separate molecules for rotation. Thanks for your help, Chris

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Re: [chimera-dev] [Chimera-users] Minimize
by Eric Pettersen 04 Aug '09

04 Aug '09

> Begin forwarded message: > >> From: Alex Gawronski <alex.gawronski(a)gmail.com> >> Date: August 4, 2009 1:28:42 PM PDT >> To: meng(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] Minimize >> >> Hello again, >> >> Is there a way to run Dock Prep, without GUI, from a script or >> command line? I tried 'start Dock Prep' with the headless linux >> version and it gave me a "ImportError: No module named Togl". >> >> Thanks, >> Alex You have to use a Python script in Chimera. Something along the lines of: from chimera import openModels, Molecule, runCommand from DockPrep import prep prep(openModels.list(modelTypes=[Molecule])) runCommand("write out.pdb") which you would then use in Chimera in a fashion similar to this: chimera --nogui structure001.pdb script.py mv out.pdb processed/structure001.pdb There are keyword arguments to the prep() function for changing it's behavior in the same fashion as the check buttons do in the DockPrep graphical interface. If you're familiar with Python you could modify the script to loop through your files directly in one instance of Chimera rather than calling Chimera once for each file. --Eric

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Re: [chimera-dev] Chimera-dev Digest, Vol 66, Issue 12
by Jean Didier Pie Marechal 31 Jul '09

31 Jul '09

Dear Tom and All, During the last months, I have been improving in chimera's world by using helps and flying through the scripts as you told me to do last year (and obviously by sending you tons of queries). I am now getting with a small group of students with whom we are developping some scripts from different level of complexity. I think that for some of them it is easier to understand the whole architecture through the programmer's reference. Thanks a lot for trying to get it back on the web. All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Divendres, Juliol 31, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 12 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Re: Programmer's reference (Thomas Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 30 Jul 2009 17:21:40 -0700 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Programmer's reference > To: chimera-dev(a)cgl.ucsf.edu > Message-ID: <4A723914.9030202(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi JD, > > We decided at or Chimera developer meeting today that we would > revive > the programmer's reference on the web. It will still be auto- > generated > from code comments, probably from a newer version of HappyDoc. > Eric > Pettersen will look into it. It may be many months away since we > have > lots of higher priority projects. > > Tom > > > -------- Original Message -------- > Subject: Re: [chimera-dev] Programmer's reference > From: Thomas Goddard > To: chimera-dev(a)cgl.ucsf.edu > Date: 7/27/09 4:58 PM > > > Hi JD, > > > > The automatically generated programmer's reference was removed > from > > the Chimera distribution because it was large and rarely useful. > When > > it was taken out of the distribution we did not set up a daily > automated > > build for a web site reference guide. I believe that used to > come from > > the automatic Chimera distribution builds. We'll discuss whether > we > > should bring this back at this Thursday's developer meeting. > > > > For development here we use dir() and help() in the IDLE shell > as > > described previously > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2008- > February/002354.html> > > Also we look directly at Python code files which are included > with all > > Chimera distributions under the chimera/share directory > > (Chimera.app/Contents/Resources/share on Mac) and we look at the > C++ > > header files which are included in distributions under > chimera/include. > > Of course we work all the time on Chimera code so these methods > may > > not be ideal for your less frequent programming needs. > > > > While we ponder this, you can use the Chimera 1.3 programmer's > > reference included with the distribution in > > > > share/chimera/helpdir/ProgrammersGuide > > > > Tom > > > > > > -------- Original Message -------- > > Subject: Re: [chimera-dev] Programmer's reference > > From: Thomas Goddard > > To: chimera-dev(a)cgl.ucsf.edu > > Date: 7/27/09 1:34 PM > > > >> Hi Tom and All, > >> > >> thanks for the answer. I knew the pdf was removed, but not the > full > >> reference. > >> Though it was complicated sometime to get to the right place, I > finally > >> got used to it and it was useful to me. > >> > >> Do you think of posting another kind of reference in the future > or will > >> you stop to provide any? > >> > >> all the best, > >> JD > >> > >> -------- Original Message -------- > >> Subject: Re: [chimera-dev] Programmer's refere > <goddard(a)cgl.ucsf.edu>>> To: Jean Didier Marechal > >> Date: 7/24/09 10:10 PM > >> > >>> Hi JD, > >>> > >>> I believe we no longer provide the programmer's reference > guide. It > >>> was automatically generated from source code comments using > HappyDoc. > >>> It's quality was so poor we stopped generating it. > >>> > >>> Tom > >>> > >>> -------- Original Message -------- > >>> Subject: [chimera-dev] Programmer's reference > >>> From: Jean Didier Pie Marechal > >>> To: chimera-dev(a)cgl.ucsf.edu > >>> Date: 7/24/09 2:34 AM > >>>> Dear All, > >>>> > >>>> It seems that we have a problem in getting to the programmer's > reference. Is there something wrong with the server? > >>>> > >>>> All the best, > >>>> JD > >>>> > >> _______________________________________________ > >> Chimera-dev mailing list > >> Chimera-dev(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > ------------------------------ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > End of Chimera-dev Digest, Vol 66, Issue 12 > ******************************************* >

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Programmer's reference
by Jean Didier Pie Marechal 31 Jul '09

31 Jul '09

Dear All, It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimecres, Juliol 22, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 7 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. small suggestion regarding savepos (Jean Didier Pie Marechal) > 2. Re: small suggestion regarding savepos (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 22 Jul 2009 13:20:56 +0200 > From: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> > Subject: [chimera-dev] small suggestion regarding savepos > To: chimera-dev(a)cgl.ucsf.edu > Message-ID: <3a0ecec54f4c.4a671238(a)uab.es> > Content-Type: text/plain; charset=iso-8859-1 > > Dear all, > > I see that when I close a session, the savepos list continues > containing the poses I defined for my anterior session. May be that > is something you want to have this way, but I was wondering if the > savepos (with an option for example) could list only the poses for > the working session. > > All the best, > JD > > > > > Dr. Jean-Didier Mar?chal > Lecturer > Computational Biotechnological Chemistry @ Transmet > Unitat de Qu?mica F?sica > Departament de Qu?mica > Universitat Aut?noma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 22 Jul 2009 11:43:20 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] small suggestion regarding savepos > To: JeanDidier.Marechal(a)uab.es > Cc: chimera-dev(a)cgl.ucsf.edu, Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <D600289F-8E55-4765-96AB-F2F4E264138C(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi JD, > I think you're right: closing a session should clear saved > positions. In tomorrow's build that's what will happen. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Jul 22, 2009, at 4:20 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > > > I see that when I close a session, the savepos list continues > > containing the poses I defined for my anterior session. May be > that > > is something you want to have this way, but I was wondering if > the > > savepos (with an option for example) could list only the poses > for > > the working session. > > > > All the best, > > JD > > > > > > > > > > Dr. Jean-Didier Mar?chal > > Lecturer > > Computational Biotechnological Chemistry @ Transmet > > Unitat de Qu?mica F?sica > > Departament de Qu?mica > > Universitat Aut?noma de Barcelona > > Edifici C.n. > > 08193 Cerdanyola (Barcelona) > > Tel: +34.935814936 > > e-mail: JeanDidier.Marechal(a)uab.es > > > > > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >

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Surface Vertices
by Alex Gawronski 27 Jul '09

27 Jul '09

Hello, I would like to write to file all the vertices of the surface of a protein corresponding to each residue. Currently I'm exporting a mesh file of the surface fragments but this requires a lot of disk space and would probably be slower then simply writing the vertex list to file. Is there a way to do this using a python script? Thanks, Alex Gawronski

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small suggestion regarding savepos
by Jean Didier Pie Marechal 22 Jul '09

22 Jul '09

Dear all, I see that when I close a session, the savepos list continues containing the poses I defined for my anterior session. May be that is something you want to have this way, but I was wondering if the savepos (with an option for example) could list only the poses for the working session. All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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How to use "getRotamers" function?
by ylei＠ecs.umass.edu 21 Jul '09

21 Jul '09

Hi all I'm trying to get the rotamers for the given residue along the backbone using Dunbrack Backbone Dependent Library. So far, I want to use getRotamers function. But when running this command in the python shell, I got this error "No module named Dunbrack". I don't know if there is a module "Dunbrack" which I should import first. Moreover, besides getRotamers, there are several other functions, e.g. getRotamerParams, extractResInfo, useRotamer, RotamerLibraryInfo, registerLibrary, useBestRotamers, etc and a class called RotamerParams in the same file. I also found there are two associated functions in the Dunbrack folder, say, dependentRotamerParams and independentRotamerParams, which are used in the above functions. Can someone help me distinguish these functions? Which one will be useful if I need a full set of rotamers for certain purpose (i.e. side-chain structure prediction) given the backbone? Thanks in advance. Sorry for disturbing others. Best, Yang

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Voronoi Volume & Mark Gerstein Lib
by Eric Gonzalez 21 Jul '09

21 Jul '09

Hi all, I tried to use the libs of Marc Gerstein to integrate the Voronoi's Volume calculus in script that calculate this volume from my PC, but I don't found how to use this libraries (I compile and install them), from script to use in Chimera. I hope that someone can help me. Thx!

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PDB file parser failing to identify chain IDs
by Sébastien Cuendet 21 Jul '09

21 Jul '09

Hi, I'm working with PDB files, opening them with: chimera.openModels.open(fileHandler, 'PDB'). Later on when I use the chainId on the residues of the molecule (accessed by residue.id.chainId). The problem is that the PDB format does not require the chaind id to be defined. When that is the case, all residues have id ' ', which is rather annoying to distinguish the chains to which they belong. Now, bringing up problems only is never really appreciated ;), so my colleague Aurelien Grosdidier and I tried to think of some solutions to split the residues into chains when loading a model from a PDB file that does not contain any chain ID. 1) Split on TER. Chains are usually separated by a TER line, which could thus be used to determine when to create a new chain. However, like the chain id information, the TER line is optional in the PDB format... 2) Compute an atom to atom distance matrix for each two consecutive residues. Since the typical distance between two atoms is known, we can compute if two residues reasonably belong to the same chain. The computations can easily be pruned when two residues belong to the same chain, which is the most frequent case. 3) Compute an atom to atom distance matrix and use it to determine which atoms belong to the same chain. This is computationnally more expensive than 2), but it must be done somewhere in Chimera to compute the bonds between the atoms that are rendered graphically. Any chance we can access this information (I did not find how)? Any comment on those solutions? Any other solutions? Any help will be appreciated! Thanks, Sebastien

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Good!
by Jean Didier Pie Marechal 20 Jul '09

20 Jul '09

Hi Conrad, OK, we'll forget qhull. But what you found from Mark Gerstein is perfect. We didn't get to this point. We have few hands and brains available for the moment, so we'll try to have a go. Should not be too difficult. I'll get you posted if succeed...or will bother you again later... All the best and thanks a lot JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: Conrad Huang <conrad(a)cgl.ucsf.edu> Data: Dilluns, Juliol 20, 2009 11:14 pm Assumpte: Re: [chimera-dev] Calculation voronoi volums in a prot. > First the bad news. I looked into qhull and it appears that > computing > the volumes for all Voronoi cells is not built-in to the software. > The > qhull FAQ gave an example for computing the volume of a single cell: > > > To compute the area and volume of the Voronoi region for input > site 5 (site 0 is the first one), use > > > > rbox 10 D2 | qvoronoi QV5 p | qconvex s FS > > My guess is that this will probably be pretty inefficient as the > number > of atoms increases. As the qhull documentation says, algorithms > that > keep intermediate convex hull results are much more efficient. > > On the good news side, the code that the "Area/volume from Web" > server > is from Mark Gerstein (see > http://www.molmovdb.org/geometry/files/libproteingeometry/README.html) > and is probably the best starting point. If you have some > programming > expertise available, it should be fairly straightforward to compile > the > calc-volume program and modify the Chimera extension to use that > instead > of the web. (We will, of course, be happy to answer any > questions.) If > not, we can talk about alternative solutions. > > Conrad > > Jean Didier Pie Marechal wrote: > > [...] > > > > Re. the server access. How the call to the server works is perfect > > for the purpose of our work and does exactly what we want. However, > > since we want to script every step of our work, it would be great to > > know if a command line equivalent to the "Area/volume from Web" > > interfase exists. As we thought there was no command to do so, we > > were wondering if qhull based calls could do the trick. > > > > Re. Voronoi calculation Conrad, having qhull providing volmetric > > values would be great. That would afford us calling the server, > eases> the script, and also allows us to understand better why in some > > cases, the calculations give strange values (not only the -1 we > > understood the origin, but other problems). > > > > If that is too complicated, as Elaine says, we will try to call the > > server directly and recover the volumes. > > > > Thanks a lot for the help, > > > > Best, JD >

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Re: [chimera-dev] Calculation voronoi volums in a prot.
by Jean Didier Pie Marechal 20 Jul '09

20 Jul '09

Dear Conrad and Elaine, thanks for your answers. Just to recenter my questions: What we are doing large statistics on a substantial set of protein structures. Some of the descriptors we need are voronoi attributes; our main interest is on the volumes surrounding atoms. Nevertheless, having a representation of the polyedra would be great (not great genial). So we explored chimera's capabilities on this. Re. the server access. How the call to the server works is perfect for the purpose of our work and does exactly what we want. However, since we want to script every step of our work, it would be great to know if a command line equivalent to the "Area/volume from Web" interfase exists. As we thought there was no command to do so, we were wondering if qhull based calls could do the trick. Re. Voronoi calculation Conrad, having qhull providing volmetric values would be great. That would afford us calling the server, eases the script, and also allows us to understand better why in some cases, the calculations give strange values (not only the -1 we understood the origin, but other problems). If that is too complicated, as Elaine says, we will try to call the server directly and recover the volumes. Thanks a lot for the help, Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: Conrad Huang <conrad(a)cgl.ucsf.edu> Data: Divendres, Juliol 17, 2009 6:48 pm Assumpte: Re: [chimera-dev] Calculation voronoi volums in a prot. > Unfortunately, the answers to both your questions is "no, it does > not do > what you want." First, the "Area/Volume from Web" tool only > obtains the > numerical values for surface area and volume; it does not get the > volume > map itself. Second, the qhull package is included for the Delaunay > triangulation used by the "Intersurf" tool and there are no tools > that > use the Voronoi diagram capabilities. > > What type of visualization are you trying to create? Since Voronoi > diagrams generate partitions separated by planes, do you want to > see all > the partitioning planes, or just polyhedra around specific atoms? > We > can look into whether qhull can generate the required data and how > hard > it would be to interface that with Chimera. > > Conrad > > Jean Didier Pie Marechal wrote: > > Dear all, > > > > We are trying to calculate voronoi's volumes around atoms in a > protein. So far we used the interfase "Area/Volume from Web" but we > have several troubles. So here the questions: > > > > 1. Is there a command line to do the server call automatically > and display resulting volumes in the viewer? > > > > 2. We know that Qhull is one of the packages embedded in chimera. > We try to see how to script voronoi calculation and read resulting > volumes but failed so far. Do you have an example on how to > generate the voronoi volumes maps from qhull in chimera? > > > > All the best, > > JD > > > > > > Dr. Jean-Didier Maréchal > > Lecturer > > Computational Biotechnological Chemistry @ Transmet > > 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 > > > > > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >

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gaussian interface: getting nuts with connectivity
by Jean Didier Pie Marechal 17 Jul '09

17 Jul '09

Dear all, I am trying to make chimera an interface for the quantum mechanical program gaussian. Pretty much everything seems to go smooth but I am getting crazy (stupid?) because I can't reproduce the geometry connectivity gaussian wants. I used tools of chimera I know for bond mapping and connectivity. But I can't get to the right connectivity format. I join you here an input file of gaussian (a ARG-ALA dipeptide). If you look at the file, the connectivity between the atoms is at the end and is in the following form: atom 1, atom 2, bond_order, atoms 3, bond_order (etc for all atoms linked to atom 1) ... atom 31 (to 37 = all terminal atoms). I have been using the different atoms attributes I know like neighbors, bonds and bondMap, but I can't see how to proceed neither I see how to use the bond order calculations as in the mol2 module. If you have time and can give me a hint, I would be extremely greatful Thank you very much, best JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Juliol 9, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Generating images in chimera with the --nogui option (Davide > Ba?) 2. Re: Generating images in chimera with the --nogui option > (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 9 Jul 2009 17:32:22 +0200 > From: Davide Ba? <dbau(a)cipf.es> > Subject: [chimera-dev] Generating images in chimera with the --nogui > option > To: chimera-dev(a)cgl.ucsf.edu > Message-ID: > <3e4b67ca0907090832r4e46b826i5dfe81842b58685a(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > my name is Davide and I'm currently working on Marc Marti-Renom's > group. > I'm trying to generate an image using chimera with the --nogui option: > > chimera --nogui --nostatus --script cmd.py > > > The file cmd.py contains the following lines: > > from chimera import runCommand > > runCommand('open input.cmm') > > runCommand('copy file image.png png') > > > but I keep getting the following error message: > > Traceback (most recent call last): > > File "/usr/src/chimera/share/__main__.py", line 65, in <module> > > value = chimeraInit.init(sys.argv) > > File "CHIMERA/share/chimeraInit.py", line 384, in init > > chimera.openModels.open(a, prefixableType=1) > > File "CHIMERA/share/chimera/__init__.py", line 1344, in open > > File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython > > File "cmd.py", line 3, in <module> > > runCommand('copy file image.png png') > > File "CHIMERA/share/chimera/__init__.py", line 2025, in runCommand > > File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand > > File "CHIMERA/share/Midas/midas_text.py", line 563, in doCopy > > File "<string>", line 1, in <module> > > File "CHIMERA/share/Midas/__init__.py", line 908, in copy > > File "CHIMERA/share/chimera/printer.py", line 1182, in saveImage > > AttributeError: '_chimera.NoGuiViewer' object has no attribute > 'pilImages'> Error while processing cmd.py: > > AttributeError: '_chimera.NoGuiViewer' object has no attribute > 'pilImages'> > (see reply log for Python traceback info) > > > > cmd.py was generated from within chimera using the "record" command of > chimera's "command line". > If I delete the line "runCommand('copy file image.png png')", the > scriptexecute with no error. > > Is it possible to generate images using the --nogui option? > > Thanks a lot for your help! > > Best regards, > Davide > > ____________ > *Davide Ba?* > Structural Genomics Unit > Bioinformatics & Genomics Department, Prince Felipe Research Center > Avda. Autopista del Saler, 16 , 46012 Valencia, Spain > Tel: +34 96 328 96 80 (ext. 1021) Fax: +34 96 328 97 01 > Email: *dbau(a)cipf.es* > Web: *http://sgu.bioinfo.cipf.es/dbau* > El document original ha estat eliminat per l'antivirus. El motiu ha estat: Fitxer adjunt amb extensió potencialment perillosa (vbs, vbe, js, jse,scr, exe, com, bat, lnk, ceo, htt, pif) Per a més informació vegeu: http://www.uab.es/si/virus_correu/

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Calculation voronoi volums in a prot.
by Jean Didier Pie Marechal 17 Jul '09

17 Jul '09

Dear all, We are trying to calculate voronoi's volumes around atoms in a protein. So far we used the interfase "Area/Volume from Web" but we have several troubles. So here the questions: 1. Is there a command line to do the server call automatically and display resulting volumes in the viewer? 2. We know that Qhull is one of the packages embedded in chimera. We try to see how to script voronoi calculation and read resulting volumes but failed so far. Do you have an example on how to generate the voronoi volumes maps from qhull in chimera? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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Non-standard residues
by Alex Gawronski 15 Jul '09

15 Jul '09

Hello, Is there a way to select only standard residues with the "select" command? I was also wondering if this would work to minimize only H bonds: runCommand('select @H') runCommand('minimize freeze unselected nogui true') If not, how can it be done? When I try the inverse (selecting everything before Hs are added), I get "ValueError: underlying C++ Atom object is missing", which I assume occurs because atoms are removed by Dock Prep. Thanks in advance! Alex Gawronski Carleton University

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