September 2010 - Chimera-users - RBVI Mailing Lists

ribbon problem
by Francesco Oteri 30 Sep '10

30 Sep '10

Dear all, I'd like to use chimera to do a picture of a circular DNA with ribbon representation. I found the two following problems: 1.If I load the .pdb files, chimera is unable to recognize the topology and shows extra-bond connecting the last base of a strand with the previous of the other strand. 2.If I load the AMBER topology, the connectivity is correctly recognized, but the first base and last are not connected by the ribbon. Is there any solution?

4 14

how to set the transparency of ribbon
by Qinghua Liao 30 Sep '10

30 Sep '10

Dear chimera's users, Could someone tell me how to set the transparency of ribbon of a protein? Thanks very much All the best, Qinghua

2 2

Dielectric ; Steepest descent
by r charbel maroun 29 Sep '10

29 Sep '10

Hi everybody, The value of the dielectric constant used by Chimera is 1, corresponding to calculations in vacuo. Is there not an easy way to change this value to, say 78 or to include a sigmoid function or the Generalized Born approach so as to mime the presence of the solvent ? I looked for it but couldn't find it : where in the {chimera_install_location}/share/MMMD/MMTKinter.py file can the value of the dielectric be changed ? Otherwise, how to mime implicitly the solvent ? Also, it seems that only the Steepest descent, and not the Conjugate gradients method, for energy minimization has been implemented in Chimera. Why is this so? It'd be so nice to have these two functionalities added as I don't know of any free academic program allowing us to do energy minimization with these options without having to parametrize every new ligand (Charmm, Namd), a painful task. Cheers, Charbel

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 89, Issue 30
by vamsi krishna 29 Sep '10

29 Sep '10

Hi all, I am very happy to see modeller interface in chimera latest version.Please help me any one how to use (steps) it for modeling. Thank you Best wishes, vamsi On 29/9/2010 3:00 AM, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.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: download of chimera 1.5 (Elaine Meng) > 2. Fwd: Stereo 3D for teaching (Nadir T. Mrabet) > 3. Re: Remove hydrogen (Elaine Meng) > 4. Re: select side chain (Elaine Meng) > 5. Re: Fwd: Stereo 3D for teaching (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 28 Sep 2010 09:22:16 -0700 > From: Elaine Meng<meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] download of chimera 1.5 > To: atila petrosian<atila.petrosian(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID:<6FB84799-504C-4FA9-8CFE-4CA7A0E2BB33(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Chimera 1.5 daily build downloads are included in the download page. You have to scroll down to the "Daily Builds" section, or click the "Daily Builds" link at the top to go directly to that section (or just click here): > > <http://www.cgl.ucsf.edu/chimera/download.html#daily> > > "alpha" is whatever is not yet an official release, so yes, right now the "alpha" downloads are version 1.5. > Elaine > > > ------------------------------ > > Message: 2 > Date: Tue, 28 Sep 2010 18:30:34 +0200 > From: "Nadir T. Mrabet"<Nadir.Mrabet(a)medecine.uhp-nancy.fr> > Subject: [Chimera-users] Fwd: Stereo 3D for teaching > To: "chimera-users(a)cgl.ucsf.edu BB"<chimera-users(a)cgl.ucsf.edu> > Message-ID:<4CA2182A.3020902(a)medecine.uhp-nancy.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Elaine, > > Could you please react to my last week's mail, forwarded (again) below? > Thanks, > > Nadir Mrabet > > > -------- Original Message -------- > Subject: [Chimera-users] Stereo 3D for teaching > Date: Fri, 24 Sep 2010 17:23:35 +0200 > From: Nadir T. Mrabet<Nadir.Mrabet(a)medecine.uhp-nancy.fr> > Reply-To: Nadir.Mrabet(a)medecine.uhp-nancy.fr > Organization: Nancy University, School of Medicine > To: chimera-users(a)cgl.ucsf.edu BB<chimera-users(a)cgl.ucsf.edu> > > > > Hi, > > I had addressed previously the question about which equipments would > perform best to display molecular structures in 3D for teaching purposes. > Greg Couch had offered to keep me up on the latest technologies offered > at the last SIGGRAPH conference. > But nothing so far. > Can anyone help me with that? > > Many thanks in advance. > > Nadir >

2 1

clustering of docking results
by Bala subramanian 29 Sep '10

29 Sep '10

Friends, I am using viewdock tool for analysing the docking result obtained from autodock. Is there any way to do some clustering of the docked conformations using the energetically best structure as the reference within chimera ? Thanks in advance, Bala

2 1

Fwd: Stereo 3D for teaching
by Nadir T. Mrabet 28 Sep '10

28 Sep '10

Hi Elaine, Could you please react to my last week's mail, forwarded (again) below? Thanks, Nadir Mrabet -------- Original Message -------- Subject: [Chimera-users] Stereo 3D for teaching Date: Fri, 24 Sep 2010 17:23:35 +0200 From: Nadir T. Mrabet <Nadir.Mrabet(a)medecine.uhp-nancy.fr> Reply-To: Nadir.Mrabet(a)medecine.uhp-nancy.fr Organization: Nancy University, School of Medicine To: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> Hi, I had addressed previously the question about which equipments would perform best to display molecular structures in 3D for teaching purposes. Greg Couch had offered to keep me up on the latest technologies offered at the last SIGGRAPH conference. But nothing so far. Can anyone help me with that? Many thanks in advance. Nadir -- Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

3 2

3D stereo
by Nadir T. Mrabet 28 Sep '10

28 Sep '10

Hi, This is for teaching purposes so that students can "walk" though 3D structures. Would it be possible to use Chimera via a 3D stereo beamer to project display on a very large screen and watch the selected structure in 3D by means of shutter glasses? If this is so, what kind of equipment would you recommend? Many thanks, Nadir -- Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.

2 2

select side chain
by Enrico Morelli 28 Sep '10

28 Sep '10

Dear all, how can I select the side chain of the residue and to color it using different color from the backbone (possibly the command line)? Thanks -- ------------------------------------------------------------------- (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 | +------------------------------------------------------------------+

2 1

Remove hydrogen
by Enrico Morelli 28 Sep '10

28 Sep '10

Dear, another question. How I can remove or can't display all the protons displayed in chimera? Thanks -- ------------------------------------------------------------------- (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 | +------------------------------------------------------------------+

2 1

download of chimera 1.5
by atila petrosian 28 Sep '10

28 Sep '10

Dear Elaine Meng chimera-alpha<https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=alpha/chimera-alpha-wi…> is the same chimera 1.5. is it true?

2 1

Chimera-users September 2010