- Chimera-users - RBVI Mailing Lists

Ensemble cluster
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, As a preamble, it is quite possible that I completely misunderstood the way to use the Ensemble cluster tool. Here is the problem I face: I opened a PDB file containing 8 models. The models have the same number of atoms, the same numbering, the format is Model Endmdl, etc. I launched Ensemble cluster in order to identify clusters. From the image below, one can see visually 2 clusters. Chimera effectively identifies 2 clusters _but _the representatives of each (in red and blue-turquoise) belongs to the same cluster. I expected one representative in each of the two clusters. May you tell me what is wrong with my understanding? Many thanks for your help, Damien ps : Is there a way to cluster according to a previously chosen RMSD?

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Command line history
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, I just installed the last release for Windows (June 07, 2013). I would like to get back the command line history I had in the previous version. I saved this command line history in a file named/chimera.cmd/. May you tell where to copy/chimera.cmd/ in the program files of my new Chimera? (I've made a search in the Windows explorer for /chimera.cmd/ but nothing was returned) Thanks, Damien

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Hydrophobicity surface
by Anne Simonsen 19 Jun '13

19 Jun '13

Dear Chimera helpers, I'm trying to make a figure showing the hydrophobic surface of one chain (chain A in attached IGA1.pdb file) with a peptide (chain B) shown as ribbon with residues, but I then get a "hole" in the A surface around the peptide (see attached figure). Can you please advice? Thank you! Best wishes, Anne -- Anne Simonsen, PhD, Professor Dept. of Biochemistry, Institute of Basic Medical Sciences University of Oslo, P.B. 1112 Blindern 0317 Oslo, Norway Visiting address: Domus Medica, room 3174 Sognsvannsveien 9 0372 Oslo Phone: +47 22 851110 Fax: +47 22 851058 Mobile: +47 99350960 email: anne.simonsen(a)medisin.uio.no http://www.med.uio.no/imb/english/research/groups/autophagy/

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adding an O in compound 1
by Ibai Gazpio 18 Jun '13

18 Jun '13

Hi all, I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use? Ibai.

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Chimeras limited capability to visualize correctly molecular structure
by Marek Maly 18 Jun '13

18 Jun '13

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera - ball and stick - 3D printing
by Francois Richard 18 Jun '13

18 Jun '13

Hi everyone, I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer. I would like to print the ball and stick representation of the molecule, including the hydrogen bond. So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond. Do you have any idea how to improve the output? Thanks a lot, Francois

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protein schematic representaton
by francesco oteri 13 Jun '13

13 Jun '13

Good morning to everybody, someone of you knows whether exist a program that creates schematic representation of a protein like the one in plot b and d of the figure: http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html Greetings, Francesco

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Missing segment confuses addH
by Sam Egel 13 Jun '13

13 Jun '13

Hi, Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera. More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz). Thank you for your time, Sam

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display of glycine atoms
by Levandoski, Mark 11 Jun '13

11 Jun '13

Hello there - I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view. Thank you very much in advance for the help, Mark P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element. Mark M. Levandoski Associate Professor of Chemistry Grinnell College 641-269-4544

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Selecting regions of a PDB structure
by Anindito Sen 11 Jun '13

11 Jun '13

Dear All, I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that. Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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