- Chimera-users - RBVI Mailing Lists

Query regarding Ksdssp assignment
by Arun Prasad Pandurangan 25 Jul '11

25 Jul '11

Dear Users and Developers, I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera? Looking forward for the advices. Thank you. with best regards, Arun Prasad

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Display of bond between CA's
by Greg Friedland 25 Jul '11

25 Jul '11

Hi, I'm trying to prepare an image from a structure in which I'd like to hide the backbone atoms except the CAs. When I do this for two neighboring residues however a long bond is drawn between the CAs. How can I hide this without hiding the CAs? Thanks, Greg

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creating multimeric units
by ALEXANDER MUCHUGIA 25 Jul '11

25 Jul '11

Hi, My name is Alexander Muchugia, I am a Bioinformatics student at Rhodes University, South Africa and I am working on modelling HIV protease. It is a dimer but Its modelled as a monomer. I was trying to look for software than can convert it as a dimer. I am enquiring if it is possible to use chimera to do it and how can I do it. Regards. Alexander.

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Chimera for Mac OSX Lion
by Victoria James 22 Jul '11

22 Jul '11

Hi there! I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? If not, will you be releasing another build soon that will be able to? Many thanks and kind regards Victoria

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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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Curved helical filaments
by Tom Goddard 11 Jul '11

11 Jul '11

Hi Andy, The "vop unbend" command can straighten the density from a curved filament. The tricky part is you need a center-line path. You could define that by placing 3 markers. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#unbend Bending a straight filament map to follow a curve is not available. This is the inverse of the vop unbend operation. You can do a fake version of this by making a helical curve around the straight density map and then using vop unbend. That won't center the filament on the helical path, but it will create something similar by straightening the helix which I think will twist the density. Tom > Hi Tom- > > Not sure if there is an option for this - > > 1. can we bend an electron density map of a filament/tube by an small > angle ? > > 2. Can we generate an helix using a density map of a filament. > An example will be that of the bacterial flagella - it has the local > helical arrangement of the flagellin molecule and then thAT > ARRANGEMENT extends over several micrometers like a "sinusoidal wave" > with different helical arrangement to the filament axis. > > Best > Andy > > > Dr. Anindito Sen (Ph.D) >

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Tear-off menus in Chimera 1.5.3 for Mac OS X
by Jeff Lawton 11 Jul '11

11 Jul '11

Hi, I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and it seems that the "tear off" feature of the menus is not available, though I was previously able to do that when running the X window version of Chimera. Is there a way to use the menu "tear off" feature in the native aqua version? Thanks! Jeff -- Associate Professor of Biochemistry Department of Chemistry Eastern University 1300 Eagle Road St. Davids, PA 19087 (610) 341-1545

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Re: [Chimera-users] distance between 2 residues
by Dedan Githae 11 Jul '11

11 Jul '11

how is the problem solved in chimera? i want to measure distance between 2 residues

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Invitation à se connecter sur LinkedIn
by Vincent Zoete 07 Jul '11

07 Jul '11

LinkedIn ------------ J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. Vincent Vincent Zoete Associate group leader chez Swiss Institute of Bioinformatics Région de Genève, Suisse Veuillez confirmer que vous connaissez Vincent Zoete https://www.linkedin.com/e/vxh6i1-gpupen7z-1e/isd/3469346511/KWdfhuHl/ -- (c) 2011, LinkedIn Corporation

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Problem with multiple monitors and NVidia 3D Vision - any suggestions ?
by Steven Ludtke 07 Jul '11

07 Jul '11

Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't go into stereo mode. Here are the relevant lines from the Xorg log file: [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 [ 9016.284] (==) NVIDIA(0): RGB weight 888 [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 [ 9018.466] (==) NVIDIA(1): RGB weight 888 [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision [ 9019.116] (II) NVIDIA(GPU-1): stereo. [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA [ 9021.570] (II) NVIDIA(1): stereo controller [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, it raises an error :^( Here are the relevant xorg.conf sections: Section "ServerLayout" Identifier "Layout0" Screen 0 "Screen0" 0 0 Screen 1 "Screen1" 2560 0 InputDevice "Keyboard0" "CoreKeyboard" InputDevice "Mouse0" "CorePointer" Option "Xinerama" "1" Option "XineramaStereoFlipping" "0" EndSection Section "Device" Identifier "Device0" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Tesla C2070" BusID "PCI:131:0:0" EndSection Section "Device" Identifier "Device1" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Quadro 4000" BusID "PCI:2:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Device0" Monitor "Monitor0" DefaultDepth 24 Option "TwinViewXineramaInfoOrder" "DFP-2" Option "TwinView" "0" Option "metamodes" "nvidia-auto-select +0+0" SubSection "Display" Depth 24 EndSubSection EndSection Section "Screen" # Removed Option "metamodes" "nvidia-auto-select +0+0" Identifier "Screen1" Device "Device1" Monitor "Monitor1" DefaultDepth 24 Option "TwinView" "0" Option "metamodes" "1920x1080_120 +0+0" Option "Stereo" "10" SubSection "Display" Depth 24 EndSubSection EndSection Section "Extensions" Option "Composite" "Disable" EndSection Anyone else have a Stereo configuration with dual monitors working ? cheers ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging Dept of Biochemistry and Mol. Biol. Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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Re: [Chimera-users] Regarding adding plane surfaces....
by Elaine Meng 07 Jul '11

07 Jul '11

On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote: > Hi Elaine, > > I have three objects in the chimera image. > All these objects are in different planes. > How to add surfaces to each of these so that they can be shown to lie in diff planes? > I have attached a typical image herewith. > > Regards, > Chinmaya Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms. The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Thanks, 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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Chimera function
by Flora Ieong 07 Jul '11

07 Jul '11

To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong

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movie script
by Jean-Francois Menetret 06 Jul '11

06 Jul '11

Hello, I am trying to make a movie to illustrate a conformational change between two PDBs; I would like to turn the objects while switching from one to the other. Could you give me some pointers ? Thank you J-F

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Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 06 Jul '11

06 Jul '11

Thanks Elaine, I did check out the CCL website; a great resource. Mickey >>> Elaine Meng 07/05/11 6:25 PM >>> Hi Mickey, I don't have experience in this area, but you might try asking on the Computational Chemistry List (www.ccl.net) as to what programs might be suitable for predicting the structure of your complex. One way is to use their web form http://www.ccl.net/cgi-bin/ccl/send_ccl_message Best, 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 Jul 2, 2011, at 1:46 AM, Mickey Branham wrote: > Thanks Elaine, > Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. > > So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. > > We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. > > Don't know if this seems interesting but any comments from you would be appreciated. > > Thanks again for your response. > > Cheers > Mickey Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

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Not Responding
by Chad Junkermeier 05 Jul '11

05 Jul '11

Hello, I have been having strange behavior lately with opening coordinate files. I am using xyz format files with up to 500 atoms. When I tell Chimera to open one of these files the computer sits for a moment and then starts reporting that Chimera is "Not Responding." I have tried this on three different Mac computers, one using OS X 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram, NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB RAM, and I don't know anything else). On each of these machines I have tried using a variety of different versions of your code, and I continually find that I have the same problem. I also just installed Chimera on a Windows XP machine and it has similar issues. The xyz files are the product of relaxing a graphene sheet in Quantum Espresso, and then copying and pasting the final configuration out of the QE output file into a xyz file. Here are a few of the things that puzzle me. First, if I place the input configuration of atoms into a xyz file, Chimera will read in the structures without any problems. The output xyz files work in VMD and in iMol. I thought that it might be an issue with the xyz data structure and transformed it to PBD and it still wouldn't load. I also wondered if it was an issue of too many decimal points (higher precision than the input file), but after reducing the number of decimal points of each coordinate on all of the atoms, it still wouldn't work. I have looked through some of the output files and there doesn't appear to be any weirdness in any of the files. Further complicating this issue is that sometimes, after if I let it sit for a while, the program magically starts working. Again, I have no problem opening other files. Does anyone have any ideas on what to do to fix this problem? Chad

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Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 05 Jul '11

05 Jul '11

Thanks Elaine, Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. Don't know if this seems interesting but any comments from you would be appreciated. Thanks again for your response. Cheers Mickey >>> Elaine Meng 06/23/11 6:23 PM >>> Hello Mickey, Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. 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 Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: > Dr. Meng > Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. > > Cheers > Mickey > > Michael Lee Branham, PhD. > University of KwaZulu-Natal > School of Pharmacy and Pharmacology > Durban, South Africa > > Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer > Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

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