- Chimera-users - RBVI Mailing Lists

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

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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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