July 2009 - Chimera-dev - RBVI Mailing Lists

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 30 Jul '09

30 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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Chimera-dev July 2009