- Chimera-users - RBVI Mailing Lists

building a alpha helix
by Anindito Sen 04 Dec '08

04 Dec '08

Dear All I was wondering if there is any tool by which can generate an alpha helix, as an extension of a truncated crystal structure docked in the density map. The possibility of the truncated portion of the protein behaving as an alpha helix has been predicted by different groups. The density map shows some empty regions (after the crystal structure has been docked) just good enough for an alpha helix to fit in. Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Transparency of ribbons
by lvyuan zhang 04 Dec '08

04 Dec '08

Hi all, I'm a new user and my question maybe a little weird to you guys. I want to make some parts of my protein, let's say "A", partially transparent, so when compared to other parts of the protein, let's say "B", these "A" parts are hardly visible (the background is white). So I set the alpha value of "A" to less than 1, such as 0.1. then I save the image with POV-ray. The resulted "A" is too dark, and it is still quite "visible". Is there any way to make partially transparent ribbons lighter, instead of darker than non-transparent ones? I would really appreciate it if any one can help resolve this problem. Thans! Cheers! Luyuan Zhang

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Software(Drug Design)
by Tarit Mitra 04 Dec '08

04 Dec '08

28, Ashfield Green Yateley Hants GU46 6AL UK Dear Sir, I am a retired scientist, and working on an honorary basis for the University of London. I work from home and go to the University in regular interval. I would very much like to use your software for drug design. I was wondering whether you would grant me a free academic licence to the software. I shall only use the software for academic purpose and not for any financial reason whatsoever. I have both Linux(Ubantu) and Windows XP. My computer has 40GB hard disk with 756MB RAM I shall be grateful if you will kindly consider my case favourably. Yours faithfully T. K. Mitra, B.Sc(London), Ph.D(London)

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opaque background
by Mueller, Juergen-Joachim 01 Dec '08

01 Dec '08

Dear all, is there a possibility to make the background invisible to be able to overlay a structure over anything? Thanks, Juergen

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Chimera rotational matrix
by Bui Khanh Huy 01 Dec '08

01 Dec '08

Hi, I notice that Chimera has slightly different in calculation of transform when I tried to rotate my EM density (200x200x200 mrc file) using Chimera. The origin of the density reported by Volume Viewer is 0,0,0 First, I print out the homologous transform matrix using: >>> om = chimera.openModels >>> mlist = om.list() >>> m = mlist[0] >>> print m.openState.xform The transformation is: 1 0 0 0 0 1 0 0 0 0 1 0 If I rotate the model using command: roll z -30 1 Then print out the transform matrix again: 0.866025 0.5 0 -36.8852 -0.5 0.866025 0 61.2937 0 0 0 1 That would be weird because I didn't do any translation. So what is really happening in Chimera when I rotate the model? Best, Huy

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How to generate submodels in a mol2 file in Chimera?
by CHIU,YEUNG 01 Dec '08

01 Dec '08

Dear friends, Hello! I'm wondering how many models and submodels in all can Chimera save into one single mol2 file? Right now I can have models only 0-9 into one single mol2 file. I think I'm going to use submodels, but how can I generate them? For instance, if I have a brunch of pdb files which contain one molecule each, I'd like to combine them into one mol2 file, which has a submodel corresponding to each molecule. (If this statement of the problem is not clear enough, please let me know). Thank you for your help and sorry to bother the others. Best wishes. Sincerely yours CHIU,YEUNG

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Increases size of labels
by Todd Weaver 25 Nov '08

25 Nov '08

Under the Actions pulldown for Label --> Other is there a way to increase the size of the lettering/numbering. When I make side by side stereo the labels are too small for publication. Thanks so much! -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281

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Laplacian filter on density maps
by Grigore Pintilie 24 Nov '08

24 Nov '08

Hi, Just wondering if it might be possible to apply a Laplacian filter on a density map in chimera. The reason I'm asking is that if the cross-correlation is computed with laplacian-filtered maps it gives more robust results for the correct alignments vs. non-correct alignments. Thanks, Greg

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Highlighting CA as spheres
by Ibrahim Moustafa 24 Nov '08

24 Nov '08

Hi Chimera team, I want to make a figure of the protein highlighting the following features: - The whole structure is shown in cartoon - The CA-atoms of some residues are highlighted as a sphere on top of the cartoon model. When trying to make that, the spheres are off in space and not exactly on top of the cartoon model. Is there a remedy for that?. So the spheres appear on top of the cartoon rather than in empty space. Also, how to turn the bonds off between consecutive CA-atoms? Thanks for help, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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changing ion appearance
by Elaine Meng 22 Nov '08

22 Nov '08

On Nov 22, 2008, at 5:17 PM, Barry Lever wrote: > Elaine- a small question. I load up various ruthenium complexes as > mol2. files into Chimera and invariably they appear as attached, > with the central Ru atom as a huge ball, and the other atoms not > appearing - how do I get rid of that huge ball or how do I make it > much smaller ?? Hi Barry, By default, ions are initially shown in the sphere representation. Any atoms can be undisplayed or shown in a different representation (wire, stick, ball-and-stick). For example, you could select it with Ctrl-click and then use "Actions... Atoms/Bonds... hide" (or in the same menu, choose some other representation such as "stick") or use commands, for example: repr ions wire - or - ~display ions If you never want ions to be shown initially as spheres, you can change the Preferences (Favorites... Preferences, choose Category "New Molecules", change "monatomic ion style" to whatever you want, click "Save"). You might want to change additional settings in that panel, for example to show the other atoms/bonds with thicker lines or in a different representation. These preferences will apply to subsequently opened structures. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Molecules> Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Identifying surface residues and write them to a file in a pdb format
by Thiruvarangan Ramaraj 22 Nov '08

22 Nov '08

Hello All, I am using Chimera molecular viewer, to identify the surface residues and then write all the identfied residues on the surface to a file in a pdb format. Any help would be greatly appreciated. Thank You Thiru

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building a alpha helix and flexing it
by Anindito Sen 21 Nov '08

21 Nov '08

Hi Elaine Got the wrong email in extension in the previous email request. Please ignore it. Here is the problem- In continuation of the process (mentioned below) I have generated the helix that needs to be added. However it seems that the helix needs to be flexed in some points to get a better fit. Can yo let me know how do that? Thanks Andy Hi Andy, There are two main possibilities: (1) With the "addaa" command you can build out from the C-term of a protein, residue by residue. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/addaa.html > (2) With the "Build Structure" tool you can create a peptide that is not attached to anything, then move it to a reasonable position and combine it with the existing protein. <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/editing/ed… > The moving/combining part of #2 can be rather difficult, so if it is a C-terminal truncation, definitely #1 is the way to go. For example, if the last residue in the structure is 309 in chain A of model #0, you could use commands like: addaa ala,310,alpha #0:309.a addaa lys,311,alpha #0:310.a addaa thr,312,alpha #0:311.a ... etc. ... If you need to extend the N-terminal end, however, approach #2 is the only choice. In Build Structure (under Tools... Structure Editing), go to the "Add Atoms" tab and choose the "peptide sequence" option. There you would just enter the sequence in one-letter amino acid codes, specify alpha-helix backbone angles, indicate the new atoms should be put in a "new model" and click Add. You don't want to put the helix in the same model as the protein because then you will not be able to move them separately. Then get the helix into position by activating/deactivating models and using the mouse (deactivating a model freezes it so that only the other models move with the mouse). Getting a reasonable position is nontrivial, unfortunately. Besides moving things interactively with the mouse, another possibility is to build enough atoms to overlap part of the protein structure and then match those overlapping parts, such as with the "match" command. Once the helix is in a reasonable position relative to the protein, you could combine the models into one model and then add a bond. If there were overlapping atoms, you would first need to delete the duplicate atoms. Perhaps you only need a rough representation, and in that case do not need to combine and bond the structures. See these previous posts for details on how to do the combining and bonding: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003255.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003238.html > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 18, 2008, at 12:55 PM, Anindito Sen wrote: > Dear All > I was wondering if there is any tool by which can generate an alpha > helix, as an extension of a truncated crystal structure docked in > the density map. The possibility of the truncated portion of the > protein behaving as an alpha helix has been predicted by different > groups. The density map shows some empty regions (after the crystal > structure has been docked) just good enough for an alpha helix to > fit in. > Best > Andy _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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selecting surface waters
by Walter Novak 21 Nov '08

21 Nov '08

Hi All, I think there might be an easy way to do this, but haven't figured it out yet. I am interested in only selecting the waters on the surface of the protein, not those that are buried. Any suggestions? Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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building a alpha helix
by Anindito Sen 18 Nov '08

18 Nov '08

Dear All I was wondering if there is any tool by which can generate an alpha helix, as an extension of a truncated crystal structure docked in the density map. The possibility of the truncated portion of the protein behaving as an alpha helix has been predicted by different groups. The density map shows some empty regions (after the crystal structure has been docked) just good enough for an alpha helix to fit in. Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Fwd: carbon-chlorine bond
by Francesco Pietra 18 Nov '08

18 Nov '08

Elaine: In the fear that docking and MD had been carried out with C in place of Cl for the ligand, I checked all. OK, correct for Cl. I noticed that when all atom names are left-justifies in column 13, Chimera reports the structures correctly.When all atom names are left-justified in column 14, Chimera does not report Cl correctly. I writing pdb files, the various programs in DOCK/Amber are not well consistent (although I did not carry out a thorough search). Dock6 writes the final pose pdb for receptor+ligand by left-justifying all atom names in column 13. Amber behaves differently according to which internal program is used. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Mon, Nov 17, 2008 at 10:58 PM Subject: Re: [Chimera-users] carbon-chlorine bond To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Eleaine: Thanks. Moving Cl to columns 13 and 14, the C-Cl bond is displayed for me too.Living with the new and the old. It will be so for quite a long time. Regards francesco On Mon, Nov 17, 2008 at 7:46 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Francesco, > I was going to write back that your PDB file from AMBER has the atom names > mis-aligned so that Chimera probably thinks the chloride is a carbon, which > would have a shorter automatic bond cutoff. However, when I put those 4 > lines from your message below in a file and open it in Chimera, the elements > are correctly identified and there is already a C-Cl bond; only the H is > unconnected. Perhaps the characters on the far right were sufficient to > identify element Cl. The H is far away and must be bonded to something else > in the complete structure. > Elaine > > On Nov 17, 2008, at 10:19 AM, Francesco Pietra wrote: >> >> Hi Elaine: >> Yes, it is a pdb file written with program ptraj (Amber) for the >> minimum energy. The chlorine atom is defined as (partial block): >> >> ATOM 14544 H1 AA1 341 76.488 57.341 49.169 >> hn >> ATOM 14545 C3 AA1 341 75.036 56.270 51.132 >> ca >> ATOM 14546 Cl AA1 341 73.973 56.486 49.780 >> cl >> ATOM 14547 N1 AA1 341 74.619 55.535 52.192 >> nb >> >> and there are no CONECT. As you said above, prmtop/mdcrd with movie do >> show a line connecting C-Cl, but I don't know if there is another way >> to extract the minimum-energy structure than that pdb file. >> >> Why are all other bonds shown correctly by Chimera in the above >> situation? Why just C-Cl not? >> >> francesco >

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Re: [Chimera-users] clustering of docking solutions
by Elaine Meng 18 Nov '08

18 Nov '08

Hi Sebastian, Are all the docked structures the same molecule, just in different positions? You are right that ViewDock doesn't have clustering, and Ensemble Cluster automatically determines the clusters without allowing you to specify an RMSD cutoff. My ideas only pertain if the structures are all the same molecule or at least contain a common set of atoms: (a) You could use Ensemble Match to compare the ensemble to itself, if the atoms in common have the same names. This would not perform clustering, but it calculates all-by-all RMSD values using a set of atoms you specify. However, these are best-fit RMSDs of the structures, while I suspect you may want the RMSDs in their current positions instead. Another caveat is that it creates a dialog that is an N x N table, which may not be manageable for a large number of structures (high N). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblematch/ense… > There is an example of using Ensemble Match at the end of the "model panel and ensembles" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html > (b) As you mentioned, you could convert to a multi-model PDB, and use the MD Movie tool's RMSD analysis to calculate an all-by-all RMSD map. However, it would require more work to extract the RMSD values (output is a grayscale map) and these are also best-fit RMSDs. This option is more practical for high N than option (a), however. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > Part 2 of the "trajectories/ensembles" tutorial includes an example of MD Movie RMSD Analysis: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p… > (c) You could use a script to do all-by-all comparisons of the structures with the "rmsd" command. This calculates current-position RMSDs rather than best-fit RMSDs. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> See these previous posts for more general information on scripts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 17, 2008, at 6:07 AM, Sebastian Kruggel wrote: > Hi all, > I am looking for a possibility to cluster docking results (multimol2 > file) in chimera. In DockView I can't find such tool and in the > EnsembleCluster method I don't see a way to set rmsd limits. > > I found a hint to the MD Analysis tool in the mailing list, ok, I > could > convert my docking solutions into pdbs and use this, but probably > there > is another simple and convenient way that I am just too blind to > see ;-) > > Maybe somebody can help? > Thanks in advance, > Sebastian

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New Chimera release candidate and version numbering
by Conrad Huang 17 Nov '08

17 Nov '08

New Release Candidate A new production release candidate addressing Microsoft Windows graphics drivers problems, particularly with integrated graphics accelerator chips, is now available. Release 1.3 candidates are available for all platforms including a Mac Aqua version that does not require X windows. New Version Numbering System With the upcoming production release of Chimera we are changing our version numbering to clarify major releases and allow us to provide critical bug fixes while working on newer versions. The upcoming release will be release 1.3. Critical bug fixes (if any) to 1.3 will be released as 1.3.1, 1.3.2, etc., and the next major release of Chimera will be release 1.4. Chimera Team

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Re: [Chimera-users] carbon-chlorine bond
by Elaine Meng 17 Nov '08

17 Nov '08

Hi Francesco, I was going to write back that your PDB file from AMBER has the atom names mis-aligned so that Chimera probably thinks the chloride is a carbon, which would have a shorter automatic bond cutoff. However, when I put those 4 lines from your message below in a file and open it in Chimera, the elements are correctly identified and there is already a C-Cl bond; only the H is unconnected. Perhaps the characters on the far right were sufficient to identify element Cl. The H is far away and must be bonded to something else in the complete structure. Elaine On Nov 17, 2008, at 10:19 AM, Francesco Pietra wrote: > > Hi Elaine: > Yes, it is a pdb file written with program ptraj (Amber) for the > minimum energy. The chlorine atom is defined as (partial block): > > ATOM 14544 H1 AA1 341 76.488 57.341 > 49.169 hn > ATOM 14545 C3 AA1 341 75.036 56.270 > 51.132 ca > ATOM 14546 Cl AA1 341 73.973 56.486 > 49.780 cl > ATOM 14547 N1 AA1 341 74.619 55.535 > 52.192 nb > > and there are no CONECT. As you said above, prmtop/mdcrd with movie do > show a line connecting C-Cl, but I don't know if there is another way > to extract the minimum-energy structure than that pdb file. > > Why are all other bonds shown correctly by Chimera in the above > situation? Why just C-Cl not? > > francesco

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Re: [Chimera-users] carbon-chlorine bond
by Elaine Meng 17 Nov '08

17 Nov '08

Hi Francesco, It only means that whatever file(s) you are reading into Chimera do not specify the bond explicitly. I can't tell from the information given whether your MD program knows the bond is there; it may know, but not write this information into the file that you input to Chimera. If the file(s) describe trajectory in the format of the MD program (AMBER? GROMOS?) and you are using the MD Movie tool in Chimera for display, all the bonds should be there. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > However, if you are doing something else like writing a PDB file from those programs, maybe the PDB file does not specify the bond explicitly, and the other viewers might have a more relaxed criterion for automatically identifying a bond. I don't think there is a way to change the automatic criteria, but you could just add a CONECT record specifying the bond to the PDB file, or just add the bond in Chimera with the command "bond" or the "Add/ Delete Bonds" section of Build Structure. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht… > Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 16, 2008, at 11:00 AM, Francesco Pietra wrote: > For a monochlorinated small alkaloid docked onto a protein model, > after molecular dynamics simulations Chimera shows the chlorine atom > as a dot, without a line to represent the bond. Before dynamics, the > C-Cl line connecting the two atoms was shown. Other viewers show the > bond both before and after MD. For the purpose of presentation, how > to set a longer C-Cl bond length as a temporary default for Chimera? > > Very likely the parameterization for chlorine in the MD suite is not > as it should. > > Thanks > francesco pietra

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clustering of docking solutions
by Sebastian Kruggel 17 Nov '08

17 Nov '08

Hi all, I am looking for a possibility to cluster docking results (multimol2 file) in chimera. In DockView I can't find such tool and in the EnsembleCluster method I don't see a way to set rmsd limits. I found a hint to the MD Analysis tool in the mailing list, ok, I could convert my docking solutions into pdbs and use this, but probably there is another simple and convenient way that I am just too blind to see ;-) Maybe somebody can help? Thanks in advance, Sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 D 20146 Hamburg Tel +49(0) 40 42838 3626

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Re: [Chimera-users] Running a job in chimera
by Elaine Meng 12 Nov '08

12 Nov '08

Dear Tuhin, The script to perform the actions (your #1 or #2) could be written in python or in Chimera commands. Just opening the python file (*.py) or Chimera command file (*.com) in Chimera will execute it. The trickier part would be how to automatically loop through your multiple structures. You could write a long Chimera command script that includes the names of the structures, or you could use a python script that loops through a list of filenames. The methods can be combined; for example, the python script could merely loop through the names and open the structures, then open a separate Chimera command script. You could also use a shell script to loop through filenames, but I guess that would be slower because it would involve starting a new Chimera for each input (#1) or set of inputs (#2). If that is easier for you, however, it is reasonable. Please see this previous posting for examples/discussion of Chimera scripts for processing multiple structures, calling a script from another script, and using aliases: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003218.html > See also Chimera nogui mode: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui> I believe all the actions you want to perform can be done with Chimera commands, for example open /location/location/frame20.pdb delete solvent & protein z>5 write format pdb relative 0 0 /location/location/frame20zone5.pdb close 0 or open /location/mystruct1.pdb open /location/mystruct2.pdb open /location/mystruct3.pdb matchmaker #0 #1 matchmaker #0 #2 These are just possibilities out of several ways to perform the tasks. For example, the top example assumes your structure is a protein, and in the bottom example, you could use "match" instead of "matchmaker" to superimpose structures. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 11, 2008, at 1:41 AM, tuhin(a)iitk.ac.in wrote: > Dear All, > I have run several simulations. But, I need to analyse a selective > number > of structures from each simulation saved at a given time step "t". > Thus, > for a 20ns simulation, starting t=0 and incrementing it by 50ps, > I'll have > ~400 individual structures. Each structure is within a waterbox, which > contains approx. 20,000 water molecules. Once I get the structures, > I need > to do the following using CHIMERA: > > 1. Open each structure and save water molecules within a cutoff > distance of > 5.0 Angstrom from the protein. Thus, I'll end-up having a shell > (<=5.0A) > of water molecules around the protein. The saved structure will be > in > .pdb format and include the protein with 5.0A water shell. > I know how to do it in CHIMERA using the commandline option/ > pulldown > menu, but, how to do it for 400 structures. Is there a way to run it > in a "Batch Job" ? > > 2. I also need to superimpose Ca-Ca atoms of 400 structures. But, I > feel > there is a limit to the no. of structures that CHIMERA could handle, > thus, at max. I would be superimposing 20-30 structures at a time. > How > could I automatize the same through a script sothat I could run it > in > batches? > > Thanks in advance. Any suggestion(s) is welcomed. > Warm regards, > Tuhin

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zone command
by Francesco Pietra 12 Nov '08

12 Nov '08

A polypeptide was docked onto a protein that already carried ligands. Then, molecular dynamics of the complex was carried out. To do this, a single PDB file was created with the program ptraj of Amber. Although ptraj removes chain labels, TER lines, etc., renumbering all the residues in a single sequence, I know, from the ligand positions, the corresponding numbering for the chains and for the polypeptide. Which is the best procedure to map around certain groups of amino acids of the protein, i.e., those that constitute the experimentally-evaluated binding site? I want to take notice of which residues of the polypeptide are most involved in the binding. Thanks francesco pietra

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Re: [Chimera-users] Powerpoint
by CHIU,YEUNG 12 Nov '08

12 Nov '08

Hi John, According to my experience, you can not directly insert the video file from Chimera into your powerpoint slides, but only a superlink to the video. Usually what I do is I set up a buttom with the superlink, and everytime I click the buttom, the video can be played by Quicktime~ If you get some other way to do it, please let me know~ thank you~ On Wed Nov 12 07:28:07 EST 2008, "Beale, John" <jbeale(a)stlcop.edu> wrote: > Can movies created in Chimera be played in a Powerpoint > presentation? If > so, how do I set it up? > > John Beale > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > Sincerely yours CHIU,YEUNG

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Powerpoint
by Beale, John 12 Nov '08

12 Nov '08

Can movies created in Chimera be played in a Powerpoint presentation? If so, how do I set it up? John Beale

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Running a job in chimera
by tuhin＠iitk.ac.in 11 Nov '08

11 Nov '08

Dear All, I have run several simulations. But, I need to analyse a selective number of structures from each simulation saved at a given time step "t". Thus, for a 20ns simulation, starting t=0 and incrementing it by 50ps, I'll have ~400 individual structures. Each structure is within a waterbox, which contains approx. 20,000 water molecules. Once I get the structures, I need to do the following using CHIMERA: 1. Open each structure and save water molecules within a cutoff distance of 5.0 Angstrom from the protein. Thus, I'll end-up having a shell (<=5.0A) of water molecules around the protein. The saved structure will be in .pdb format and include the protein with 5.0A water shell. I know how to do it in CHIMERA using the commandline option/pulldown menu, but, how to do it for 400 structures. Is there a way to run it in a "Batch Job" ? 2. I also need to superimpose Ca-Ca atoms of 400 structures. But, I feel there is a limit to the no. of structures that CHIMERA could handle, thus, at max. I would be superimposing 20-30 structures at a time. How could I automatize the same through a script sothat I could run it in batches? Thanks in advance. Any suggestion(s) is welcomed. Warm regards, Tuhin

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How to make bonds between two pdb files
by Ann Spevacek 06 Nov '08

06 Nov '08

Hello - I am trying to make a bond between a protein and a polysaccharide chain in Chimera and am not quite sure how to do it. I am also curious as to whether the program will take into account interactions such as sterics when it generates the bond. Any guidance will be greatly appreciated! Thanks, Ann Spevacek Millhauser Lab UCSC

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successive minimizations: can we use a unique protein setup?
by Jean Didier Pie Marechal 06 Nov '08

06 Nov '08

Hi everyone, I want to do the following: 1. minimize a region of a structure 2. change some part of the region by hand (like swap a residue) 3. minimize once more. and this 2 or three times. However, each time I want to minimize I have to pass through the all setup of the protein (add H, hist protonation, and so one). Couldn't we keep the information of the first setup and directly fo through the minimization? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Novembre 5, 2008 2:00 am Assumpte: Chimera-users Digest, Vol 67, Issue 4 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Using match (Omar Davulcu) > 2. Re: Using match (Eric Pettersen) > 3. Re: Models or chain (Eric Pettersen) > 4. removing side chains (Matthew Dougherty) > 5. Re: removing side chains (Eric Pettersen) > 6. Re: Using match (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 3 Nov 2008 14:53:19 -0800 > From: "Omar Davulcu" <davulcuo(a)ohsu.edu> > Subject: [Chimera-users] Using match > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <001301c93e06$f7394020$e5abc060$@edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > > I'm using the match command with a cutoff to align specific regions of > related enzymes. It appears to work fine and remove residue pairs > above the > cutoff, but is there a way to list those residue pairs which were > (or were > not) removed? > > > > Thanks for any help! > > Omar Davulcu > >

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Using match
by Omar Davulcu 04 Nov '08

04 Nov '08

Hi, I'm using the match command with a cutoff to align specific regions of related enzymes. It appears to work fine and remove residue pairs above the cutoff, but is there a way to list those residue pairs which were (or were not) removed? Thanks for any help! Omar Davulcu

3 2

removing side chains
by Matthew Dougherty 04 Nov '08

04 Nov '08

I have a session that someone has given me. It consists of 24 monomers in two states, each monomer colored differently. In the model panel I see only two IDs. I need to do a morph showing just the ribbons. Because the overall number of atoms is quite large, I want to strip off the side chains in order to reduce the computation. Is there an easy way to do this? Or do I have to go back to individual monomers, strip off the side chains, recolor, and recombine them, before morphing? thanks, Matt

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Re: [Chimera-users] Models or chain
by Eric Pettersen 04 Nov '08

04 Nov '08

Hernando Sosa wrote: > Hi Elaine, > > The problem I have is actually not with chimera itself. I can > display all the models etc nicely within it. However, I want to make > now a PDB file of a multi-protein complex in a format that can be > deposited in the PDB database. Then I run into problems if the models > are separated by Model ENDMDL lines or have chains with the same > letter > identifier. I was hoping to be able to generate a multi-protein PDB > file from my chimera fitting without having to manually edit a lot of > lines in the multimodel PDB file. Any suggestions on how to best do > this > would be appreciated. > Hi Hernando, Elaine kind of mentioned this in passing in another posting, but you can now do what you wanted to do above with the new "combine" command (also available as the Combine button of the Model Panel). It's in the current daily build and upcoming release candidate/production release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Coloring snapshots using time as attribute
by Ibrahim Moustafa 03 Nov '08

03 Nov '08

Dear Chimera team, I have several snapshots from simulation loaded as different models. I wonder if there is a way to color them coded according to time as an attribute, e.g. Red-white-blue for t0 -> t. Thanks in advance, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Re: [Chimera-users] How to add change to multiple molecules
by CHIU,YEUNG 03 Nov '08

03 Nov '08

Hi Yang You mean adding "charge"? I think you can add charge to all of the models as long as you check the box referred to them at the bottom. If you want to add charge to some models only, you can ~disp all, then display one by one and add charge to them. I hope this would help. Good luck! On Sun Nov 02 20:32:46 EST 2008, zhouyang <zhouyang(a)mail.shcnc.ac.cn> wrote: > Hi > Recently I wanna add change to a series of molecules for DOCK6 > which are stored in a single .mol2 file. It seems that the > Chimera GUI can just add change for one molecules at one > operation. I wonder how to add change to all of them? > Alternatively I just suppose to use 'split' shell command to > seperate these molecules to single files and then add change to > them. Then the key point is whether Chimera can run in > command-line mode so that I can achieve by writing a shell > script? > Thanks in advance > Yang > zhouyang(a)mail.shcnc.ac.cn > > 2008-11-03 ?????? ZHOU Yang > Master Candidate > Drug Discovery and Design Center > Shanghai Institute of Meteria Medica > China Academy of Sciences > 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Shanghai, China > (Postcode: 201203) > > Mobile: 86-137-6430-7897 > MSN: zhouyang_pku(a)hotmail.com > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > Sincerely yours CHIU,YEUNG

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How to add change to multiple molecules
by zhouyang 02 Nov '08

02 Nov '08

Hi Recently I wanna add change to a series of molecules for DOCK6 which are stored in a single .mol2 file. It seems that the Chimera GUI can just add change for one molecules at one operation. I wonder how to add change to all of them? Alternatively I just suppose to use 'split' shell command to seperate these molecules to single files and then add change to them. Then the key point is whether Chimera can run in command-line mode so that I can achieve by writing a shell script? Thanks in advance Yang zhouyang(a)mail.shcnc.ac.cn 2008-11-03 周阳 ZHOU Yang Master Candidate Drug Discovery and Design Center Shanghai Institute of Meteria Medica China Academy of Sciences 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Shanghai, China (Postcode: 201203) Mobile: 86-137-6430-7897 MSN: zhouyang_pku(a)hotmail.com

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Fwd: Combining fragments for RESP charges
by Francesco Pietra 31 Oct '08

31 Oct '08

Sorry I used the wrong address for the message below. ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Fri, Oct 31, 2008 at 8:34 AM Subject: Combining fragments for RESP charges To: chimera-users-request(a)cgl.ucsf.edu I was reading Ross Walker's tutorial A1, in the suite of tutorials for Amber. When deriving RESP charges for an unusual molecule covalently bound to a protein, the unusual molecule is first detached from the protein and then further divided into fragments. RESP charges are derived for the fragments, then the fragments are recombined using Sirius visualization program. The recombined fragments are then attached to the protein, again using Sirius. Can these recombinations be carried out with Chimera? Thanks francesco pietra

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morph-coordinates and camera movements
by Matthew Dougherty 30 Oct '08

30 Oct '08

I was generating a morph of atoms and wanted to rotate the camera 242 degrees on the x axis. I am thinking there may be several ways to do this, such as per-frame script in the morph tool or through the movie recorder script. Is one way better than the other? What would the scripts look like? Thanks, Matt

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directory within Chimera ??
by Barry Lever 30 Oct '08

30 Oct '08

Elaine: I know you are busy .. but as a fairly new user....when I restore a previous session.. can I extract from Chimera, the names of the input data files that were used to create that molecule and subsequent manipulations- I am especially interested to know where I can locate the name of the input geometry file that set up the molecule. In future I will know to include that information in the overall session file name but for now..... Thanks so much Barry -- A. B. P. Lever Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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multiple Chimera windows on Mac
by Elaine Meng 30 Oct '08

30 Oct '08

On Oct 30, 2008, at 8:07 AM, Chin-Hsien (Emily) Tai wrote: > > One quick question, is there any way to have several sessions of > Chimera running at the same time so that we can compare/rotate > different domain parsing results of the same structure at the same > time? > Hi Emily, I assume you are using a Mac... Yes, you can have multiple Chimera instances, as many as you want, if you start Chimera from the Terminal window. For example, I have Chimera version 1.2540 installed as /Applications/Chimera2540, so to start it from Terminal I would type: /Applications/Chimera2540.app/Contents/MacOS/chimera Actually I don't really type that because it is too troublesome, and instead have an alias in my home directory .tcshrc file (or .cshrc file). If you don't have either of these files you can just create a file by that name in your home directory and put the alias in it, in my case: alias chimera /Applications/Chimera2540.app/Contents/MacOS/chimera Then after you source that file or log in again, simply typing "chimera" (or whatever you used as the alias) starts Chimera. In a second Terminal window, you can enter "chimera" for a second running Chimera, etc. I have multiple different Chimera versions with different aliases, for example, a recent daily build is on my Desktop: alias chinew ~/Desktop/Chimera.app/Contents/MacOS/chimera Even if you have only one version, you can start it as many times as you want from different Terminal windows. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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scripts in Chimera
by Ben Keshet 29 Oct '08

29 Oct '08

Hi, I am reviewing a large number of structures (docking results). I uses the ViewDock tool which is great and makes life much easier. Still, for every file I open with ViewDock, I repeat the same set of commands before actually reviewing the poses, that is (initially only the receptor structure is open, with only ribbon shown): 1. open the ligands mol2 file. 2. color by element 3. choose atoms within 6A from the ligands (by selecting the ligand, than select zone<6A). 4. show the selected atoms. This is to show only receptor atoms within 6A of the ligand. Is there a way I can "record" this sequence or write some simple script that I could run after opening the ligands mol2 file? Thanks! Ben

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volume planes display loop
by Benoit Zuber 28 Oct '08

28 Oct '08

Hi, I have got some questions regarding plane display of volumes: Is there a way to cycle through a limited range of planes? For example if the thickness of my volume is 300, is it possible to cycle from z = 100 to z = 120, instead of from z = 0 to z = 299? Is there a way to make the cycling through the planes start in the other direction than when it stopped last time? For example, I click stop while the display is cycling from low z value to high z value. If I then click start, the display is going to cycle again from low to high z value but I would like it to cycle from high to low z value. Is it possible to specify a starting plane and an end plane, and to have the display going from the starting plane to the end plane only once (without cycling)? Finally, can all of this be specified through the command line? Cheers, Ben Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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Flushing output during the script execution
by Lukas Palatinus 27 Oct '08

27 Oct '08

Hello all, I am using Chimera as a visualization tool for small-molecule electron densities obtained by ab initio structure solution. I want to create a small script that will make Chimera read and display the intermediate electron densities as they are produced during the iterative structure solution process. I am not skilled in Python, but I could make a simple Python script by copying and modifying scripts previously posted in this list. Here is the script: from chimera import runCommand as run from os.path import exists from time import sleep map_file= 'test.xplor' while exists(map_file): run('close all') run('open ' + map_file) sleep(1) I am sure this is not the most elegant way to achieve what I need, but it should do the job. What the script should in my opinion do is to read and display the file test.xplor, then wait one second, close the map and reopen it again, until the file test.xplor is deleted. The script does >>almost<< that, it opens the volume viewer, reads the map, but it does not display the map in the main Chimera window. Only after the file test.xplor is deleted, the last map is displayed. Can anybody give me a hint what am I doing wrong? I am using Chimera 1.2540 on Mac OS X 10.4. Thanks in advance for any help. Best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

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forget previous error
by Jean Didier Pie Marechal 27 Oct '08

27 Oct '08

Sorry, I made a mistake and found my problem. All the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Octubre 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 66, Issue 22 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. volume planes display loop (Benoit Zuber) > 2. Re: volume planes display loop (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 24 Oct 2008 16:36:42 +0100 > From: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> > Subject: [Chimera-users] volume planes display loop > To: chimera users list <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4901EB8A.9040102(a)mrc-lmb.cam.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > I have got some questions regarding plane display of volumes: > Is there a way to cycle through a limited range of planes? For > example > if the thickness of my volume is 300, is it possible to cycle from > z = > 100 to z = 120, instead of from z = 0 to z = 299? > > Is there a way to make the cycling through the planes start in the > other > direction than when it stopped last time? For example, I click stop > while the display is cycling from low z value to high z value. If I > then > click start, the display is going to cycle again from low to high z > value but I would like it to cycle from high to low z value. > > Is it possible to specify a starting plane and an end plane, and to > have > the display going from the starting plane to the end plane only > once > (without cycling)? > > Finally, can all of this be specified through the command line? > > Cheers, > Ben > > > Beno?t Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber(a)mrc-lmb.cam.ac.uk > > > > ------------------------------ > > Message: 2 > Date: Fri, 24 Oct 2008 10:31:44 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] volume planes display loop > To: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> > Cc: chimera users list <chimera-users(a)cgl.ucsf.edu> > Message-ID: <49020680.2070802(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ben, > > The current Chimera daily builds have a more flexible volume > plane > cycling interface. In the planes panel it now has a switch > > Cycle through [20] planes at speed [30] > > It lets you play through a specified number of planes centered on > the > currently shown plane. You start it by clicking a switch and stop > it > the same way. There is no control to stop after N planes, and the > initial direction of play is the same as when you last stopped > playback. > There is currently no Chimera command equivalent which would > obviously > be handy for making movies. I've attached a Python script which > can be > used with Chimera commands (example given in script) to control > exactly > which frames to show in a movie. Note that the frame rate is only > relevant for real-time cycling in Chimera. Movie recording > captures > every new frame no matter how slow they are rendered and plays in a > movie player at 25 frames per second (adjustable with a movie > encode > command option). Chimera movie recording capabilities are very > limited > now but it is an area we intend to improve. > > Tom > > > Benoit Zuber wrote: > > Hi, > > > > I have got some questions regarding plane display of volumes: > > Is there a way to cycle through a limited range of planes? For > example > > if the thickness of my volume is 300, is it possible to cycle > from z = > > 100 to z = 120, instead of from z = 0 to z = 299? > > > > Is there a way to make the cycling through the planes start in > the other > > direction than when it stopped last time? For example, I click > stop > > while the display is cycling from low z value to high z value. If > I then > > click start, the display is going to cycle again from low to high > z > > value but I would like it to cycle from high to low z value. > > > > Is it possible to specify a starting plane and an end plane, and > to have > > the display going from the starting plane to the end plane only > once > > (without cycling)? > > > > Finally, can all of this be specified through the command line? > > > > Cheers, > > Ben > > > > > > Beno?t Zuber > > MRC Laboratory of Molecular Biology > > Hills Road > > Cambridge > > CB2 0QH > > United Kingdom > > +44 1223 402209 > > bzuber(a)mrc-lmb.cam.ac.uk > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 66, Issue 22 > ********************************************* >

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Problem with sum?
by Jean Didier Pie Marechal 27 Oct '08

27 Oct '08

Hi guys, I got back to the script on inertia axis calculation and I had the following error when running it on the built of th 15/10/2008 on my linux box: Traceback (most recent call last): File "/home/jd/Desktop/scripts/chimera/inertia_model.py", line 73, in <module> axes, d2, center = inertia_ellipsoid(m) File "/home/jd/Desktop/scripts/chimera/inertia_model.py", line 13, in inertia_ellipsoid mass = sum(amass) TypeError: 'float' object is not callable then I just try in the python shell: i=[1,2,3] sum(i) and I have the same prob. sum(i) Traceback (most recent call last): File "<pyshell#38>", line 1, in <module> sum(i) TypeError: 'float' object is not callable Some input? all the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Març 19, 2008 8:43 pm Assumpte: Chimera-users Digest, Vol 59, Issue 19 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Principal axis of inertia (Tom Goddard) > 2. problem with 17/03 build linux 64 (Jean-Didier Mar?chal) > 3. Un-tile (Jim Nettles) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 19 Mar 2008 12:00:33 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Principal axis of inertia > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47E162D1.5070108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Eric, > > Just ignorance -- didn't know Chimera could tell me the atomic > mass. > Attached is the same script only using atomic mass instead of > atomic number. > > Tom > > Eric Pettersen wrote: > > Just wondering why you weighted by atomic number rather than mass > > > (a.element.mass)? > > > > --Eric > > > >

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Re: [Chimera-users] coloring seperate domains
by Elaine Meng 23 Oct '08

23 Oct '08

On Oct 22, 2008, at 1:52 PM, Chin-Hsien (Emily) Tai wrote: > > We would like to use Chimera as a visualizing/figure drawing tool to > compare different domain parsing schemes and we are wondering how to > automate the process as much as possible. The tasks are: > 1.fetch a PDB > 2.select Chain (for example B) > 3.Invert (all models) > 4.Atoms/Bonds delete > 5.chain trace only > 6.backbone only > 7.Ribbon show rounded > > I am wondering if there is a simple way to combine step 1 to 4 to > display only specified chain in PDB? > Then rotate the structure to minimize domain overlapped area. > > Then color each domain according to different parsing schemes, for > example: > scheme1 "color red #0:1-38.A 150-190.A; color green #0:39-149.A; > color blue #0:192-347" > scheme2 "color red #0:1-30.A 160-195.A; color green #0:31-159.A; > color blue #0:196-347" > > Can Chimera read a script and displays different domains in > different colors? > Thanks for your advice in advance! > Cheers, > Emily, Dear Emily, You can definitely do all those steps in a script, except I'm not sure how to automatically orient the structure to best show the domains. I'll discuss the other parts first. A Chimera command script is just a text file containing the same things you would enter at the command line. If you name the file something.com or something.cmd it will automatically execute when opened in Chimera (with File... Open or the command "open"). Chimera can also execute python scripts (something.py) in the same way. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > There are many possibilities for either type of script, but here are some example Chimera commands: open 2mnr delete ~ :.a ribbon ribrep rounded ~disp color red :3-132 color dodger blue :133-359 copy png file 2mnr.png This set of commands fetches PDB structure 2mnr, deletes everything that is NOT chain A, displays ribbon, uses the rounded ribbon style, undisplays all atoms, colors the specified residue ranges, and saves an image in PNG format. You don't have to specify the chain in the coloring command since there is only one chain left. Each of these commands has a manual page if you want to see details (for example, there are other image formats such as TIFF). You can try the commands in the Command Line to see what works before putting them into a script. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> For saving images, you might want to make the background white (set bg_color white) before using the script, or after opening each structure use the ribbons preset and then a publication preset (preset apply int 1; preset apply pub 1) instead of ribbon and ribrep rounded. <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/print.html#tips> There are some fancier approaches that may facilitate processing a large number of structures. You can separate the structure-specific and general commands using aliases: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png # # the following general commands could be put in a separate file # open mypdb delete ~ mychain preset apply int 1 preset apply pub 1 color red dom1 color dodger blue dom2 color yellow dom3 color magenta dom4 copy png file output close 0 This structure only has two domains, so I clear any previous dom3 and dom4 assignments from previous structures. There will be error messages when commands refer to nonexistent aliases, but they can be ignored. The reason you might want to separate the specific and general commands is that all of the general commands can then be put in a second command file (for example named "process.com" ) that is opened by the first script. The second script file could be in the same directory (folder) as the first, or you could specify its whole pathname. alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png open /Users/meng/Desktop/process.com # # now go to next structure # alias mypdb 4enl alias mychain :.a alias dom1 :1-141 alias dom2 :142-436 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/4enl.png open /Users/meng/Desktop/process.com [... etc.] Putting the general commands in a separate file minimizes the number of lines in the primary command file. However, it may still be tedious if you are processing a very large number of structures. Since I don't know python, I would probably write a script or program (in some other language) to make the long main Chimera command file. If you know python, another approach is to make the main script python instead of Chimera commands, and have it cycle through multiple structures. You could call the Chimera commands in my examples from inside the python script. Finally, now about orienting the structure to best show the domains. The only way I can think of with Chimera commands is to use "align" to put domains 1 and 2 front and back, then rotate 90 degrees, for example: align dom1 dom2 turn y 90 That worked pretty well in my tests. Those commands could be in the general script (process.com in my example), assuming all the structures have at least two domains, before the image-saving command. There are some other possibilities that require python; I'll get back to you if we come up with something good. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Chimera-users Digest, Vol 66, Issue 20
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Hi All, I figured it out. The problem turned to be the resolution of the files that did not play in the powerpoint. Editing the movie to have a lower resolution enabled the file to play fine in the powerpoint. I wonder if there can be an option to determine the resolution in the output file from Chimera to avoid such problems with powerpoint and also, this can be added to the tips on Chimera site for making the movie for use in powerpoint: "make sure of the produced file to match the projector and the computer. Usually, something like 800x600 should work" Thanks to Elaine for her help. Ibrahim On 10/22/08 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Question about movie in powerpoint (Ibrahim Moustafa) > 2. Re: Question about movie in powerpoint (Elaine Meng) > 3. Re: orthogonal views (Elaine Meng) > 4. Re: orthogonal views (Tom Goddard) > 5. Re: orthogonal views (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Oct 2008 13:05:51 -0400 > From: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Subject: [Chimera-users] Question about movie in powerpoint > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C524D5AF.343C%I.moustafa(a)psu.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera team who is always giving the best support, > > I have a question regarding movie playing in power point and hope you can > help. > > I'm setting a power point presentation and want to play some movie (.avi > MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; > however, if I'm in the presenter view mode it does not play and gives me a > black screen. > I tried to re-insert the movie, change the view size, put everything in the > same place...but none of these solved the problem. > > The funny thing is that other movies bigger in size can play fine in the > presenter view mode. These have the same format (avi MSMPEG-4v2) and created > using the same program. > > Do you have any idea how to resolve this issue? Any advice is more than > welcome. > > Also, I noticed that sometimes the movie, that is known to be working > fine, does not work for unknown reason. > Especially in the case of 2 movies in the same slide. Any tips to have two > movies in the same slide to work in a more robust way is really appreciated. > > Really appreciating your help, thanks; > Ibrahim

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orthogonal views
by Thomas C. Marlovits 22 Oct '08

22 Oct '08

Hi Chimera's ... is there an easy way to create orthogonal views at the same time of a molecule ? The idea is to open a (pdb) file and visualize the molecule from orthogonal directions at the same time in one viewer. Rotation/ movemements of the molecule should be done then on all three views at the same time of course. Maybe you have already implemented such an option (similar to the stereo viewing ...) Tx, -T. ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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Question about movie in powerpoint
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Dear Chimera team who is always giving the best support, I have a question regarding movie playing in power point and hope you can help. I'm setting a power point presentation and want to play some movie (.avi MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; however, if I'm in the presenter view mode it does not play and gives me a black screen. I tried to re-insert the movie, change the view size, put everything in the same place...but none of these solved the problem. The funny thing is that other movies bigger in size can play fine in the presenter view mode. These have the same format (avi MSMPEG-4v2) and created using the same program. Do you have any idea how to resolve this issue? Any advice is more than welcome. Also, I noticed that sometimes the movie, that is known to be working fine, does not work for unknown reason. Especially in the case of 2 movies in the same slide. Any tips to have two movies in the same slide to work in a more robust way is really appreciated. Really appreciating your help, thanks; Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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About Amber residue number renumbering
by Francesco Pietra 22 Oct '08

22 Oct '08

Hi Elaine: At the end of a long journey of ACE/NME capping a fractionated model, I would not leave the impression that I like the way Amber treats the layout of pdb files. With Chimera I had all HETATM capping groups on one side and the ATOM of protein stretches on another side, conserving the residue number they had in the unabridged model. Straightforward to relate to the starting crystallographic work Now, after Amber forced (forced against me) manipulation, the ACE/NMR residues are intermingled with the standard amino acid, all ATOM, and take part to the overall sequential numbering. As the number of atoms in ACE differs from NME, and the stretches are many, headache in relating residue numbers imposed by Amber to residue numbers in the original crystallographic work from which I started. Regards francesco pietra

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Error when fetching pdb by ID
by Kenward Vaughan 21 Oct '08

21 Oct '08

Hmm... is this my system or outside it? I'm at home behind a firewall and have never seen such an error before. I'm not sure where I should look for an answer... Fetch by ID. The error log: Opening 1ai2 Error reading 1ai2: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') Done opening 1ai2 It doesn't fail at work, so I'm suspicious of my home network. ??? Both my workstation and gateway/firewall are Debian/Sid boxes. What port is the call made on?? Thanks for any ideas! Kenward -- ."^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Chair, Physical Science Department |,;| Bakersfield College / ', \ 1801 Panorama Drive / o O \ Bakersfield, CA 93305 (oOoOOoOo) http://www2.bc.cc.ca.us/kvaughan ---========--- ???$$MM$$???

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Fwd: Pruning pdb graphically
by Francesco Pietra 21 Oct '08

21 Oct '08

Hi Elaine: LEaP does not understand capping, with a pdb file that Chimera understands perfectly. I have asked for light at both the Amber and Dock sites. Even Dock uses LEaP for amber score. LEaP adds and exta H to the terminal/beginning and OXT to the terminal/last. Moreover, it tries to join the first ACE with last NME. I have not tried separating the capping residue with TER. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Tue, Oct 21, 2008 at 10:34 AM Subject: Re: [Chimera-users] Pruning pdb graphically To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Elaine: I had fully protonated histidine and left the chain amino group of lysine in basic form! No excuse for that. Now the charge is 5.0000 so that I expect that dockprep (avoiding add-h!) will work. In my (brief) experience, Chimera is an excellent tool also for capping, especially if Add-H is revised for the cases of capped residues. In some cases (12 residues capped in my case) that is important. Also because I want to run MD under various pH conditions, so that capping will change (constant pH MD is not possible with Amber under explicit medium conditions). That Amber has updated to PDB rules is good news. Perhaps I was so suspicious because a few days ago I found a bug with the latest version of ambpdb (Amber's tool to get a pdb file from inpcr/prmtop): the N-hydrogen names for LEU as first residue are written incorrectly. A revised ambpdb is forthcoming. Regards francesco On Tue, Oct 21, 2008 at 12:49 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > After looking at more parameter files, I now believe that Amber and PDB atom > names in standard residues, including hydrogens, are the same. My previous > information was old (I haven't run Amber for 10 years!), sorry about that. > You would still need to worry about correctly naming any atoms changed or > added with Build Structure, though. > > Besides the Amber *lib files mentioned before, you can also look up the > standard atom names in the links from this PDB page: > http://remediation.wwpdb.org/downloads.html > > Elaine > > > On Oct 20, 2008, at 2:39 PM, Elaine Meng wrote: > >> I forgot to mention that usually you don't need to worry about the atom >> names, as Add Charge knows which PDB names go with which Amber >> names/charges, and AddH uses the standard names. >> >> I think you only have to worry about the names of atoms that were changed >> or added "manually" in Build Structure, and if the nonhydrogen atoms have >> the standard names (PDB = Amber for nonhydrogen atoms in standard residues), >> AddH will use correct names for the hydrogens later added to those atoms. >> If you use hydrogens added by Build Structure, however, you have to fix >> their names. >> >> Elaine >> >> > >

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Residue Accessibility
by Luis Alberto Alvarez 21 Oct '08

21 Oct '08

Hello, I am trying to calculate the relative surface accessibility of residues (It will come to getting the solvent accessibility I guess) and the only information I found is from a post in the mailing list dating to 2005 ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000482.html)I am just wondering if there is anything new in this front or I should just follow the 2005 instructions. Thank you -- Luis Alvarez alvarez(a)lcp.u-psud.fr Laboratoire de Chimie Physique Université Paris-Sud à Orsay microscope: 01 69 15 30 31 (80% du temps) bureau: 01 69 15 56 15

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