- Chimera-users - RBVI Mailing Lists

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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adding pseudo bonds
by Jean Didier Pie Marechal 12 May '09

12 May '09

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 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: 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 > ********************************************* >

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