- Chimera-users - RBVI Mailing Lists

rebuild DNA
by Damien Larivière 14 Apr '11

14 Apr '11

Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien

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Problem for docking result analysis
by Bishwajit Das 12 Apr '11

12 Apr '11

Hi, I load a docking results in .pdb format,now how can i view inter-molecular bonding information with chimera. please help me. -- * BISHWAJIT DAS*** KOLKATA

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Merging of two pdb files
by Monisha Hajra 11 Apr '11

11 Apr '11

Hi, I have modeled one protein. I have pdb file of the protein. I want to merge the protein with one co-factor (I have the pdb file for the same). Can I merge them in one file using Chimera? If not, then any other tool can you suggest? Regards Monisha

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NMR average structure
by Lucio Ferella 11 Apr '11

11 Apr '11

Hi all, I need to calculate an average structure (or select the most representative member of), from an NMR emsemble structures in Chimera. Is it possible? Thanks for any helps. Lucio

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recording path through centroid
by Francesco Pietra 11 Apr '11

11 Apr '11

Hello: Is it anything new about recording path by the way of the centroid? I did not use it since September 2000. It worked nicely, though -being at illustrations for a candidate publication - my question is whether it has been improved further. thanks francesco pietra

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Hydrophoic and Hydrophilic solvent accessible surface area
by Monisha Hajra 09 Apr '11

09 Apr '11

Hi Team, Can I calculate Hydrophoic and Hydrophilic solvent accessible surface area in Chimera? If so, let me know how? Really appreciate help. Regards Monisha

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Labeling 3D structures in Chimera (and saving them as such)
by Bilal Asif 08 Apr '11

08 Apr '11

Hello, I am a senior undergraduate student at Stony Brook University, part of a team currently attempting to design an introductory biology lab for biology undergraduates. We are attempting to use Chimera as a way to introduce students to structural biology and research. However, we have run into a problem, one which we hope you can help us solve. We have discovered that if one attaches a label to a molecule in Chimera, one cannot save it as a .pdb, and open it again with the same labels attached. Is there a way to preserve labels attached to 3D structures, perhaps by saving it in a different file format? Thank you for your time and consideration. Any insight would be greatly appreciated. Bilal Asif Stony Brook University

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problems in chimera display
by manidip_rs＠iicb.res.in 08 Apr '11

08 Apr '11

  I have downloaded and installed chimera-1.5.3-linux_x86_64.bin, release date April 05,2011.  But after opening a volume data the volume is appearing as random slices.  I have checked all the other necessary requirements. I am using RHEL 5.4 and NVIDIA graphics.  Please suggest.                                                                                                                                                                                                      Thanks,                                                                                                                                                               Manidip Shasmal, Research Fellow,                                                                                                                                                               Indian Institute of Chemical Biology, kolkata -700032 Do not Remove: [HID]20110408124249826[-HID] **************************************************** VirusFree, Spamfree, power packed email service. ****************************************************

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Controling the configuration of chiral atoms.
by vincent zoete 08 Apr '11

08 Apr '11

Dear Chimera team, We are very satisfied daily users of Chimera for drug design and protein engineering applications in our lab. Congratulations for your great work! I would like to come back on the point raised by Dr. Charbel MAROUN recently. Having the possibility to change the configuration of whatever chiral atom would be very useful for drug design applications. It's true that we can do it using other software like Pymol or HyperChem, to cite just two of them arbitrarily. But it would be much more convenient to rapidly and graphically do it in Chimera, without the need to switch to another program for that particular and single action. We are often working with D-amino acids and chiral small molecules. We apreciate a lot the "Build Structure" module to construct or modifiy such compounds, and allowing more control on the chiral center configuration would be very useful. Do you think you could consider adding such chirality inversion command in the future? Sincerely, Vincent Zoete, Molecular Modeling group - SIB www.click2drug.org =========================================================== Hello, Sorry, Chimera does not do that. I am pretty sure that SYBYL and probably some other programs will do it, but you may want to ask on a more general list such as CCL.net for a more certain and detailed answer about other programs. 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 Jan 28, 2011, at 6:15 AM, R. Charbel Maroun wrote: > Hi everybody, > Is there an easy and quick way to invert the chirality of an atom, say a Ca ? > Greetings, > ----------------------------------------- > R. Charbel MAROUN, Ph.D., H.D.R.

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Hydrogen bond cut off
by Simon Sham 07 Apr '11

07 Apr '11

Hi, First, I don't have access to the reference by JE Mills in Journal of Comp. Aided Design 1996. Secondly, can someone please tell me that in chimera is the cut off distance between the donor and acceptor atoms 3.5 angstroms and cut off angle 35 degrees? Thanks for your help in advance. Simon

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Problem for selecting the Recepter and ligand
by Bishwajit Das 07 Apr '11

07 Apr '11

Hi I am using chimera,i am a new user of this and i open a docking model in .pdb format. Now my question is how i seen that model which is recepter and which is ligand.How i differentiate with recepter and ligand with two another colour. Please help me with step by step Thank you -- * BISHWAJIT DAS*** KOLKATA

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salt bridges
by Simon Sham 07 Apr '11

07 Apr '11

Hi, I have tried to find out salt bridges with chimera. According to the archive: "findhbond selRestrict both saveFile ~/mydir/myfile" 1. I could not find "selRestrict" under "FindHbond". I am using the latest version of CHimera. Thanks for your help in advance. Best, Simon Sham

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Scrollbar in Structure/sequence associations
by Lucio Ricardo Montero Valenzuela 06 Apr '11

06 Apr '11

Hello. I want to suggest that a vertical scrollbar be added to the Structure/sequence associations dialog box, because whenever there are more than ~17 models, the last ones are not reachable. Lucio

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Suggestion
by Davis, Derick C. (MU-Student) 04 Apr '11

04 Apr '11

Hello, I was wondering if the developers have considered creating an application of Chimera for the iPhone or iPad? If not, they should :) Thank you, Derick Davis

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Map's Box size
by יוכבד 04 Apr '11

04 Apr '11

Hi Can I please get your help with map resizing. I have a map with a box size 250,269,108. To run a map fitting script I need the map to have a cubic size. Using the volume viewer- Region min max step x - I was able to play with the box size the problem is I can't get the entire map into a cubic box (Z axis is to small). Is there a way to enlarge the box on the Z axis? Thank you Yocheved

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Thermal ellipsoids are not updated when playing multi-frame PDB trajectory
by Lukasz Walewski 01 Apr '11

01 Apr '11

Hi, I am looking at the trajectory with thermal anisotropy factors that change from frame to frame, i.e. I have a multi-frame PDB file that contains ATOM and ANISOU records. The components of the anisotropy tensors change during the simulation (the data I am analyzing has a redefined meaning). I am able to properly read and play the trajectory. Ellipsoid representation of the thermal U factors works excellent for a single frame. However it seems that the ellipsoids are not updated when I play the trajectory, i.e. the atoms move as expected but the ellipsoids retain both their positions and shape from the first frame. Is there any way around ? In any case I find Chimera wonderful software that I came upon only recently. Thanks guys for developing it! With best regards, Lukasz

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Script for getting the map values of fitted residues.
by Robert Ford 29 Mar '11

29 Mar '11

I was wondering if there was a script available that would get the map density values of amino aid residues in a model fitted to an EM or X-ray density map and then write the data to a text file? Essentially what I need is something that does something like this (but not laboriously by hand) e.g. in command line mode select #1:1.B then I use Tools>Volume Data>Fit in Map and click 'Update' to get the average map density value for the atoms in amino acid residue number 1 in chain B of model 1. Many thanks for your help Bob Ford, Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, 131 Princess St., The University of Manchester Manchester M1 7DN, UK. Tel: +44(0)161 2004187 Fax: +44 (0)161 3068918 bob.ford(a)manchester.ac.uk www.ls.manchester.ac.uk

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Ask a question
by ding kevin 29 Mar '11

29 Mar '11

Hi, I am a freshman to use Chimera. When I run "add charge" of ligand by the tutorial, and the error below appears. I would like to know the reasons and how could I solve this problem. Thank you very much! Charge model: AMBER ff99SB Assigning partial charges to residue ARA (net charge +0) with am1-bcc method Running ANTECHAMBER command: D:/drivers/Chimera 1.5.3rc/bin/amber11/bin\antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 -fi mol2 -o c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (ARA) cygwin warning: (ARA) MS-DOS style path detected: c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 (ARA) Preferred POSIX equivalent is: /cygdrive/c/users/dingzh~1/appdata/local/temp/tmpkghulj/ante.in.mol2 (ARA) CYGWIN environment variable option "nodosfilewarning" turns off this warning. (ARA) Consult the user's guide for more details about POSIX paths: (ARA) http://cygwin.com/cygwin-ug-net/using.html#using-pathnames (ARA) /usr/bin/antechamber.exe: error while loading shared libraries: ?: cannot open shared object file: No such file or directory (ARA) Error: cannot run ""D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit (ARA) Running: "D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Failure running ANTECHAMBER for residue ARA Check reply log for details -- Zhaoyang Ding East China University of science and technology Shanghai China

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recovering saved pseudobonds; or convert pseudo to bond?
by Kelly Dryden 29 Mar '11

29 Mar '11

Hi, I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? Thanks, Kelly

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Re: [Chimera-users] [chimera-dev] Energy Minimisation Citation
by Nancy 29 Mar '11

29 Mar '11

Thank you very much for your explanations, I greatly appreciate it. Nancy On Mon, Mar 28, 2011 at 1:47 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Konrad, > Thanks for the MMTK citation link. The force field information is in the > Chimera minimization man page, for example: > > < > http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/minimize/min… > > > > To summarize, Amber ff99 is used for standard residues and monatomic ions, > Antechamber/GAFF for nonstandard residues. Of course, the page above also > mentions MMTK and links to its documentation. 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 Mar 28, 2011, at 10:24 AM, Konrad Hinsen wrote: > > > On 28 Mar, 2011, at 5:26 , Nancy wrote: > > > >> I used the "Minimize Structure" feature of Chimera to minimize several > ligand molecules in preparation for docking (with the "Gasteiger" charges > option). I need to cite this in an article that I am to submit for > publication, and I need a bibliography of the software, including a > description of the minimisation algorithm, force field, etc... Please let > me know how I should go about this? > > > > The minimization code used by Chimera comes from MMTK, whose reference is > this paper: > > > > > http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2 > > > > The force field is some dialect of Amber, though I don't know which one > exactly is used by Chimera. I hope someone else can provide that > information. > > > > Konrad. > >

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(no subject)
by Hernán Costa 28 Mar '11

28 Mar '11

Hi I need to obtain mutation on differents sites on a protein but i can´t. How can I create a mutual mutation an know if the rotamer selected is Ok? Thanks Hernán Costa

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Energy Minimisation Citation
by Nancy 28 Mar '11

28 Mar '11

Dear All, I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option). I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc... Please let me know how I should go about this? Thank you very much, Nancy

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RMSD Calculation
by Nancy 27 Mar '11

27 Mar '11

Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy

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displaying DelPhi results
by Knut Langsetmo 26 Mar '11

26 Mar '11

Hi, I have done a DelPhi calculation on my protein, and when I try to display it, I get the error: "File cam.phi, format delphi Record size 1852798752 > file size 26826676" Any suggestions would be greatly appreciated. Thanks, --Knut

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Automated RMSD Calculations
by Nancy 25 Mar '11

25 Mar '11

Hi All, I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations? Thanks in advance, Nancy

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Chimera production release candidate (1.5.3)
by Elaine Meng 25 Mar '11

25 Mar '11

A Chimera production release candidate (version 1.5.3) is now available: <http://www.cgl.ucsf.edu/chimera/download.html> Please try it and report any problems. The 1.5 series includes 64-bit versions and will be the last for X11 on Mac (not to worry, the native Mac versions will still be supported). See the release notes for changes relative to previous versions of Chimera: <http://www.cgl.ucsf.edu/chimera/1.5.3/docs/relnotes/1.5.html> Relative to 1.5.2, version 1.5.3: - corrects line width in saved images (affects mesh, silhouette edges, and other lines such as H-bonds) - fixes error on Windows associated with non-Unicode usernames - turns multisampling off by default on Macs (it was associated with bad behaviors on some Mac systems) 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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installation problem
by estrella＠cartuja.csic.es 23 Mar '11

23 Mar '11

Hi, I´ve tried hardly to intall the last Chimera version for Windows (chimera 1.5.3rc), but at the phyton execution time, I have this message: "Unable to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this error and it possible solution in internet, without any success. Could you help me? Thanks so much Estrella

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Re: [Chimera-users] chimera help...please...
by Eric Pettersen 23 Mar '11

23 Mar '11

On Mar 23, 2011, at 2:32 AM, Amit Kumar wrote: > > Dear Pettersen, > first of all I like to thanks you as i am getting always nice > graphics from chimera software and hope you still involve in > improving it to compete all over good structure visualizers.... > I am a frequent user of this visualizer and already cited in all my > papers internationally published. I am struggling in getting ... I'm happy you've gotten good results with Chimera, and thanks for the citations -- they help us get our funding renewed! > 1) user guide of UCSF Chimera in pdf version as whole If you go to the Chimera home page and click on the "Documentation" link, there will be a list of links to various documentation. One of those links will be for a PDF of the 1.5 version of the User's Guide. It's about 12.5 MB (828 pages). The Chimera documentation was always designed to be hyperlinked web pages, so the PDF version is not as well organized or concise as it would be if the documentation was PDF-based. I hope you know that the HTML User Guide is bundled with each Chimera download and therefore all the Help buttons in dialogs, the "help" command, and the various functions in the Help menu just access your local copy and don't go over the web. > 2) if i build structure - add atom in structure ----whether we can > plced the atom at my desired place or coordination...if yes > how...and whether i can dragg that atom specifically to some unique > place....how? The atom gets placed in the center of the view, so if you can get the center of the view to be your desired location then you're set. Otherwise, you can use the "Movement Mouse Mode" tool (in the Movement tools category) to move the atom wherever you want it positioned. > 3)whether we can allign the specific atom/residue and accordingly > whole molecule....how? Although i use match maker that allign whole > molecules but my specific residue miss out Use the "match" command to match specific atoms/residues. Open the command line (Favorites->Command Line) and type "help match" for details. As an example if you wanted to match residue 14 in model 0 with residue 20 in model 1 (and they were the same residue type with the same atom names) then "match #0:14 #1:20" will move model 0 so that its residue 14 will be superimposed on model 1's residue 20. > 4)how i can allign heteroatom like in my case i am trying to allign > heme from different hemoglobin molecule with maximum efficiency...as > heme are chemically same for both molecule it should allign > perfectly and accordingly their globin (apoprotein) part... Similarly, if the hemes have the same number of atoms and the same atom names then something like "match #0:HEM #1:HEM" would work (also assuming only one heme per model). If the hemes have differing numbers of atoms or different atom names then you would have to use a more detailed match command where you actually specify the atom names so Chimera knows which atoms to pair up in the match. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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DNA atomic structure fitting with an envelope
by Damien Larivière 22 Mar '11

22 Mar '11

Dear all, James Stroud or Thomas Bishop webservices among others enable to create a portion of DNA in the PDB format. Is it possible in Chimera to import a mesh envelop (see image), the PDB structure of the DNA portion and to force the DNA to fit with the envelope (which has the length and the diameter of the DNA portion)? Many thanks for your help Damien ps: As far I understand, the MDFF tool by Klaus Schulten allows to conform a PDB structure to a mesh (interesting for cryoEM). I have not tested it yet.

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Offsetting residue numbering
by Sumitro Harjanto 22 Mar '11

22 Mar '11

Hi Elaine, Is there a way to introduce a systematic offset to the residue numbering in a model? The numbering in my model is different from the convention. Eg. the methionine that's supposedly in position 5 is labeled as MET 4, alanine in position 6 as ALA 5, and so on. I can't do it manually cos there are many residues. Is there an easy way to resolve this other than using a script to automatically assign the labels? It'll be good if i can resolve this from the root , such that my atom specification is also consistent with the naming convention I use. :) Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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matchmaker output
by Tiziano Tuccinardi 18 Mar '11

18 Mar '11

Dear all, I am using MatchMaker for aligning about 100 structures, and it works very well!! Is it possible to automatically save the pairwise alignment without opening the MultAlignViewer? Due to the large number of structures, I cannot use the Match-Align tool but it would be enough to save the pairwise alignments Thanks in advance Tiziano -- +++++++++++++++++++++++++++++++++++++ Tiziano Tuccinardi, PhD Dip. Scienze Farmaceutiche Via Bonanno 6, 56126 PISA Tel ++39 050 2219595 Fax ++39 050 2219605 E-mail tuccinardi(a)farm.unipi.it <mailto:tuccinardi@farm.unipi.it> http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/ Adjunct Assistant Professor SbarroInstitute for Cancer Research and Molecular Medicine Centerfor Biotechnology TempleUniversity PhiladelphiaPA 19122 (USA) +++++++++++++++++++++++++++++++++++++

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Movie frames are blank
by Gökhan Tolun 17 Mar '11

17 Mar '11

Dear all, I am trying to create a very simple movie, but my movies turn out blank. I am using the Spin Movie example script on http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html My movie seems to render, and the movie file is created, but when I open the file and play it, its just a blank (all black) video. When I examined the captured frames, theyre also all blank black frames. If I choose Save image, it saves it just fine, so I guess the image capturing algorithm for movies is different the one for saving the images. This is on Windows 7 64-bit, Chimera 1.5.2, Intel Mobile 965 express Chipset GPU (its a TabletPC, hence the GPU). Any suggestions to fix this would be appreciated. Thank you. _______________________________________ Gökhan Tolun, M.S., PhD. Post-doctoral Research Associate Lineberger Comprehensive Cancer Center University of North Carolina 450 West Dr., CB#7295, Room 11-119 Chapel Hill, NC, USA 27599

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Average Backbone B-factor
by Simon Sham 17 Mar '11

17 Mar '11

Hi, I need to read a pdb file and calculate the average backbone (CA, C, & N) B-factor for each residue and compare it with the result some MD. Is there anyway I can do it in Chimera? Thanks, Simon

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Re: [Chimera-users] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? the exception message as follow: ------------------------------------------------- Executing test.py... Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open models = func(filename, *args, **kw) File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 10, in <module> for arg_k, arg_v in opts: NameError: name 'opts' is not defined Error while processing test.py: NameError: name 'opts' is not defined File "test.py", line 10, in <module> for arg_k, arg_v in opts: See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing -t: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing test: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. ---------------------------------------------------------- At 2011-03-15 09:02:09，"Greg Couch" <gregc(a)cgl.ucsf.edu> wrote: (This is really achimera-dev(a)cgl.ucsf.edu mailing list question.) My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up. So in the beginning of your Python script, add: import chimeraInit chimeraInit.init(nogui=True, silent=True) before using chimera's modules. But, in general, you would be better off running those python scripts with chimera. For example: % chimera --nogui --silent script.py That would set up the the appropriate environment for chimera, execute the python script, and exit. And you would be protected against any future changes in how chimera is initialized. If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera). If you want to install other Python packages into chimera's Python that have a setup.py file, use: % chimera --nogui --silent setup.py install It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details). Right now, chimera is using Python 2.7. HTH, Greg

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radial clipping
by Kelly Dryden 16 Mar '11

16 Mar '11

Hi, I would like to radially clip a density map. There are nice ways to do radial coloring, but I haven't found anything that allows a similar cropping (preferably with capping). Is there an easy way to do this? I do not want to erase the density, but rather be able to see the surface at varying radii, just as you can do with planes. (At the moment, I can only run v1.4). Thank you, Kelly

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Re: [Chimera-users] [chimera-dev] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric

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I am having a problem
by Burt Goldberg 15 Mar '11

15 Mar '11

Dear, Chimera, as I opened the program it prompted me to re-register. I tried 3 time but got a Error message PKCS7. HELP!!!! Burt -- Burt Goldberg, PhD Professor of Chemistry & Biochemistry Chemistry Department Affiliated Research Professor Medical Parasitology New York University School of Medicine New York University

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Re: [Chimera-users] Selection through bond and fragment naming
by Jean Didier Pie Marechal 15 Mar '11

15 Mar '11

Dear all, thanks a lot for your answers. I seem to have a problem though. When running the script, one way or another I always ends up with something like: a.residue.removeAtom(a) AttributeError: 'NoneType' object has no attribute 'removeAtom' AttributeError: 'NoneType' object has no attribute 'removeAtom' File "M:\REUNIONS\dibuixos\Manipulate_structure\newres.py", line 20, in <module> a.residue.removeAtom(a) See reply log for Python traceback. I think I got the origin of the problem but can't figure out how to solve it. What I observed is that, before running the script if I do the following after selecting my atoms: >>> for a in at: print a.residue I have the following list printed UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 but doing the same AFTER having run the script gives : None UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 ... It seems like the residue type of the first atom disappeared. Any clue? all the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Divendres, Març 11, 2011 8:29 pm Assumpte: Re: [Chimera-users] Selection through bond and fragment naming > On Mar 11, 2011, at 7:42 AM, Jean Didier Pie Marechal wrote: > > > Hi, > > > > I have a system from which I only have xyz coordinates. What I > would > > like to do is to define myself residue attribute on different > > fragments of the molecules. Could you tell me how (or if there is > a > > way to ): > > > > 1. expand a selection to bonding atoms (i.e. I click on one atom > and > > expand selection through one bond after each actions) This would > be > > of the easiest way for me to select the fragments I want to. > > Hi JD, > My only idea as to how to do this is with a short Python script: > > from chimera.selection import currentAtoms, addCurrent > addAtoms = set() > for a in currentAtoms(): > addAtoms.update(a.neighbors) > addCurrent(addAtoms) > > You could then use the open command to run it: > > open <script folder location (e.g. ~marechal/scripts)>/expand.py > > which you could short to "xp" with the alias command: > > alias ^xp open blah-blah/expand.py > > > > > 2. set a residue attribute to the given selected fragment. I > think I > > remember how to do so in scripting, but what is the command line > to > > do so? > > So, do you really want to set a residue-level attribute, or do you > want to organize the selected atoms into a residue? Setting a > residue- > level attribute for the atoms is easy: > > setattr r myAttrName my-attr-val sel > > Organizing the atoms into a residue again requires Python, and not > as > simple a script as for your first question, e.g.: > > # script designed to run under "runscript" command, therefore has > an > "arguments" variable available... > try: > rname, rnum = arguments > except ValueError: > raise chimera.UserError("must supply residue name and number > arguments") > > try: > rnum = int(rnum) > except ValueError: > raise chimera.UserError("residue number (second arg) must be an > integer") > > atoms = chimera.selection.currentAtoms() > if not atoms: > raise chimera.UserError("No atoms selected") > > # make a new residue > newRes = atoms[0].molecule.newResidue(rname, "A", rnum, ' ') > > # withdraw atoms from their current residues > for a in atoms: > a.residue.removeAtom(a) > if len(a.residue.atoms) == 0: > a.molecule.deleteResidue(a.residue) > > # add atoms to new residue > for a in atoms: > newRes.addAtom(a) > > So you would run this script with the command "runscript blah- > blah/ > newres.py TYR 1", which could again be shorted using aliasing: > > alias ^nr runscript blah-blah/newres.py $1 $2 > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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registration and user group
by SteffenVfx 15 Mar '11

15 Mar '11

Hi there. I've been trying to register with you all for some time, but it always comes back with a registration error. I'd like to enroll in your mailing list and user group forum. can you pass along my information? thanks casey *Steffen VFX ~the science of storytelling~* *| Casey Steffen M.S. | President/Chief Creative Officer | 211 6th Ave. #2a | Brooklyn, NY 11215 | **Web:**www.steffenvfx.com | **Twitter:**SteffenVfx<http://twitter.com/steffenvfx> | **Blog:**http://blog.steffenvfx.com | **Phone:347-875-0423 |*

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bond selection
by Elisabeth Ortega 11 Mar '11

11 Mar '11

Dear Chimera Dev. Team, I have a little question for you. How can I select a bond using the Command Line (or the IDLE)? Thanks in advance. Elisabeth Ortega-Carrasco Universitat Autònoma de Barcelona

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Selection through bond and fragment naming
by Jean Didier Pie Marechal 11 Mar '11

11 Mar '11

Hi, I have a system from which I only have xyz coordinates. What I would like to do is to define myself residue attribute on different fragments of the molecules. Could you tell me how (or if there is a way to ): 1. expand a selection to bonding atoms (i.e. I click on one atom and expand selection through one bond after each actions) This would be of the easiest way for me to select the fragments I want to. 2. set a residue attribute to the given selected fragment. I think I remember how to do so in scripting, but what is the command line to do so? Kind regards, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es

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error: from DockPrep import prep
by wascm 11 Mar '11

11 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ####################################### Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ################################################# how can i solve this problem? best wishes Tao Cui

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error: from DockPrep import prep
by wascm 11 Mar '11

11 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ----------------------------------- Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ---------------------- how can i solve this problem? best wishes Tao Cui

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Re: [Chimera-users] using chimera command in batch mode
by cuitao＠webmail.hzau.edu.cn 10 Mar '11

10 Mar '11

Dear sir I am so grateful to you for your detailed answer. Thanks a million. best wishes Tao Cui ------------------ 原始邮件 ------------------ >From: Eric Pettersen <pett(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: "cuitao(a)webmail.hzau.edu.cn" <cuitao(a)webmail.hzau.edu.cn> >Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >Subject: Re: using chimera command in batch mode >Date: Wed, 9 Mar 2011 13:11:31 -0800 > On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: Dear sir: I have seen one message you posted in dock-fans mail list. http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html The batch mode solution you privided is really helpful to me. I wnat to know if I can complete similar batch mode works for other applation? for example, delete all H atoms, save molecule to pdb format and writedms. Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Internal water molecules
by Tom Goddard 10 Mar '11

10 Mar '11

Hi John, Here's an idea about how to define internal water molecules and identify them in Chimera. Make a density map of the molecule at some resolution, say 5 Angstroms, using the Chimera "molmap" command, then define internal waters to be the ones that are located at a point above a certain density threshold. You can use the Chimera "Values at Atom Positions" dialog (menu Tools / Volume Data) to get the interpolated density map value at each atom position. It assigns the density value to each atom. Then you can use the Render by Attribute dialog (menu Tools / Structure Analysis) to select just those atoms with values above the threshold density. Then you can intersect that list of atoms with waters since it will also include protein atoms. All this is easy to do but since you want to do it for many frames of a molecular dynamics simulation you need a script that can be run for each MD frame. Unfortunately the values at atom positions and the render by attribute selection capability don't have Chimera command equivalents. But those capabilities (like all Chimera capabilities) can be used with a Python script. I could provide you a script if this sounds useful. Also I'll add to our feature request list the need for Chimera commands that would allow you to do it without resorting to Python. Tom > Hello, > > Is it possible, in Chimera, to select only the internal water > molecules of a protein structure? I need to find out how many water > molecules enter the protein structure from the outside during a > molecular dynamics simulation. > > Thanks! > > John

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Re: [Chimera-users] castp visualization
by Elaine Meng 09 Mar '11

09 Mar '11

On Mar 9, 2011, at 9:06 AM, Irene Newhouse wrote: > Remember a few days ago, I sent you an image from a Chimera castp visualization & it looked really weird, with strips connecting two apparently disconnected regions? Well, I put up PyMol & its castp viewer & it manages to plot the surface understandably - blackish represents the 'outside' of the cavity... I think my protein is nonetheless somewhat pathological, because if I try to render the same surface in mesh, it swells to occupy nearly the whole molecule, which is not right - mesh & solid should enclose the same volume. However, the solid rendering does reproduce where the substrate goes, and how on earth it gets in there is now my problem:-) > > I just tried something else -- I have the new Chimera on my linux station, & that's where I was seeing the odd renderings. On my PC, I have the previous version of Chimera & it shows the same surfaces as PyMol! The image chasurfs.png shows the odd effects [from the current release on my linux station], for only one of the dimer units [I thought maybe the dimer was the issue. No.] Possibly the surface rendering of cavities in the current release of Chimera is correct most of the time, but it looks as if it's not for a protein as odd as this one. For debugging purposes, the PDB is 1X09 [I used Chimera to generate the other dimer unit]. > Hi Irene, Given your observations, it may be a graphics driver problem on your linux machine. I.e. the salient difference may be the platform, not the Chimera version. However, wasn't what you sent before from Surfnet, not CASTp? In any case, my understanding is that the same Chimera code is used on the different platforms, and I don't think these tools have been changed for months. I just tried "open castp:1x09" in the 1.5 release and a recent daily build (v1.6 Feb 24) and looked at a few pockets, and the surfaces seemed fine. Since I deal with the user interface and not programming or hardware issues, I included the list in case others have suggestions or comments. Best, Elaine

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Re: [Chimera-users] using chimera command in batch mode
by Eric Pettersen 09 Mar '11

09 Mar '11

On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: > Dear sir: > > I have seen one message you posted in dock-fans mail list. > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > The batch mode solution you privided is really helpful to me. I > wnat to know if I can complete similar batch mode works for other > applation? for example, delete all H atoms, save molecule to pdb > format and writedms. > > Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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select by atom number
by Francesco Pietra 09 Mar '11

09 Mar '11

Hello: Is any trick to select by atom number? Having NAMD files with CHARMM FF, i.e., SEGID and no chain ID, I find now difficult to use CHIMERA the way I used it. Thanks francesco pietra

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color bond distance, angle and so on
by Jean-Didier Maréchal 09 Mar '11

09 Mar '11

Hi guys, How can I change the color of the labels associated to distance between atoms, angles etc (both the for the text and the dashes). Thanks a lot JD **************************** Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es

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Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues
by Elaine Meng 08 Mar '11

08 Mar '11

On Mar 8, 2011, at 1:03 PM, Ingmar Buerstel wrote: > Dear Elaine, > thanx a lot for your quick answer. In fact I have already a modelled structure (made with swiss model) of the protein. > I was looking for a possiblitiy to fit a 4Fe4S-cluster in the position of the original cluster. The cysteines are conserved, thus, I just need to copy/paste the 4Fe4S-cluster into my structure. I would be glad, if you could help me concerning this problem. Dear Ingmar, You could superimpose your model and the related structure that does contain this cluster (residue SF4) and then merge the SF4 residue into your model. However, the result may be rough, depending on how well the structures match in 3D. It might be better to start over and use Modeller as described in my previous message, because it can make a model that already includes the cluster. However, if you want to try the superimposing approach, here are more details. (a) In Chimera, open your model and then open the known related structure that contains the cluster. (b) Superimpose the two structures, for example with the Matchmaker tool. Here is some discussion of different ways to superimpose structures in Chimera. You will want to make sure that the structures match well at the four cysteines. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (c) Delete everything in the known structure except for the part you want to paste into your homology model, and then combine the two models into one. For example, if your model is open as #0 in Chimera and the known structure is open as #1, you could use commands delete #1 & ~:sf4 combine #0,1 The delete command gets rid of all atoms in #1 except the SF4 residue. The combine command creates a new model, #2, by merging the SF4 residue in #1 with the homology model in #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> You can save the new model #2 to a file (for example, with File... Save PDB). However, you would hope that the cysteine sidechains in your model are pointing in the correct orientations to bind the cluster. If not, you might have to paste in those residues from the known structure too, and delete them from your homology model, before merging. Then you might have to manually text-edit the PDB to add bonds between the merged cysteines and the rest of the homology model. Again, it might be better just to start over and use a modelling method that can include the cluster in the first place. 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 > > > > Subject: Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues > > From: meng(a)cgl.ucsf.edu > > Date: Mon, 7 Mar 2011 09:38:45 -0800 > > CC: chimera-users(a)cgl.ucsf.edu > > To: ingmar_b(a)hotmail.com > > > > Dear Ingmar, > > It sounds like you want to model your whole protein including the 4Fe4S cluster, am I right? Or is there a structure of your protein but that does not include the cluster? > > > > I would not recommend modeling this "from scratch" (building one atom by one atom) in Chimera but instead, homology-modeling your protein and cluster from the structure of a related protein that contains the cluster. Of course, this all depends on the existence of a known structure for a related protein. > > > > Chimera includes an interface to the Modeller program for homology-modeling. To use it, you would have to first go to the Modeller website > > <http://www.salilab.org/modeller/registration.html> > > and register to get a license key (free for academic use). In Chimera, you could choose "Tools... Sequence... Blast Protein," paste in the sequence of your protein, and then blast it against the PDB to see if there are any structures related to your protein. If there is a hit that seems good enough to you, you could use the Blast results dialog to open the structure and also the alignment of the two sequences. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html> > > Then, in the sequence alignment window, choose "Structure... Modeller Tools" to show the interface to Modeller. Use "Advanced Option" to "Include non-water HETATM residues from template" so that the FeS cluster will be included in the model. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> > > > > Or, you could simply see if there is already a model of your protein available in ModBase by using "File... Fetch by ID" in the Chimera menu. However, those models probably wouldn't contain the FeS cluster. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > > > Some related references I just saw but didn't read in detail: > > > > Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. > > <http://dx.doi.org/10.1007/s00775-003-0445-8> > > > > Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. > > (2002) J.Mol.Biol. 315: 1155-1166 > > <http://dx.doi.org/10.1006/jmbi.2001.5292> > > (goes with PDB entries 1iqz, 1ir0 ... I see that the residue name of the cluster is SF4, so you could also use the searching tools at the PDB website to find structures that have this cluster) > > > > I hope this helps, > > Elaine > > > On Mar 6, 2011, at 6:44 AM, Ingmar Buerstel wrote: > > > Dear users, > > > i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. > > > > > > So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster > > > Thanx in advance, > > > Ingmar > >

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