- Chimera-users - RBVI Mailing Lists

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 18 Nov '03

18 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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how to edit pdb file
by solomon 15 Oct '03

15 Oct '03

dear sir, 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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Re: bug? (HETATMs)
by Eric Pettersen 06 Oct '03

06 Oct '03

On Saturday, October 4, 2003, at 10:21 AM, solomon wrote: > when i open a pdb format file like below: > HETATM ................................. > HETATM ................................. > HETATM ................................. > ... > ... > ... > HETATM ................................. > > then I find that all the HETATM type atoms are bonding each other. All > the HETATM need a ter card to split them. As for HETATM type, I think > maybe there is some wrong with chimera. > best regards > gaokeng xiao Dear Gaokeng, As far as know, Chimera will connect HETATM segments of all standard PDB files (i.e. those distributed by the RCSB) correctly. That being said, Chimera has to do a lot of guessing when it comes to connecting non-standard PDB files (which I'm pretty sure is the kind of file you're talking about here). One thing to keep in mind with HETATMs is that they don't necessarily imply a chain break. Also, they are supposed to have CONECT records detailing their connectivity. So for instance, part of PDB entry 1f1j looks like this: ATOM 3688 OG SER B 602 58.714 25.290 29.976 1.00 66.81 O TER 3689 SER B 602 HETATM 3690 C ACE C 701 29.751 29.860 -0.650 1.00 52.20 C HETATM 3691 O ACE C 701 28.552 30.100 -0.812 1.00 55.72 O HETATM 3692 CH3 ACE C 701 30.801 30.183 -1.675 1.00 52.54 C ATOM 3693 N ASP C 702 30.252 29.308 0.427 1.00 51.48 N The ACE residue in the HETATM records is connected to residue 702 (as detailed in the CONECT records for the file). So in summary, you can have sequences like these where the HETATM residues are connected: ATOM ATOM HETATM HETATM HETATM ATOM ATOM -or- HETATM HETATM HETATM ATOM ATOM Now the really big problem is that the SCOP web site returns "PDB" files with just these kinds of sequences but with _no_ CONECT records! So, Chimera guesses as best it can in this situation. The rule of thumb that it uses is that HETATMs are connected unless they occur somewhere after a TER card with no intervening ATOM record. Explicit CONECT records can add connectivity. So for your file of all HETATMs where nothing should be connected, there is a silver lining: in order to get nothing connected you just have to add a _single_ TER card at the beginning of the file, like this: TER HETATM ................................. HETATM ................................. HETATM ................................. --Eric

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graphics accelorator choice of chip
by David Griffiths 02 Oct '03

02 Oct '03

Since Fire GL2 is now discontinued does anybody have experience of latest graphics acceloratots for use on chimera It has been suggested to me that the following should be OK but does anybody have experience of using them ? NVidia Geforce FX 5600/5900 ATI 9700/9500. david griffiths d.g.griffiths(a)herts.ac.uk

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Re: [Chimera-users] how to color ribbons?
by Elaine Meng 20 Aug '03

20 Aug '03

Hi Mario, I'll include two different ways you could do this in Chimera 1.1700: ---------------- with menu ---------------- Actions... Atoms/Bonds... hide Actions... Ribbon... show Actions... Ribbon... edged Actions... Color... white Select... Structure... secondary structure... helix Actions... Color... red Select... Structure... secondary structure... sheet Actions... Color... cyan Select... Clear selection ---------------- with commands ---------------- ~display ribbon ribrepr edged ribcolor white ribcolor red :/isHelix ribcolor cyan :/isSheet ---------------- In both approaches, first the atoms are undisplayed, then the ribbon is turned on. The step setting the ribbon type to "edged" is optional; you could use whichever ribbon type you want. Then, I make everything white before making helices red and strands cyan. The reason I don't use the turn descriptor is that it only applies to explicit PDB TURN records, whereas in most cases, the PDB only contains HELIX and SHEET records. You could just put the commands in a plain text file, for example named "sscolor.com," and then use the command "source sscolor.com" to execute all the commands in the file. (The file must be in the working directory; otherwise you will have to include the whole path in the source command.) I hope this helps! Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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