- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] delphi potenital map viewing
by Thomas Goddard 05 Dec '03

05 Dec '03

Hi Klaas, The Delphi Viewer is the only tool that can color a molecular surface according to the potential value. Can you email me the Python traceback you get when the "_cubes error: ..." occurs? This shows exactly where in the code the error happened. You find it by looking at Favorites/Reply Log. Having the traceback alone might be enough for me to figure out and correct the problem. If you could put the phi file on the web so I could download it I would almost certainly be able to figure out the problem. The Delphi Viewer is supposed to be able handle maps of any size. It will be much slower than volume viewer, but it should not generate an error with a large map. Tom > Date: Fri, 05 Dec 2003 21:10:20 +0100 > From: Klaas Decanniere <Klaas.Decanniere(a)pandora.be> > Reply-To: Klaas.Decanniere(a)pandora.be > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] delphi potenital map viewing > > Thomas Goddard wrote: > > >Hi Klaas, > > > > The size of the Delphi potential map Chimera can display is only > >limited by the size of your computer memory. > > > > If you open a large map it does not get shown immediately if the map > >is larger than 1 Mvoxels (~100^3). > > > > > > When I tried using the "delphi viewer" option, I get _cubes error: grid > index out of range > Using the volume viewer I can indeed load everything. > Is there a way to tie the volume viewer thing to a molecular surface? > With a colour gradient showing different levels of potential? (As in the > Molecular surface option in the Delphiviewer) > Or maybe I can save the subsampled map somehow and then read it into the > delphiviewer thing? > > Thanks again for your help. > > Klaas > > P.S.: I like the program more each day. > P.P.S.: If you ever have a day with nothing to do: the automatic > fetching of pdb files doesn't work for me as I'm behind a proxy server.

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delphi potenital map viewing
by Klaas Decanniere 04 Dec '03

04 Dec '03

Hello, Thinking that more is better I ended up with Delphi potential maps on a rather large grid which I would like to visualize with chimera (gsize=213) Chimera seems to think the grid is to large. Is there an easy way to have chimera accept bigger grids (speed is not really an issue)? Alternatively, what is the largest grid that chimera can accept? Thanks for your help. Klaas Decanniere

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ribbon+atoms
by Elaine Meng 25 Nov '03

25 Nov '03

Dear Soren, Thanks for the compliments - we're trying! You're right that in recent versions of Chimera , showing ribbon turns off the backbone atoms. There is an easy workaround: open two copies of the same molecule, use one copy to show ribbon and the other copy to show atoms. The reason for the behavior is when the ribbon is drawn as a smooth curve, it does not exactly pass through the backbone atoms. Often one wants to show just the ribbon and certain side chains, and the current behavior is to extend the side chain to meet the ribbon (even when the backbone atoms are not on the ribbon) so that they are not floating in space. However, we agree that sometimes one will want to display both the ribbon and the backbone atoms, and in the future there will a preference to switch between: (a) show ribbon, not backbone atoms, and extend the side chains to meet the ribbon (b) show ribbon and whatever backbone atoms are displayed by the user, do not extend side chains to meet the ribbon Until this switchable preference becomes available, we hope that the suggested workaround will let you do what you want. Sincerely, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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ribbon+atoms
by Soren M. Kristensen 25 Nov '03

25 Nov '03

Dear Chimera developers You have createdt an absolutely brilliant program. I have a small question/suggestion about displaying atoms and ribbons simultaneously. When displaying a number of backbone atoms and then putting on a ribbon, then some of the atoms dissapear in release 1700 and onwards. Is there a way to avoid this behaviour? It basically means that I am stuck with the pre-1700 version, but maybe there is some parameter I can tweak to make it work in the new versions? I would be grateful for your help. I reproted this as a bug some 6 months ago, but was told that it was supposed to be like this. I measure experimental values for selected backbone atoms and display them as colorcoded spheres on top of a ribbon to indicate what is measured different places in the structure. If you have suggestions to acieve this behaviour in another way I would be grateful. Thank you in anticipation, Søren -- Søren M. Kristensen, Ph.D. Phone: (+45) 3532 0301 University of Copenhagen FAX: (+45) 3535 0609 Department of Chemistry E-mail: smk(a)kl5.ki.ku.dk H. C. Ørsted Institutet http://kl5.ki.ku.dk/~smk Universitetsparken 5 Room: C508 DK-2100 København Ø Denmark

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some CADD tools released
by gentamicin5 19 Nov '03

19 Nov '03

Dear all, I have written some CADD tools, and the details are described below. All of these programs are released under GNU/GPL. You can download them from: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------- CADD tools (linux & irix) pscan_2.2.0 PSCAN is a small but a practical tool for finding any potential binding site of a protein. It can picture the size and appearance of a binding site, and point out the possible pharmacophore.Thus it is helpful for drug design. While running DOCK, QCPE_MS is necessary for autoMS and even the next step sphgen. QCPE_MS, however, is a commercial package. Now, PSCAN and SPHBOX can do the same job. After removing all dots outside of the target binding site by SPDBV (or others), and choosing several positions you are interesting, run SPHBOX to generate sph and box files. pmol2q_2.1.1_rc2 PMOL2Q is a specific file format converter for protein pdb file to mol2 file with adding hydrogens and partial charges. From v2.1.1, PMOL2Q can also output pdbq and pdbqs format. (The pdbqs format is added solvation data according with ADDSOL in AutoDock) It can recognize each amino acid and reconstruct the coordination precisely. The bond length of 109 pm for C-H, 101 pm for N-H, 96 pm for O-H and 134 pm for S-H are used for adding hydrogens.You can choose to add global hydrogens or only polar hydrogens. KOLL and AMBER95 partial charges are available in PMOL2Q. PMOL2Q can also check probabel error of protein coordination, including incomplete atom_missing residues and atom bumps. Hydrogens will not be added on incomplete residues if they exist. You need to fix it by other program before converting file format. (ex. SPDBV can fix the incomplete residues by mutate function) dbfilter_2.2.1 DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-molecular built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Common_atoms_only, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Big_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. ----------------------------------------------------------------- 每天都 Yahoo!奇摩海的顏色、風的氣息、愛你的溫度，盡在信紙底圖 http://tw.promo.yahoo.com/mail_premium/stationery.html

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Fwd: MidasPlus version 2.1 (1997/02/04)
by Robin Parsons 17 Nov '03

17 Nov '03

Begin forwarded message: > From: Devleena Mazumder <devleena(a)chem.ucsb.edu> > Date: Fri Nov 14, 2003 6:04:37 PM US/Pacific > To: Robin Parsons <rparsons(a)cgl.ucsf.edu> > Subject: Re: MidasPlus version 2.1 (1997/02/04) > > Dear Robin, > Thanks for your email. > I have installed Chimera. Its easier to use than Midas. Unfortunately, > I > dont see the label3d option in it that was available with Midas. So, I > am > unable to get labels in neon. > Thanks > Devleena > > On Thu, 6 Nov 2003, Robin Parsons wrote: > > :>To: Devleena, > :>University of California, Santa Barbara, > :> > :>Thank you for your interest in our MidasPlus molecular modeling > :>software. You should know, however, that MidasPlus 2.1 is the final > :>version of MidasPlus and will not be developed further. You may wish > :>to explore our next generation of molecular modeling software, > Chimera. > :> You can look over Chimera's capabilities on our web site at: > :> > :>www.cgl.ucsf.edu/chimera/ > :> > :>In addition, Chimera is offered at no cost to educational and > :>non-profit institutions. > :> > :>Please contact me if you have any further questions. > :> > :>Robin Parsons > :>UCSF Computer Graphics Lab > :>Resource for Biocomputing, Visualization and Informatics > :>600 16th St., Room N-472B, Box 2240 > :>San Francisco, CA 94143-2240 > :>Commercial Carrier Zip Code: 94107 > :>tel. 415-476-1540 > :>fax 415-502-1755 > :>rparsons(a)cgl.ucsf.edu > :> > :> > > > > _______________________________________________________________ > DEVLEENA MAZUMDER-SHIVAKUMAR > PhD Candidate, Dept of Chemistry & Biochemistry > UNIVERSITY OF CALIFORNIA SANTA BARBARA > http://www.chem.ucsb.edu/~devleena/ > > **Although the past gives us lessons, it does not > give the whole answer to what must be done now.** > > Robin Parsons UCSF Computer Graphics Lab Resource for Biocomputing, Visualization and Informatics Assistant to Thomas Ferrin, PhD 600 16th St., Room N-472B, Box 2240 San Francisco, CA 94143-2240 Commercial Carrier Zip Code: 94158 tel. 415-476-1540 fax 415-502-1755 rparsons(a)cgl.ucsf.edu

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quick question
by vreyes 30 Oct '03

30 Oct '03

To Whom It May Concern: Our system is SUN Solaris 64bit Sparc III. Should I select #4 from the list below when downloading Chimera? 1.) SGI IRIX Platforms 2.) i386 Linux Platforms 3.) Mac OS X using X windows 4.) Tru64 UNIX 5.0/5.1 Platforms 5.) Microsoft Windows Platforms Please let us hear from you ASAP. Thanks very much for your help. V. Reyes San Diego Supercomputer Center Structural Bioinformatics group

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Delphi controller
by Marco Sette 21 Oct '03

21 Oct '03

Dear all, I'm trying to use the Delphi controller but I have problems to interface Delphi to Chimera.I created a link to Delphi under the Chimera directory but it does not seems the correct way. Is there some place to look to solve this problem ? I use Linux RedHat 9.0 Thanks, Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Delphi under Chimera
by Marco Sette 20 Oct '03

20 Oct '03

Dear all, I'm trying to use the Delphi controller but I have problems to interface Delphi to Chimera.I created a link to Delphi under the Chimera directory but it does not seems the correct way. Is there some place to look to solve this problem ? I use Linux RedHat 9.0 Thankks to all. Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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by solomon 15 Oct '03

15 Oct '03

Hi, I'm a new chimera user. Now I have some difficult to use chimera. How can I save the amino acid that I select as a new .pdb file. For example, I select the amino acids that is around the ligand within 10 A,and I want to save these residues as an another .pdb file. How can I do? Best regards, xiaogaokeng

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