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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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
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
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
