- Chimera-users - RBVI Mailing Lists

Controling the configuration of chiral atoms.
by vincent zoete 07 Apr '11

07 Apr '11

Dear Chimera team, We are very satisfied daily users of Chimera for drug design and protein engineering applications in our lab. Congratulations for your great work! I would like to come back on the point raised by Dr. Charbel MAROUN recently. Having the possibility to change the configuration of whatever chiral atom would be very useful for drug design applications. It's true that we can do it using other software like Pymol or HyperChem, to cite just two of them arbitrarily. But it would be much more convenient to rapidly and graphically do it in Chimera, without the need to switch to another program for that particular and single action. We are often working with D-amino acids and chiral small molecules. We apreciate a lot the "Build Structure" module to construct or modifiy such compounds, and allowing more control on the chiral center configuration would be very useful. Do you think you could consider adding such chirality inversion command in the future? Sincerely, Vincent Zoete, Molecular Modeling group - SIB www.click2drug.org =========================================================== Hello, Sorry, Chimera does not do that. I am pretty sure that SYBYL and probably some other programs will do it, but you may want to ask on a more general list such as CCL.net for a more certain and detailed answer about other programs. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 28, 2011, at 6:15 AM, R. Charbel Maroun wrote: > Hi everybody, > Is there an easy and quick way to invert the chirality of an atom, say a Ca ? > Greetings, > ----------------------------------------- > R. Charbel MAROUN, Ph.D., H.D.R.

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Hydrogen bond cut off
by Simon Sham 07 Apr '11

07 Apr '11

Hi, First, I don't have access to the reference by JE Mills in Journal of Comp. Aided Design 1996. Secondly, can someone please tell me that in chimera is the cut off distance between the donor and acceptor atoms 3.5 angstroms and cut off angle 35 degrees? Thanks for your help in advance. Simon

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Problem for selecting the Recepter and ligand
by Bishwajit Das 07 Apr '11

07 Apr '11

Hi I am using chimera,i am a new user of this and i open a docking model in .pdb format. Now my question is how i seen that model which is recepter and which is ligand.How i differentiate with recepter and ligand with two another colour. Please help me with step by step Thank you -- * BISHWAJIT DAS*** KOLKATA

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salt bridges
by Simon Sham 07 Apr '11

07 Apr '11

Hi, I have tried to find out salt bridges with chimera. According to the archive: "findhbond selRestrict both saveFile ~/mydir/myfile" 1. I could not find "selRestrict" under "FindHbond". I am using the latest version of CHimera. Thanks for your help in advance. Best, Simon Sham

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Scrollbar in Structure/sequence associations
by Lucio Ricardo Montero Valenzuela 06 Apr '11

06 Apr '11

Hello. I want to suggest that a vertical scrollbar be added to the Structure/sequence associations dialog box, because whenever there are more than ~17 models, the last ones are not reachable. Lucio

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Suggestion
by Davis, Derick C. (MU-Student) 04 Apr '11

04 Apr '11

Hello, I was wondering if the developers have considered creating an application of Chimera for the iPhone or iPad? If not, they should :) Thank you, Derick Davis

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Map's Box size
by יוכבד 04 Apr '11

04 Apr '11

Hi Can I please get your help with map resizing. I have a map with a box size 250,269,108. To run a map fitting script I need the map to have a cubic size. Using the volume viewer- Region min max step x - I was able to play with the box size the problem is I can't get the entire map into a cubic box (Z axis is to small). Is there a way to enlarge the box on the Z axis? Thank you Yocheved

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Thermal ellipsoids are not updated when playing multi-frame PDB trajectory
by Lukasz Walewski 01 Apr '11

01 Apr '11

Hi, I am looking at the trajectory with thermal anisotropy factors that change from frame to frame, i.e. I have a multi-frame PDB file that contains ATOM and ANISOU records. The components of the anisotropy tensors change during the simulation (the data I am analyzing has a redefined meaning). I am able to properly read and play the trajectory. Ellipsoid representation of the thermal U factors works excellent for a single frame. However it seems that the ellipsoids are not updated when I play the trajectory, i.e. the atoms move as expected but the ellipsoids retain both their positions and shape from the first frame. Is there any way around ? In any case I find Chimera wonderful software that I came upon only recently. Thanks guys for developing it! With best regards, Lukasz

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Script for getting the map values of fitted residues.
by Robert Ford 29 Mar '11

29 Mar '11

I was wondering if there was a script available that would get the map density values of amino aid residues in a model fitted to an EM or X-ray density map and then write the data to a text file? Essentially what I need is something that does something like this (but not laboriously by hand) e.g. in command line mode select #1:1.B then I use Tools>Volume Data>Fit in Map and click 'Update' to get the average map density value for the atoms in amino acid residue number 1 in chain B of model 1. Many thanks for your help Bob Ford, Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, 131 Princess St., The University of Manchester Manchester M1 7DN, UK. Tel: +44(0)161 2004187 Fax: +44 (0)161 3068918 bob.ford(a)manchester.ac.uk www.ls.manchester.ac.uk

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Ask a question
by ding kevin 29 Mar '11

29 Mar '11

Hi, I am a freshman to use Chimera. When I run "add charge" of ligand by the tutorial, and the error below appears. I would like to know the reasons and how could I solve this problem. Thank you very much! Charge model: AMBER ff99SB Assigning partial charges to residue ARA (net charge +0) with am1-bcc method Running ANTECHAMBER command: D:/drivers/Chimera 1.5.3rc/bin/amber11/bin\antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 -fi mol2 -o c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (ARA) cygwin warning: (ARA) MS-DOS style path detected: c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 (ARA) Preferred POSIX equivalent is: /cygdrive/c/users/dingzh~1/appdata/local/temp/tmpkghulj/ante.in.mol2 (ARA) CYGWIN environment variable option "nodosfilewarning" turns off this warning. (ARA) Consult the user's guide for more details about POSIX paths: (ARA) http://cygwin.com/cygwin-ug-net/using.html#using-pathnames (ARA) /usr/bin/antechamber.exe: error while loading shared libraries: ?: cannot open shared object file: No such file or directory (ARA) Error: cannot run ""D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit (ARA) Running: "D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Failure running ANTECHAMBER for residue ARA Check reply log for details -- Zhaoyang Ding East China University of science and technology Shanghai China

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