November 2008 - Chimera-users - RBVI Mailing Lists

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

2 1

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

2 3

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

3 2

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

1 1

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

2 1

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

2 1

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

2 2

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

2 1

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 >

2 1

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

2 2