- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Structure -> Match in a script
by Eric Pettersen 20 Jul '11

20 Jul '11

On Jul 20, 2011, at 2:09 PM, Sierk, Michael wrote: > Eric, > > Thanks for the script! It works but I have a couple of issues still: > > 1) The second sequence in the alignment is not automatically being > associated with the second structure. (It looks like the first > sequence/structure association is done automatically, but not the > second.) I can do it manually with Structure->Associations (with > zero mismatches), and then the script works. Is there a way to > create the second association via either the Chimera command line or > using python? Is that association supposed to occur automatically > as well? AFAIK the second sequence should associate. If you send me the alignment and the structures (or tell me their PDB codes if they're standard PDB entries) I can investigate (send them off-list!). > 2) What I am trying to do is load in two molecules and 3 different > sequence alignments of the two molecules. In my Chimera script I > make 2 copies of the 2nd molecule (using "combine") and color them > differently. I would like to then do the Structure->Match process > for each of the 3 alignments. Does the "findMAV" function in the > mavMatch.py script return all instances of MAVs or just one? I know > the titles so could I perform 3 different mav.match statements, one > for each MAV instance? Well, this is a more complicated scenario than what the script I wrote really handles -- since you have multiple MAV instances and only want certain open structures to associate with each instance despite the fact that those structures are identical. So it needs two scripts! Here's the approach: In your Chimera script: 1) Open the three alignments. 2) Open the first Python script (no-auto-assoc.py) to turn off auto- association in the MAV instances. 3) Open your two structures, "reference" structure first (more specifically, in a lower model number than the matching structures) 4) Make the two copies, or just open the second structure two more times. 5) Run the second Python script (assoc-and-match.py) to associate the reference structure with the first sequence in all the alignments, and one copy of the matching structure with the second sequence in each alignment, and then match them. --Eric

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problem with a script calculating distance between residues
by Damien Larivière 20 Jul '11

20 Jul '11

Dear all, The script below has been validated for me by the Chimera team sometimes ago. In fact this script does not work each time I run it: When reaching the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... Chimera can remained fixed on the current PDB file as if it faces problem to open it. I'm forced to close Chimera which does not respond anymore. The exit code is 805306369. I attached dockSL0009.pdb and dockSL0010.pdb. What can I do to report this bug (which may be due to something external to Chimera; my Chimera version is 1.5.2 Build 32411; my plateform is Windows 7 64 bits) since I have to brutally stop Chimera, and know more about this problem? Many thanks for your help Damien from chimera import runCommand as rc #from chimera.tkgui import saveReplyLog for i in range(1, 101): rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) rc("distance :246.C@CB :297.A@CB") rc("distance :246.C@CB :297.B@CB") rc("close all") #rc("saveReplyLog('replyLog%04d.txt')" % i)

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Structure -> Match in a script
by Sierk, Michael 20 Jul '11

20 Jul '11

All - I would like to write a command file that will automatically read in two structures and a corresponding alignment file, then perform the superposition (and coloring, etc.). I can read in the pdb and pir files using the command line, and I can do the superposition in the Multalign Viewer using Structure->Match, but I cannot figure out how to do the superposition based on the sequence using the command line. I think if there was a way to select the residues that are aligned in the sequence alignment I could use the "match" command, but I don't see a way to do that. Is there an attribute analogous to mavPercentConserved that corresponds to "aligned"? Or is there an automatically generated region based on the sequence alignment? Thanks, Mike Sierk +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Michael Sierk Email: michael.sierk<AT>email<dot>stvincent<dot>edu Assistant Professor of Bioinformatics Phone: (724) 805-2367 Saint Vincent College Office: Physics 205 ----------------------------------------------------------------------------------------------------------------------------------------- "There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact." -- Mark Twain. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Re: [Chimera-users] Listing hydrogen bond geometries
by Elaine Meng 18 Jul '11

18 Jul '11

Hi Greg, For FindHBond, Chimera "imagines" the possible locations of hydrogens given the atom types (element, hybridization state) of the heavy atoms. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon…> "When there are no explicit hydrogens on a potential donor atom, FindHBond will use the donor atom type to infer their presence. For functional groups where the hydrogen positions are well-determined by the positions of the nonhydrogen atoms, the H-bonds detected in the presence and absence of explicit hydrogen atoms should be virtually identical. For functional groups where the hydrogen position is not well-determined (such as rotatable hydroxyls), the presence of an explicit hydrogen atom will limit the detected H-bonds to those appropriate for the observed position, instead of all of its possible positions." If you want explicit hydrogens, you could use Chimera's AddH tool (under Tools... Structure Editing) or addh command. By default, it will look at the surroundings and try to place hydrogens to make hydrogen bonds. However, it does not exhaustively optimize the H-bonding network of the whole structure. The goal is to determine reasonable positions based on immediate surroundings in a fairly short time. However, if you add explicit hydrogens and then use FindHBond, there will be fewer possibilities listed, as explained above. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> For the next level of computational intensity in adding hydrogens, we recommend the "Reduce" program from the Richardson lab. From the bottom of the AddH page, "When a more intensive approach is desired, the program Reduce (developed by the Richardson Laboratory) is a good alternative. Reduce places hydrogens to optimize local H-bonding networks and avoid steric overlaps, while flipping certain sidechains 180 degrees as deemed appropriate to fulfill these criteria. Asparagine and glutamine sidechains may be flipped to switch their terminal N and O atoms, and the imidazole ring of histidine may be flipped to switch N and C identities. The protonation state of histidine is adjusted based on the local environment. Reduce is available free at http://kinemage.biochem.duke.edu: • for on-line use as part of the MolProbity service, on a file uploaded or chosen by PDB code (individual sidechain flips can be accepted or rejected) • for download (from the Software section) to run on most platforms and is described in: Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Word JM, Lovell SC, Richardson JS, Richardson DC. J Mol Biol. 1999 Jan 29;285(4):1735-47. " I hope this helps, Elaine On Jul 18, 2011, at 2:16 PM, Greg Friedland wrote: > Hi Elain, > Thanks very much for you response and sorry for the delay in getting back to you. > > I am trying to determine the potential hydrogen bonding potential (i.e. the ability to form these bonds) from hydrogen-less structures (they are from the PDB). I have been trying to model in the hydrogens but it is not trivial since there are many hydroxyls, which can rotate about their dihedrals. (if you have suggestions on how to model these hydrogens it'd be great to know about them). > > So until I can get a good model with the hydrogens attached I am wondering how Chimera is able to determine potential hbonds from heavy atom positions only. Any insight you can provide would be appreciated. > > Cheers, > Greg

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Listing hydrogen bond geometries
by Greg Friedland 14 Jul '11

14 Jul '11

Hello, I would like to list the hydrogen bond geometries between two models. I have found the feature to do this in the FindHBond panel but it only lists the distances not the angles. This information appears to be used in identifying the hydrogen bonds however, so is it possible to extract this information as well? If not, can you suggest another tool that could do this? Thanks, Greg

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(no subject)
by efratk＠techunix.technion.ac.il 14 Jul '11

14 Jul '11

Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat

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(no subject)
by efratk＠techunix.technion.ac.il 14 Jul '11

14 Jul '11

Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat

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saving coordinates from a session and re-opening them in another one
by Boaz Shaanan 14 Jul '11

14 Jul '11

Hi I save selected & displayed coordinates (using save pdb) from a session, in order to incorporate them into another session. It’s a selected zone around the active site. When I open them in the new session they look strange. Also, the saved coordinates don’t always contain the full set of displayed coordinates (I’ve done this several times on different structures and it seems particularly but not just on pdb’s with aniso card). I’m attaching the session whose coordinates I saved + the saved coordinates (I hope that’s OK with the BB policy). Please help me figure out the problem. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail:bshaanan@bgu.ac.il Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan

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DMS output format
by Efrat Kligun 13 Jul '11

13 Jul '11

Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat

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3D chimera
by Bigley, Andrew 11 Jul '11

11 Jul '11

Dear Chimera Developers, The recent advances in 3D technology is affording some unique opportunities to people interested. I have recently seen advertisements for new glasses free 3D smart phones. Can you adapt chimera for such a platform and hence convert a smart phone into a portable 3D protein viewer that would allow manipulation of the view through typical touch screen commands? Andrew N. Bigley, Ph.D.

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