March 2011 - Chimera-users - RBVI Mailing Lists

Searching chimera-users archive
by Tom Goddard 08 Mar '11

08 Mar '11

Hi Conrad, Searching the Chimera mail archives from the Chimera documentation web page does not work at all well. http://www.cgl.ucsf.edu/chimera/docindex.html I tried searching for "Beale" and it produced no results. > Your search - *Beale site:www.cgl.ucsf.edu/pipermail/chimera-users > -filetype:gz* - did not match any documents. > > Suggestions: > > * Make sure all words are spelled correctly. > * Try different keywords. > * Try more general keywords. > * Try fewer keywords. > There is a message in August 2010 from John Beale. If I search for that message using www.google.com (chimera "startup options" John Beale) I do get the message. So it has been indexed. Some other revealing problems. Searching the Chimera archives from the documentation page for "chimera" produces only 20 hits, all but 5 are attachments. Likewise a search for "windows" produces just 4 hits (one from 2005, one 2006, one 2007, one 2010). Obviously this isn't working. Maybe we should remove the search field from the documentation until we have time to fix it because users (even ones who should know better like me) sometimes believe the search results that there are no archived messages on the topic. Tom > On Mar 8, 2011, at 10:58 AM, Tom Goddard wrote: > >> Hi Eric, >> >> How do I reply to an old chimera-users message and keep my reply in >> the same mailing list thread? I guess there is some mail header line >> that allows the mailing list to recognize which messages belong to >> the same thread. But I don't have the old chimera-users email I want >> to reply to. The web interface to the archive doesn't appear to >> provide a way to reply. > > Well, I don't know for sure, but I assume it is threaded based on the > In-Reply-To header and/or the References header. Now, the archive > doesn't show you either of those so I assume they're buried in some > internal location, so you're stuck. Besides, threading is broken > across month boundaries anyway, so isn't the point moot really? > > --Eric >

2 1

saving charmm layout
by Francesco Pietra 08 Mar '11

08 Mar '11

Hello: Is it possible to save pdb conserving as much as possible charmm layout (in particular the segments (P1, P2, etc)? I find speedy to edit graphically with Chimera but, afterward, much time is required to restore charmm layout. thanks francesco pietra

2 1

How to model a 4Fe4S cluster on conserved Cys residues
by Ingmar Buerstel 07 Mar '11

07 Mar '11

Dear users, i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster Thanx in advance, Ingmar

2 1

question on volume viewer usage
by Bala subramanian 04 Mar '11

04 Mar '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have three pdb files (of same protein) and for each pdb file, i have an electro static potential file (.dx file). I opened the three pdb files and then the .dx potential files successively through volume viewer. Each time i open the .dx file, the isosurfaces are mapped on to the first pdb file. Why is it so ?. 1) Precisely 1.dx should be mapped on 1.pdb, 2.dx on 2.pdb...etc. How can i do this ? 2) Is there any way to have a universal setting of volume display options. Like in isosurface threhold (+2 and -2 in my case), color for +ve and -ve surface, transparency etc. Because presently i am doing these settings individually for each .dx file. Thanks, Bala

2 1

1 out of many helices shown as pipe
by odonnell＠chem.fsu.edu 03 Mar '11

03 Mar '11

Hi all, I have a pdb with many alpha helices but I only want one or two to stand out as a pipe. I tried highlighting that particular sequence(s) and going to Depiction => pipesAndPlanks but it will change all of them. Many thanks for a push in the right direction. -Jason ------------------------------------------------------------------------- Sent via webmail for Chemistry & Biochemistry @ Florida State University https://webmail.chem.fsu.edu -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

ambient lighting mode for simple drawing style missing
by Benda, Christian 03 Mar '11

03 Mar '11

Hi possibly a simple question but it has kept me buffled for two weeks now, so I decided to ask: how can I set lighting mode to ambient? I am trying to create images using a simple drawing style like exemplified in http://www.cgl.ucsf.edu/chimera/ImageGallery/ p53 simple drawing or Clathrin but I don't find ambient lighting mode in the viewing tools - lighting menu. The only options given are lights (head light, 1, 2) or quality (normal, glossy). I am using Chimera 1.5 build 30417 fir darwin 64bit, aqua on a MacBook Pro with Mac OS X 10.6.6. Many thanks in advance Christian ________________________________ Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: benda(a)biochem.mpg.de

3 4

Re: [Chimera-users] Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 03 Mar '11

03 Mar '11

Thank you, I had missed the settings on that other place. Now it works quite well. (barring some issues with external monitor) I also noticed that overlay setting in same menu should be on or whole desktop would get blurry (with or without stereo glasses on). -vpk On 3/1/11 10:36 PM, Greg Couch wrote: > If both Chimera and PyMol are complaining, then you've haven't > configured OpenGL stereo correctly. The NVidia Quadro driver > configuration has two places to setup stereo. There are the > "Stereoscopic 3D" settings that are not helpful for chimera (except for > making NVIDIA's stereo image viewer work). So in addition to that, you > want to setup stereo in the "3D Settings / Manage 3D Settings" dialog. > In there, turn on "Stereo - Enable" and select the appropriate kind of > stereo in "Stereo - Display mode". > > Good luck, > > Greg > > On 02/28/2011 09:11 PM, Veli-Pekka Kestilä wrote: >> >> I have done all of these and as I said in my original e-mail I got the >> full screen tests nvidia provides working. Problem is that when I try to >> start Chimera or PyMol it fails complaining that 3d vision mode isn't >> available. So question still basically is if it's possible to get it >> working with Quadro 880M >> >> On 2/23/11 4:40 PM, Sabuj Pattanayek wrote: >>> also see : >>> http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#NVidia_NVision… >>> >>> . It has some instructions on how to setup 3d vision on windows. >>> >>> On Wed, Feb 23, 2011 at 8:36 AM, Sabuj Pattanayek<sabujp(a)gmail.com> >>> wrote: >>>> IIRC there's an option in the windows nvidia configuration utility >>>> that enables and disables nvidia 3d vision. I assume that's the setup >>>> you're trying to use, so check that to see if it's enabled or >>>> disabled. >>>> >>>> 2011/2/23 Veli-Pekka Kestilä<veli-pekka.kestila(a)helsinki.fi>: >>>>> Hi Tom, >>>>> >>>>> On 2/22/11 8:12 PM, Tom Goddard wrote: >>>>>> Hi Veli-Pekka, >>>>>> >>>>>> This is either a driver configuration problem or driver limitation or >>>>>> driver bug. Your driver is from Oct 2010 and there are newer ones. >>>>>> The >>>>>> following 266.58 driver was released Jan 18, 2011 and the notes >>>>>> say it >>>>>> adds support for various "3d vision notebooks". Maybe the new >>>>>> driver is >>>>>> needed. >>>>>> >>>>>> http://www.nvidia.com/object/notebook-win7-winvista-64bit-266.58-whql-drive… >>>>>> >>>>> I installed back the newest driver and problem still persist. So it's >>>>> problem either with driver or the card. >>>>> 880M isn't very high end on the Quadro Cards. >>>>> >>>>>> If it is a driver configuration problem, I don't know about that. Our >>>>>> expert on stereo and Windows is on vacation this week but can >>>>>> advise you >>>>>> next week. >>>>> Seems that I will be waiting for that. Thank you for your reply. And >>>>> hope to hear from you next week. >>>>> >>>>> -vpk >>>>> >>>>>> Tom >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have problem with Nvidia Quadro FX 880M and Stereoscopic view. >>>>>>> When I >>>>>>> switch the stereoscopic view on in Chimera it gives me following >>>>>>> error: >>>>>>> >>>>>>> stereo viewing (Unable to find hardware stereo support >>>>>>> (couldn't choose pixel format >>>>>>> Couldn't configure togl widget)). >>>>>>> >>>>>>> I have installed the Quadro drivers version 259.57 in Windows 7 >>>>>>> 64bit. >>>>>>> And separate 3D driver for Quadro. >>>>>>> >>>>>>> Greetings, >>>>>>> Veli-Pekka Kestilä >>>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> University of Helsinki / Institute of Biotechnology / >>>>> veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, >>>>> Biocenter 3 >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

1 0

odd output from surfnet
by Irene Newhouse 03 Mar '11

03 Mar '11

I'm trying to get an image of channels in the attached protein. It's actually a dimer, & the surfaces looked bizarre for the dimer, so I thought maybe surfnet was choking on the repeated residue numbers when you use chain ID, so I clipped it down to the monomer. That' still odd. I've attached a png of the result, using the defaults, & the pdb file of the monomer. What am I doing wrong? Is there a way to get the n largest channels, instead of all of them? Thanks! Irene Newhouse

2 5

morph problem
by Andres Palencia 02 Mar '11

02 Mar '11

Dear Chimera Users, I am trying to morph the complex1 and complex2 from the same system (protein-RNA) to make a video monitoring the conformational changes. As complex 1 is missing one domain and a helix (not visible in the crystal structure), I need to remove these parts in complex 2 to have an equal number of atoms in both complex and could morph it. The resulting video is not so nice because shows the gaps corresponding to the missing part. So, to avoid that, I have modelled the missing part in the complex 1 to have the same atoms, and afer morph it again to make the video, but this is not working. In the transition between complex 1 and complex 2, the RNA encounter one helix on the way that needs to move out to let the RNA to get the position observed in complex 2. If I take out this helix, the video can perfectly be done, but still is not perfect because show gaps. Anybody could give an idea in how to solve the problem? We need the video to include in a publication,. Thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

2 1

3-D
by Jason Bouvier 02 Mar '11

02 Mar '11

Hi, how do I view proteins in 3-D in Chimera? And would I use standard 3-D glasses or are special ones required? I viewing in stereo with some old 3-D glasses that I had around but to no avail. Thank you. Cordially, Jason Bouvier Jason Bouvier | Graduate Student, <http://mcb.illinois.edu/departments/biochemistry/> Biochemistry | <http://www.life.illinois.edu/gerltlab/research.html> Gerlt Lab | <http://www.igb.illinois.edu/> Institute for Genomic Biology | Rm 3200 | <http://illinois.edu/> University of Illinois at Urbana-Champaign | 1206 W. Gregory Dr. | MC-195 | Urbana, IL 61801 | office 217.333.2673 | lab 217.333.2699 | <mailto:jbouvier@illinois.edu> jbouvier(a)illinois.edu

2 2