- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Display all rotamers
by Elaine Meng 09 Dec '08

09 Dec '08

On Dec 6, 2008, at 9:35 AM, daniel.hilger(a)lrz.uni-muenchen.de wrote: > > I´m really sorry for my imprecise question. I will concretize it. I > know > the rotamer tool, but I don´t want to replace only one rotamer into > another. I will have them all in the structure and in the according > pdb-file. With the rotamer tool, it is only allowed to choose one > rotamer > out of the rotamer list before clicking "Apply". This is my problem, > and I > didn´t found an appropriate answer in the manual and help menu. Hi Daniel, I'm sorry for misunderstanding - It's true that Apply only puts one copy in the structure, but if you don't Apply and simply keep the Rotamer list dialog and choose all of its lines, that displays all of the rotamers at the same time. Maybe that would allow you to do what you want. The Rotamer list dialog allows calculating clashes and H-bonds, plus selecting the rotamer atoms so you can control their appearance with the Actions menu. The issue is that the structure can't have multiple indistinguishable atoms (with the same name and residue number). We have talked about allowing multiple rotamers to be applied to the structure by giving them different "alternate location" ID codes, but that has not been implemented yet. Also, some residues may have more rotamers than the number of possible alternate location ID codes. Nevertheless we will make sure it is on one of our requested features lists. So currently you can't save PDB with multiple rotamers, but you can save/restore the session in the state where all of the rotamers are displayed. I hope this helps, Elaine

2 1

SpaceNavigator with Linux
by Juan M Vanegas 08 Dec '08

08 Dec '08

Hi, I just purchased a space navigator and would like very much to get it working with Chimera on linux. I don't know if you are aware of the spacenav project (http://spacenav.sourceforge.net/) it is a GPL alternative to the proprietary drivers. I would be willing to help with some of the coding/testing, I know a little bit of programming and I have the device. Thanks for the great work with Chimera. Cheers, Juan

2 1

Named selection for subset of markers
by Giovanni Cardone 08 Dec '08

08 Dec '08

Hi all, I am trying to save a selection of a subset of markers as a named selection. However, the named selection results empty: is it a normal behavior? I am using Chimera version 1 build 2552. Thanks in advance, Giovanni

3 4

chimera startup problem
by Jinzhong Lin 08 Dec '08

08 Dec '08

Hi, I installed lastest chimera build (1.3.2576) on 32-bit linux platform. When I ran chimera I got for following error message Traceback (most recent call last): File "/opt/sciencetools/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/opt/sciencetools/chimera/share/chimeraInit.py", line 361, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "/opt/sciencetools/chimera/share/chimera/tkgui.py", line 2520, in initializeGUI master.tk.call('tix', 'initstyle') _tkinter.TclError: expected integer but got "9.5" Can anyone help me out? P.S. I opened the tkgui.py file and comment line 2520: master.tk.call('tix', 'initstyle') Chimera start without the error and seems usable, But I am not sure if this is appropriate. Best, lithlin

2 1

Maintaining Color and Formatting Selections for New Molecules
by Eric Ganz 08 Dec '08

08 Dec '08

Now that I have formatted and colored one molecule, I would like to maintain the color and formatting selections for a series of new molecules. How should I do this?

2 1

Re: [Chimera-users] Labeling the surface representation
by Elaine Meng 08 Dec '08

08 Dec '08

Hi Mehdi, I misunderstood your question. I thought you meant the atomspec balloons that temporarily pop up when you put the mouse over the atoms, and the previous instructions apply to those. Your picture shows the regular residue labels. To show a residue label, the residue's ribbon or some of its atoms must be displayed. It is OK for the surface to also be shown, but then the problem is that the surface usually covers up the residue labels so you can't see them. You can make the surface transparent to see the labels inside (see "Actions... Surface... transparency..." in the menu or use the command "surftransparency"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surftransparency.html > If you are displaying these labels to make a figure, another suggestion is to use 2D Labels. You have to enter the text of a 2D label yourself, but you can move it to any position in the window. 2D Labels are independent of the structure and how it is displayed. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.… > Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 7, 2008, at 11:31 AM, Mehdi wrote: > Thank you for your detailed information. I could not still figure > out how to label the residues on surface representation. I have > attached the figure (for instance) showing the ribbon representation > with a few amino acids labeled but if I want to achieve the labeling > on the surface the labels,unlike the ribbon, do not appears on it. I > also followed the tutorial but the atomspec balloons were not > observed on the surface as soon as the ribbon or simple stick > representation are hided.Do I have to keep the simple bond or ribbon > representation in order to keep the atomspec balloon and labels > observable?

1 0

show CA as sphere and ribbon
by lvyuan zhang 07 Dec '08

07 Dec '08

Hi, I want show one of the CAs in a single protein chain as a sphere. But it looks like that I have to hide the ribbon to let the sphere show. Is there anyway that I can show the CA as sphere and also allow the ribbon to remain? I looked at the gallery and I didn't find anything that can help me, so here I am to ask for help from you again. Thanks first! Cheers! Luyuan

2 1

I got it.
by lvyuan zhang 07 Dec '08

07 Dec '08

I saved the CA atoms as another pdb file, and then import it, and show atoms as sphere. ________________________________ From: lvyuan zhang <gleanerly(a)yahoo.com> To: chimera-users(a)cgl.ucsf.edu Sent: Sunday, December 7, 2008 4:42:20 PM Subject: show CA as sphere and ribbon Hi, I want show one of the CAs in a single protein chain as a sphere. But it looks like that I have to hide the ribbon to let the sphere show. Is there anyway that I can show the CA as sphere and also allow the ribbon to remain? I looked at the gallery and I didn't find anything that can help me, so here I am to ask for help from you again. Thanks first! Cheers! Luyuan

1 0

Labeling the surface representation
by Mehdi 07 Dec '08

07 Dec '08

I am a new user of chimera, I would like to know how to label the residues in surface representation like the same action for ribbon! It simply works for ribbon but unfortunately I could not get it to work for surface. Mehdi

2 1

The Macromolecular Modeling Blog
by Nir London 06 Dec '08

06 Dec '08

Hi all, We've started a new blog on all that is related to Macromolecular Modeling http://rosettadesigngroup.com/blog/ We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears. On its background there is an image of a protein-protein complex I've created using chimera, can any of you suggest a nicer figure for the background ? The best image anyone will send me will be used as background (with due credits :) please check it out and tell me what you think... Cheers, Nir London. Rosetta Design Group http://rosettadesigngroup.com

5 5