- Chimera-users - RBVI Mailing Lists

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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