- Chimera-users - RBVI Mailing Lists

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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