- Chimera-users - RBVI Mailing Lists

Ligand Binding to Homodimeric Proteins
by Nancy 17 Jan '10

17 Jan '10

Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine a potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other protomer. Therefore, a ligand should bind with equal probability and affinity to both sides of the protein. However, when I perform a molecular docking simulation (using an X-Ray crystal structure), the ligand preferentially binds to one side of the homodimer. Is this outcome likely the result of errors inherent in the X-Ray crystal structure, as one would expect identical binding to both sides? Thank you very much. Nancy

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adding hydrogens and charges
by Elaine Meng 17 Jan '10

17 Jan '10

> 1 how can i calculate the charges for molecular. > to calculate the charges both for ligand and receptor > individually. > if i want to do docking,if i must calculate charges. > 2 how can i add hydrogen for HIS. Maybe , no exact position for HIS. > how can i add hydrogen directly? > thank you very much! > Hello, Use the Dock Prep tool (in menu, Tools... Structure Editing... Dock Prep). It can do several things to prepare a structure, including adding hydrogens and charges. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.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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Re: [Chimera-users] [chimera-dev] Calculating RMSD
by Elaine Meng 15 Jan '10

15 Jan '10

Hi Victor, I'll CC the chimera-users(a)cgl.ucsf.edu list -- that address is better for general Chimera "user" questions, while chimera-dev is more for "programmer" questions, i.e. involving python or other code. The "rmsd" command does not automatically use serial number to pair the atoms. You can control the order by specifying the residues and their atoms in the command. Of course, that can be painful if you want to include very many atoms in the calculation. If the order is not given in the command, "the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number" as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> You can see command manual pages using the "help" command, e.g.: help rmsd What approach is best depends on your particular case -- whether these are multi-residue macromolecules or single-residue small molecules, and how many atoms you want to include in the calculation. If they are single-residue small molecules, you might just modify the mol2 files so that the atoms you want to pair have the same names in the two structures (but unique within a structure). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 15, 2010, at 2:11 AM, Victor Muñoz wrote: > Hi, > I want to calculate the RMSD between two mol2 structures in place. > The two structures are different forms of the same structure. I > haver modified the mol2 so that the two of them have the same > serialNumber in their respective atoms. The problem is that when I > use the command rmsd #model1 #model2, it return an incorrect value > of the rmsd, as the value showed is too high, about 5, when it > should be about 1 (the two structures are very similar). Is there > any way to calculate the RMSD value in place correctly or I am > doing anything wrong? > Thanks for your help. >

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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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