July 2007 - Chimera-users - RBVI Mailing Lists

Chimera on Linux
by Beale, John 30 Jul '07

30 Jul '07

I have been using Chimera on a Linux-equipped laptop for a long time. All that I had to do to get the software working was to download the appropriate version of Chimera and click on the executable. I am trying to install Chimera on a new Linux workstation. I downloaded the program for Linux, but when I try to run the executable I get a message that says that the software downloaded is for MS-DOS and not Linux, and I am unable to install Chimera. Has anyone run into this problem, and is there a fix for it? John Beale

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CSB 2007 Molecular Visualization tutorial
by Conrad Huang 30 Jul '07

30 Jul '07

Scooter Morris and Conrad Huang will be giving an introductory molecular visualization tutorial using Chimera on August 13 at CSB 2007 (the Conference on Computational Systems Bioinformatics) in San Diego. Interested folks can visit http://www.lifesciencessociety.org/CSB2007/index07.html for more information on CSB 2007. The tutorial abstract is attached below. An Introduction to Molecular Visualization Tutorial at the Computational Systems Bioinformatics (CSB) conference (AM2) University of California, San Diego August 13, 2007 Abstract Projects such as Structural Genomics are providing increasing numbers of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools. Attendees will learn the basics of molecular visualization and will be provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own data to the visualization. Outline: 1. Introduction to Molecular Visualization 2. Available Tools 3. Using UCSF Chimera 4. Scenarios of use 5. Extending Chimera

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Fwd: CCL: hydroxide for dock
by Elaine Meng 25 Jul '07

25 Jul '07

Begin forwarded message: > From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner- > chemistry(a)ccl.net> > Date: July 25, 2007 7:50:36 AM PDT > Subject: CCL: hydroxide for dock > Reply-To: "CCL Subscribers" <chemistry(a)ccl.net> > > Hi, everyone, > I'm preparing structures with Chimera for docking with Dock6. There > is a Zn-coordinating hydroxide that I want to keep in the > structure. When I prepare dock files, Chimera always treat it as a > water. Is there any way to define it as a hydroxide in Chimera? > Thanks, > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan_+_mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ Dear Yubo, I could answer more precisely if I could see the file, but without seeing it, I recommend: (a) looking at the residue name of the hydroxide in the text of the file. Is it WAT or HOH? If so, you could edit it to a different name, say XOH or HOM. (b) then, run Dock Prep in Chimera including hydrogen addition and all the steps before that (but don't assign charges or write the Mol2 file). (c) check the structure; if hydrogen is added where you didn't want it, simply delete it. For example, Ctrl-click to select an atom and use "Actions... Atoms/Bonds... delete" in the menu to delete it. The protonation states are intended to be reasonable at physiological pH, but if a group is expected to have a perturbed pKa (for example, in an active site or near an ion), it is a good idea to check it and manually add/delete hydrogens as needed. ( more details in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html ) (d) run Dock Prep again with only the steps AFTER hydrogen addition (charge assignment and Mol2 file output) turned on. If it asks for the net charge of XOH (or whatever you named it), indicate -1. (e) that procedure will use Antechamber to calculate the partial charges on the hydroxide O and H. If, however, you already know the charges you want to use for these atoms, you can edit the charge values in the output Mol2 file. In that case you wouldn't even have to go through all these steps, but could simply also delete the extra hydrogen from the Mol2 file, if you can figure out which line it is! I just realized this last point, so it wasn't in my original reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Windows Vista
by Jason M Walraven 23 Jul '07

23 Jul '07

I just installed the latest version of Chimera on my Windows Vista operating system (home basic). Everything seems to work perfectly, except that the colors appear to be messed up. The colors appear darker than on my previous computer (with Windows XP). Has anyone else had this problem? All colors in all other programs are normal on my computer except for in Chimera. I assume it is a compatibility issue, but I don't know enough about it to say that for sure. jw

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Re: [Chimera-users] Reading a data set from a text file
by Thomas Goddard 17 Jul '07

17 Jul '07

Hi Kyaw, I see what you've done and see that you have a set of (x,y,z) coordinates. But I'm not sure what you want or what these coordinates represent. To make a surface out of a set of points you need to know which points are next to each other. In Chimera you need a set of points, and a set of triangles, each triangle defined by 3 integer indices into the set of points that give the triangle vertices. If you can define the set of triangles I can tell you how to make the surface. Tom Kyaw Zeyar Myint wrote: > Hello Tom, > I apologize for not being able to respond to you earlier. The > set of view vectors that I want to make surface out of it are in (x, y, > z) coordinates. > > So far, I've done a quick and 'rough' way of using these vectors for > display. What I did in chimera was that I wrote a mini plugin which > makes a .bild > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> file with a > set of cylinders, given a set of vectors. > Each cylinder is centered at origin (0,0,0) and drawn according > to the vector (which is from my set of view vectors). So if the V(x,y,z) > has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by: > /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 / in .bild file. > Then .bild file is fed into chimera and then a set of cylinders > is displayed. In a sense, each cylinder represents each view vector in > the set. But this is just a quick solution. > If you can share some ideas of how to better do this, please let > me know. I'd really appreciate your help. > > Thanks a lot! > Kyaw > (P.S: I've attached .bild file which you can display in chimera and see > what inside using a text editor.) > > ------------------------------------------------------------------------ > > > On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote: > >> Hi Kyaw, >> >> I'm not sure I understand what type of data you want to display in >> Chimera. Is it a list of density values, or is it a list of x, y, and >> z coordinates? If it is density values in text rather than binary, >> you could reformat it into XPLOR format >> >> http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html >> >> which can be read into Chimera. >> >> Tom >

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presets criteria
by Roberta King 17 Jul '07

17 Jul '07

Hello, I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket? This is a useful shortcut, but I would like to understand the specific criteria. Thank you very much, Roberta ******************************** Roberta S. King, Ph.D. Associate Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 16 Jul '07

16 Jul '07

Hi Pasquale, You can definitely open multiple PDB files and move them independently. By default everything will move together, which might even be what you want. However, if you don't want them to move together, you can freeze any structure in place ("deactivate" it), move the other(s), and then "activate" the first structure again if you want it to be movable. There are several ways to control activation/deactivation; probably the easiest is to open the Model Panel (Favorites... Model Panel). Then just uncheck/check the box in the Active column to freeze/ unfreeze a model. We use the word model to mean the contents of a structure file (PDB, Mol2, etc.), so if you read in two separate PDB files, there would be two models listed in the Model Panel. Alternative ways of controlling activation/deactivation are with the little checkboxes under the Command Line and using the command "select". You would still be able to minimize multiple models as a single system by choosing all of them in the "Minimize Structure" dialog. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote: > well in order to make the dimer i used two separate pdb files and > imported them both into the same gaussian gjf file. then i imported > that file as a mol2 file into chimera, so unless i can manipulate > separate pdb files in chimera then that would be great but i cannot > figure out how to move separate pieces of my dimer. > > On 7/15/07, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Pasquale, > I had one long-shot possibility for getting the correct atom and > residue names - did you start with a PDB file before the guassian > calculations? If so, that file may have had the correct atom and > residue names. If that starting file had all the same atoms > (including hydrogens) and the order of the atoms is exactly the same > in that gaussian output, you could simply replace (probably with a > script) the coordinates in each line of the starting PDB file with > those from the gaussian output. That would only work if the order is > exactly the same, however. > > Otherwise it would be extremely tedious to figure out which > coordinates go with which atom/res/number. > Best, > Elaine

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ValueError: More than 2 coplanar positions specified!
by Mike Gretes 13 Jul '07

13 Jul '07

Hello, When trying to calculate hydrogen bonding between two molecules, I get the error: "ValueError: More than 2 coplanar positions specified!" I have successfully calculated h-bonding between two other similar molecules, so I'm not sure what the problem is (I have no alternate conformations or anything weird in the PDB files I don't think... is there anything that usually triggers this error?) thanks! mike ___________________ Michael Gretes PhD Candidate (Structural Biology) Senior Graduate Trainee, Michael Smith Foundation for Health Research NCJ Strynadka Laboratory Dept. of Biochemistry, University of British Columbia Life Sciences Center, 2350 Health Sciences Mall Vancouver, BC Canada V6T 1Z3 phone 604 822 7729 fax 604 822 5227 ____________________

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Forward of moderated message
by mailman-bounces＠cgl.ucsf.edu 13 Jul '07

13 Jul '07

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 11 Jul '07

11 Jul '07

Hi Pasquale, As Eric figured out, your mol2 file does not contain substructure information. For the structure to be read by Chimera as a series of residues, there would need to be residue information in each line in the @<TRIPOS>ATOM section and then a corresponding @<TRIPOS>SUBSTRUCTURE section at the bottom. You would have to edit that information into your file. Otherwise, the structure appears as one big residue. Mol2 format description: http://www.tripos.com/mol2/mol2_format8.html ATOM section - need substructure ID and name (residue number and name) for each atom http://www.tripos.com/mol2/mol2_format33.html#1370 SUBSTRUCTURE section - more information on those substructures (residues) To get an example mol2 file, open a PDB file of a protein in Chimera, add hydrogens if you want those in your example, and then write it out as Mol2 (File... Save Mol2...) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote: > Hi Pasquale, > If your structure all got put into a single residue named UNK, > that typically means that your file was missing the @SUBSTRUCTURE > section (http://www.tripos.com/mol2/mol2_format33.html#1370) > There is an entry in our bug database (#3518) for better handling > of files with missing @SUBSTRUCTURE sections. I will add your name > to that report so you'll know when it gets fixed. For now, you > will have to edit your file and add an @SUBSTRUCTURE section "by > hand". > > --Eric >> >> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote: >> >>> Hey Elaine, >>> My structure is currently being labeled as one big residue >>> (UNK) and when I minimize it it says it does not recognize the >>> residue, so it seems like the calculation program is using >>> residue parameters and not those for specific atoms. Also, my >>> structure contains a Zn(II) metal center and I was wondering if >>> the parm files would detect it as such if it actually used the >>> atom types. I attached my mol2 file so you can check it out. Thanks >>> -Pasquale Iacono

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