January 2010 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] adding an atom at the centroid of a blob
by Jean Didier Pie Marechal 14 Jan '10

14 Jan '10

Thanks a lot Elaine for answering me, I was indeed interested in both user interfase ...as well as the python shell one... 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: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dimecres, Gener 13, 2010 11:26 pm Assumpte: Re: [chimera-dev] adding an atom at the centroid of a blob > > On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote: > > > Hi everyone, > > I have obtained cavities for a given atom selection using surfnet > > > and I want to put an atom at the centroid of the main blob. I > know > > how to do this for a selected set of atom but I am struggling > with > > the surfaces. > > > > At this point, I splitted it (accelator Sc) and then I can select > > > the blob I am interested in. But how could I create a particular > > object for this blob? From there, how could I add an atom (i.e. > > helium) and the centroid of the blob? > > Thanks for any help, > > JD > > Hi JD, > > Now that you have your one surface piece selected (and nothing > else), > you could use the command "focus sel" or menu item "Actions.. > Focus" > to center the view on it, then add the atom at the center of view > with the Build Structure tool (under Tools... Structure Editing). > You would go to the "Add Atoms" tab in that tool, choose "atom" and > > click "Add." > > It may not be the centroid of the blob as calculated from its > vertices, but the center of its bounding box. You may want to try > it > and see if the result is sufficient. > > That's the user interface way. Maybe you meant in python -- if so, > > somebody else will have to answer! > > Best, > > Elaine >

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importing colored VRML file into cinema 4d
by odonnell＠chem.fsu.edu 14 Jan '10

14 Jan '10

Hello, I'm curious if anyone has had difficulty importing a colored VRML 3D object into Cinema 4D. I have exported a colored VRML file from chimera but the color is lost when opening it in the 3D graphics program Cinema 4d. Reopening the VRML file in chimera shows the color is there. Thanks in advance for your time. -Odie ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [Chimera-users] [chimera-dev] adding an atom at the centroid of a blob
by Elaine Meng 13 Jan '10

13 Jan '10

On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote: > Hi everyone, > I have obtained cavities for a given atom selection using surfnet > and I want to put an atom at the centroid of the main blob. I know > how to do this for a selected set of atom but I am struggling with > the surfaces. > > At this point, I splitted it (accelator Sc) and then I can select > the blob I am interested in. But how could I create a particular > object for this blob? From there, how could I add an atom (i.e. > helium) and the centroid of the blob? > Thanks for any help, > JD Hi JD, Now that you have your one surface piece selected (and nothing else), you could use the command "focus sel" or menu item "Actions.. Focus" to center the view on it, then add the atom at the center of view with the Build Structure tool (under Tools... Structure Editing). You would go to the "Add Atoms" tab in that tool, choose "atom" and click "Add." It may not be the centroid of the blob as calculated from its vertices, but the center of its bounding box. You may want to try it and see if the result is sufficient. That's the user interface way. Maybe you meant in python -- if so, somebody else will have to answer! Best, Elaine

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Looping with Chimera commands
by Yasser Almeida Hernández 12 Jan '10

12 Jan '10

Hi... It's possible run a Chimera's command iteratively? I have loaded several structures (more than 300) and i want to superimposed them to a reference structure. How i perform the matching command for every structure iteratively? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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movie
by Alex Perálvarez Marín 12 Jan '10

12 Jan '10

Hi, I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance. Alex.

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problem to download chimera
by Gabriele Gucciardo 12 Jan '10

12 Jan '10

Dear Chimera developers, I have some problem to download Chimera. I'm trying to download the Chimera software. Once I clicked on the "download link" in the home web page of chimera, a new blank page was opened but nothing happened. I'm currently using Mac os X 10.4.11. I used browser safari 4.0.4 and Firefox 3.5.7, both gave same results. Kind regards, Gabriele Gucciardo School of Chemistry & Chemical Biology College of Life Sciences UCD, Belfield, Dublin 4 Ireland 00353 1 7162972 gabriele.gucciardo(a)ucd.ie

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showing conservation
by Elaine Meng 07 Jan '10

07 Jan '10

On Jan 7, 2010, at 6:30 PM, gytjyb wrote: > hello, > 1 how can i use this software to do molecular dynasty? > 2 can you tell me how to asure conservation sequence through > protein alignment. > maybe this is just for basic knowledge,but i am a freshman. > Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just to me. (1) maybe you mean molecular dynamics - sorry, Chimera does not do molecular dynamics. (2) I recommend going through some of the Chimera tutorials. There are some beginner tutorials and others that include showing conservation and aligning protein structures. You can see the tutorials by choosing "Help... Tutorials" from the Chimera menu, or by going to our web site: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> Also, I have my own page on where you can get sequence alignments for viewing in Chimera: <http://www.cgl.ucsf.edu/home/meng/sources.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Permission to use image in educational textbook
by Carolyn Arcabascio 07 Jan '10

07 Jan '10

To Whom It May Concern: I am writing to you from the Photo Research department of Jones and Bartlett Publishers. I am currently working on the second edition of an educational textbook by Dr. Lynne Cassimeris and colleagues titled, "Lewin's Cells." The authors of this project have requested to use the image shown here: http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/actin/actin.html A hi-res version of the image has been downloaded from the website. I'd like to inquire how best to proceed with obtaining permission to use this figure. WE do have our own standard permission letter, and if this would be acceptable, I'd be happy to follow up and address the letter to the appropriate contact. Thank you very much for your time. I look forward to hearing from you. Kind regards, Carolyn -- Carolyn Arcabascio Assistant Photo Researcher Jones and Bartlett Publishers LLC 40 Tall Pine Drive Sudbury, MA 01776 Phone: 978-579-8284 Fax: 978-579-8331 www.jbpub.com

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Sphere radius
by Yasser Almeida Hernández 07 Jan '10

07 Jan '10

Hi... Can i change the radius of the sphere atoms representation ...? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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Re: [Chimera-users] adding hydrogens
by Eric Pettersen 06 Jan '10

06 Jan '10

On Dec 29, 2009, at 1:01 PM, Ravinder Abrol wrote: > We have Chimera installed and I hadn't thought of using > it to add hydrogens. I just tried it and it worked. > We have many pdbs that we need to run this on, so I found a --nogui > mode in > chimera. I tried using this to load a pdb and added hydrogens to > waters > using: > addh hbond true spec :hoh > but this command adds hydrogens to many of my Histidines also, which > I don't > want. Seems like spec option is not working? Do you know a way > around this? Hi Ravi, The "spec" argument to addh only specifies models. addh will always add hydrogens to the entire model(s) specified. To protonate water and yet preserve current histidine protonation you will have to get tricky. Namely, change the name of delta-protonated histidines to HID, epsilon-protonated to HIE, and doubly-protonated to HIP, then use "useHisName true" in the addh command. You can script this as: setattr r type HID :HIS@hd1,dd1,td1 #handle deuterium/tritium as well setattr r type HIP :HID@he2,de2,te2 setattr r type HIE :HIS addh useHisName true [+ any other args you want] setattr r type HIS :HIE:HIP:HID # set residue name back to HIS write [your args] --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Chimera-users January 2010