- Chimera-users - RBVI Mailing Lists

A request
by Soumya Ghosh (Systembiologie) 18 May '09

18 May '09

Dear Chimera, Thanks for giving such a wonderful software for molecular modelling. I am a PhD student in Germany and using the CHIMERA programme for my molecule. I want to increase the font and the font size of the highlighted amino acid in my protein and thats why I was trying in the Command: Tools - Utilities - Colour key where there is a option for font size but so far remain unsuccessful. Can you kindly advise me how I should proceed. Waiting eagerly for your kind reply, Soumya Ghosh, TUM, Freising, Germany

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Verify integer/non-integer charges in mol2
by Francesco Pietra 18 May '09

18 May '09

Hi: I assigned Amber ff99SB charges to a proven pdb file of standard amino acids and capping groups (ACE NME), saving as mol2. Conversion to a pdbqt file with ATD (autodock tool) resulted in non-integer charge (-5...). Unless something occurred that escaped my attention, the protein has -5.00000 charge. My question: how to verify a posteriory the total charge in the Chimera-written mol2 file, in order to trace back were I have blurred things? I don't see the total in the mol2 file. Thanks francesco pietra

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Morphing with two models
by Enrico Morelli 18 May '09

18 May '09

Dear all, I'm a new chimera user and I'm asking about morphing. I've two models and I'm able to move one to contacts the other. But what if I need to move both to converge on a specific center? There is some shortcut? Thanks to all -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

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apple ui
by Nils Becker 15 May '09

15 May '09

hi, just a quick user interface suggestion: it would be great if mouse-over over all directory listings (when choosing files to load etc) could activate the mouse wheel for both x and y scrolling. right now, only placing the cursor directly over the scroll bars allows scrolling by mouse wheel, and there is only one mouse wheel axis to scroll with. i am on mac is x 10.5.6 and using a recent native snapshot cheers, nils

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Floating exception
by hsosa＠aecom.yu.edu 14 May '09

14 May '09

Hi, I am having the following problem with the latest production version of Chimera (1.3) on a linux computer. Chimera crash and exit after doing some actions like rotating a molecule several times or simply trying to open the side-view window. After the program ends there is a Floating exception message in the console. The problem occur with the latest production release (1.3) and daily build versions but not with an older production version of chimera (1). I installed the latest nvidia driver but this didn't solve the problem. I am running the old linux 2.4 kernel (Suse 9.0) and I am not sure if this has anything to do with the problem . I am hesitant to upgrade the OS and break all the other programs that now work in this machine (you got to love linux :-)) Thanks Hernando Computer: Dual Xeon processor. Graphic card: NVIDIA Quadro4 XGL 9800 OS: Linux Suse 9.0 UCSF Chimera 1.3 Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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DMS citation
by Ben Keshet 14 May '09

14 May '09

Hi, I have used DMS to calculate accessible surface prior to the usage of Dock6. Is there any specific citation for the DMS application? Thank you, Ben Keshet Chemical Engineering UMBC

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surface spanning multiple models
by Nils Becker 14 May '09

14 May '09

Hi, is it possible to define surfaces that seamlessly span multiple models? when i define a surface category spanning multiple models, i always get distinct surfaces around each model. saving as a single pdb and re-importing does not help, since then i have the same problem with multiple submodels... thanks for any help! cheers, nils

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Multiple sequence alignment
by Avner Schlessinger 13 May '09

13 May '09

Dear Chimera experts, Once I create multiple structure alignment i was wondering how I can view the corresponding multiple sequence alignment. when I try to view it through the MultiAlignViewer it shows all possible pairwise alignments with the sequence of the first structure rather than all the sequences together. Thanks! Avner -- Avner Schlessinger, Ph.D. Department of Bioengineering and Therapeutic Sciences Mission Bay, Byers Hall 1700 4th Street, Suite 501 University of California, San Francisco San Francisco, CA 94158-2330 Tel +1 (415) 514-4258 Fax +1 (415) 514-4231

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a small suggestion
by Jean Didier Pie Marechal 13 May '09

13 May '09

Hello everyone, just a small suggestion to the team. Could it be possible that, when clicking on a given angle/torsion in the Structure measurments panel, the involved atom/bond get selected in the visualizer? cheers 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-users-request(a)cgl.ucsf.edu Data: Dimarts, Maig 12, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. Re: chimera performance (Greg Couch) > 2. adding pseudo bonds (Jean Didier Pie Marechal) > 3. Re: adding pseudo bonds (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 11 May 2009 14:32:22 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera performance > To: Bala subramanian <bala.biophysics(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0905111420070.1959390(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > I have had bad luck with NVidia drivers packaged as RPMs. Instead > I > recommend that you uninstall the RPM you got from rpmfusion.org and > install the NVidia driver from NVidia at > <http://www.nvidia.com/Download/index.aspx>. The "Nvidia.com > Binary > Installer" option given the webpage you cited. As mentioned there, > the > disadvanatge of NVIdia's driver is that you need to reinstall it > every > time your update your kernel -- otherwise the X server won't start. > After > a successful install (and reboot), glxinfo should tell you which > OpenGL > renderer you have and chimera should work too. > > Good luck, > > Greg > > On Fri, 8 May 2009, Bala subramanian wrote: > > > Dear Greg, > > After installing nvidia graphics drivers, i am not able to open > chimera. I > > have attached the xconfig file and the output of glxinfo as text > files.> > > *[cbala@ramana ~]$ chimera > > Traceback (most recent call last): > > File "/usr/local/chimera/share/__main__.py", line 65, in <module> > > value = chimeraInit.init(sys.argv) > > File "/usr/local/chimera/share/chimeraInit.py", line 361, in init > > tkgui.initializeGUI(exitonquit, debug_opengl) > > File "CHIMERA/share/chimera/tkgui.py", line 2525, in initializeGUI > > File "/usr/local/chimera/lib/python2.5/site- > packages/PIL/__init__.py",> line 309, in checkConfig > > > > File "/usr/local/chimera/lib/python2.5/site-packages/Togl.py", > line 27, in > > __init__ > > Tkinter.Widget.__init__(self, master, "togl", cnf, kw) > > File "/usr/local/chimera/lib/python2.5/lib-tk/Tkinter.py", line > 1930, in > > __init__ > > (widgetName, self._w) + extra + self._options(cnf)) > > _tkinter.TclError: could not create rendering context > > Couldn't configure togl widget* > > > > I installed the nvidia driver as follows. I installed it based on > the> information given in the nvidia install guide in the following > link.> > > http://www.mjmwired.net/resources/mjm-fedora-nvidia.html#pci_id > > > > su -c 'rpm -ivh > > http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release- > stable.noarch.rpm> ' > > su -c 'rpm -ivh > > http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree- > release-stable.noarch.rpm > > ' > > su -c 'rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-rpmfusion-*' > > su -c 'yum install kmod-nvidia' > > > > Then i gave the following command > > > > nvidia-xconfig as root. Then i restarted the system. Now i am > able to see > > nvidia display setting. When i give chimera, it dosent work. > > > > Bala > > > > On Thu, May 7, 2009 at 8:44 PM, Greg Couch <gregc(a)cgl.ucsf.edu> > wrote:> > >> Looking at your chimera benchmark scores and at the scores on > the web page, > >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, it > looks like > >> you don't have the NVidia graphics driver installed. And that > would make a > >> *huge* difference. To double-check, run the glxinfo command and > look at the > >> "OpenGL renderer string:" line, it should have NVIDIA in it > instead of Mesa. > >> To get the NVidia drivers, go to < > >> http://www.nvidia.com/Download/index.aspx>. > >> > >> - Greg > >> > >> > >> On Thu, 7 May 2009, Bala subramanian wrote: > >> > >> Dear Greg, > >>> You are right. Previously it was normal but now it is slow. I > havent>>> updated > >>> the kernel. I checked and noticed that i dnt have any memory > intensive>>> background jobs also. > >>> > >>> I did benchmarks with two chimera versions 1.3 (attached file > chim_test)>>> and > >>> chimera 1.4 (attached chim_test1). > >>> My graphics card is nVIDIA GETFORCE 9300MG, VRAM: 256 MB. I dnt > know how > >>> to > >>> compare and judge what is going wrong. I wud appreciate your > help on the > >>> same. > >>> > >>> Thanks, > >>> Bala > >>> > >>> So it was formerly fast on the same computer? This could > happen on a > >>> Linux > >>> > >>>> computer if you updated the kernel and forgot to reinstall the > graphics>>>> driver (from ATI or NVidia, the open source 3D drivers > still need work, > >>>> but > >>>> are improving). Another possibility, on all operatings > sytems, is that > >>>> there is a background process that is using a lot of CPU or > memory, so > >>>> chimera doesn't have the resources it used to. > >>>> > >>>> If you just want to check the graphics performance, then you > can use the > >>>> Benchmark tool in Tool / Utilities to guage the current > performance. And > >>>> then you can compare to the reported scores to see if your > graphics>>>> performance is reasonable (the Show button in the > Benchmark tool brings > >>>> up > >>>> the web page). > >>>> > >>>> - Greg > >>>> > >>>> > >>> > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 May 2009 17:19:46 +0200 > From: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> > Subject: [Chimera-users] adding pseudo bonds > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <165553c1104b.4a09afb2(a)uab.es> > Content-Type: text/plain; charset=iso-8859-1 > > Dear all, > > what is the way to add pseubond between metal and chelating atoms? > if you could tell me what are the "mouse driven" and "script > driven" manner I'll be very pleased.... > 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 > > ----- Missatge original ----- > De: chimera-users-request(a)cgl.ucsf.edu > Data: Diumenge, Maig 10, 2009 9:00 pm > Assumpte: Chimera-users Digest, Vol 73, Issue 11 > > > Send Chimera-users mailing list submissions to > > chimera-users(a)cgl.ucsf.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.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. Protonate heteroatoms only (Francesco Pietra) > > 2. Re: Protonate heteroatoms only (Eric Pettersen) > > > > > > ------------------------------------------------------------------ > -- > > -- > > > > Message: 1 > > Date: Sat, 9 May 2009 23:35:37 +0200 > > From: Francesco Pietra <chiendarret(a)gmail.com> > > Subject: [Chimera-users] Protonate heteroatoms only > > To: chimera <chimera-users(a)cgl.ucsf.edu> > > Message-ID: > > <b87c422a0905091435q4a1671e2td61284cf092e7fb6(a)mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi: > > Is there a command in Chimera to protonate (Sybyl-type) the > > heteroatoms only (or deprotonate the other elements from a fully > > protonated protein)? > > thanks > > francesco pietra > > > > > > ------------------------------ > > > > Message: 2 > > Date: Sat, 9 May 2009 15:27:55 -0700 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Subject: Re: [Chimera-users] Protonate heteroatoms only > > To: Francesco Pietra <chiendarret(a)gmail.com> > > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30(a)cgl.ucsf.edu> > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > del HC > > > > will delete all hydrogens bonded to carbons (their IDATM types > are > > HC). > > --Eric > > > > Eric Pettersen > > USCF Computer Graphics Lab > > > > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote: > > > > > Hi: > > > Is there a command in Chimera to protonate (Sybyl-type) the > > > heteroatoms only (or deprotonate the other elements from a fully > > > protonated protein)? > > > thanks > > > francesco pietra > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users(a)cgl.ucsf.edu > > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > End of Chimera-users Digest, Vol 73, Issue 11 > > ********************************************* > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 May 2009 08:39:11 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] adding pseudo bonds > To: JeanDidier.Marechal(a)uab.es > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <06B51782-B5EB-487A-B770-ACA04AA2D738(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi JD, > The "user interface" (i.e. no programming) way is to create a text > file listing the desired pseudobonds and their colors and read it > in > with PseudoBond Reader. The tool and file format are described here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.… > > > > I don't know the python way, but perhaps looking in the code for > PseudoBond Reader will help ( share/PBReader/ within your Chimera > installation). > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On May 12, 2009, at 8:19 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > > > what is the way to add pseubond between metal and chelating atoms? > > if you could tell me what are the "mouse driven" and "script > driven" > > manner I'll be very pleased.... > > all the best, > > JD > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 73, Issue 13 > ********************************************* >

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Compiling chimera from source code
by cdlau＠ucsd.edu 13 May '09

13 May '09

Dear Madam/Sir, I am currently involved in a project which requires compiling the Chimera source code from scratch. I have been using: http://www.cgl.ucsf.edu/chimera/sourcecode.html for reference, and I understand that surfacing library is not available due to licensing issues. Because I am not interested in using this feature, I wanted to know if it was still possible to compile the Chimera source code. I know that it will be difficult but any knowledge or past experience that may help me would be greatly appreciated. Thanks in advance, Chris

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