June 2009 - Chimera-users - RBVI Mailing Lists

Morphing Code Request!
by Eric J. Choi 11 Jun '09

11 Jun '09

Hello, chimera-users, Hi, my name is Eric Choi and currently I am interning at the Ren Lab at mission bay for Dr. Ren. For one of my assignments, I was to make a video of a conformation change of PPAR-GAMMA, from open to closed structure with the addition of a ligand. Upon trying to make this happen, I realized that I need the morphing python code(I believe it is) to be able to complete this step. This is what the movie making tutorial told me in the part "Ligand Flying into Unbound Conformation". If I could get the command to make the morph(python code) that would be great. Thank you! -Eric Choi

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map saving
by Jean-Paul Armache 09 Jun '09

09 Jun '09

hello, i would like to ask you a question concerning map manipulations. sometimes i need to manually fit a map into another map, but when saving the map in the new position, it doesn't retain the coordinates. it simply overlays with the original, unmoved maps. is there something i need to do in order to save it in the new position afore hand ? best regards, jean-paul armache

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movie making
by Schulz-Gasch, Tanja 09 Jun '09

09 Jun '09

Hi there, I used Chimera so far only for making pictures. Now I am doing the first movie steps. I want to combine features like hide, show, rock,... with the MD Movie module to show a morph between different protein conformations. How can this be done? The movie should start with the display part (using hide, show, rock,...) followed by the morphing. However, when using the MD movie module the morph starts at frame 1. Thanks, Tanja __________________________________________ Dr. Tanja Schulz-Gasch F. Hoffmann-La Roche Ltd Pharmaceuticals Division PRCBLM Bldg. 92/2.10D CH-4070 Basel Switzerland Tel. +41(0)61 68 88309 Fax. +41(0)61 68 86459 http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html <http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html> Email: tanja.schulz-gasch(a)roche.com <mailto:tanja.schulz-gasch@roche.com> "The information transmitted in this message is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you receive this message in error, please contact the sender and delete the material from any computer."

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loading chimera
by Bala subramanian 08 Jun '09

08 Jun '09

Friends, I installed chimera 1.4 ( build 27677) build in Fedora 10. The installation was successful but when i run chimera, chimera opens with the following message. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. In addition, when i try to capture a high resolution image (300 dpi), chimera closed itself with following message. X Error of failed request: GLXBadPbuffer Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 75435 Current serial number in output stream: 75437 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x19e767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x19e90e] #2 /usr/lib/libX11.so.6 [0xb690e9] #3 /usr/lib/nvidia/libGL.so.1 [0x6536ffd] Kindly write me what is going wrong. Thanks, Bala

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Segementation Fault
by Kshatresh Dutta Dubey 08 Jun '09

08 Jun '09

Respected Sir, I am using chimera since five months. It was running without any error. But today when i am starting chimera it is giving error like segmentation fault. Kindely help me for this problem. Thanks in advance. Kshatresh Dutta dubey

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Displaying surface residues...
by Yasser Almeida Hernandez 05 Jun '09

05 Jun '09

Hi all... I want to know if its possible display surface residues via python script. The idea is import the chimera module inside the script, and it receive (the script), the pdb file to analyze. The script is to run in a classical bash terminal... Thanks.. ---------------------------------------------------------------- Correo FENHI

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chimera on GM945
by Dmytro Kovalskyy 04 Jun '09

04 Jun '09

Hi there, I experience porblems with chimera running on Lenovo X60t in Linux. graphics: intel GM945 I have two installations on the notebook: WinXP and Linux (ALT Linux 4.1.1). Chimera's benchmark under Windows returns preety nice values (see http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, pre-pre last line, Lenovo ThinkPad X60 Tablet 6363WDP). However under linux I can not get even something reasonable to post Surf - 1 Mesh - 26 Contouring 149 Solid 1 Recoloring 5 Is it natural or due to some bugs in Linux drivers/X/kernel? Thanks in advance Dima -- ----------------------------------------------------- Dmytro Kovalskyy, PhD D.Kovalskyy(a)enamine.net Molecular Modelling Group Leader tel.: +38 044 537 32 18 Enamine ltd. fax : +38 044 537 32 53 23, Matrosova str. 01103 Kiev, Ukraine

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Residues that interact with active site
by Abeer Shokeer 03 Jun '09

03 Jun '09

Hello I have a model structure of my protein and I would like to determine which residues that could take part in active site. Can I do that with Chimera? Thanks for your help Abeer

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Deleting parts of secondary structures
by Anindito Sen 03 Jun '09

03 Jun '09

Dear All I have a Chimera session in which I have 6 sets of PDB files (ribbon representation) showing variability in the structures. However I wish to display only few of the subunits. Questions are: 1. How do I delete undesired subunits from all the chains on the command line 2. How do I select particular residues from specific chains (not all the 6).. Thanks 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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ribbon transparency
by hsosa＠aecom.yu.edu 02 Jun '09

02 Jun '09

Hi, Is there a command to control the transparency of a ribbon representation or the whole model ?. I'm trying to fade in an out a molecule (in ribbon + wire atom representation) in movie. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Chimera-users June 2009