Hi Elaine, The problem I have is actually not whith chimera. itself. I can display all the models etc nicely within it. However, I want to make now a PDB file of a multi-protein complex in a format that can be deposited in the PDB database. Then I run into problems if the models are separated by Model ENDMDL lines or have chains with the same letter identifier. I was hoping to be able to generate a multi-protein PDB file from my chimera fitting without having to manually edit a lot of lines in the multimodel PDB file. Any suggestions on how to best do this would be appreciated. Thanks Hernando Elaine Meng wrote:

Hi Hernando, Sorry, Chimera does not have an option for changing chain IDs.

However, in Chimera I find it more convenient to work with structures read as multiple models as opposed to multiple chains in a single model:

- you can easily toggle which are shown and which are active (movable with the mouse) using the Model Panel http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html

- you can move one relative to another, whereas you cannot move one chain relative to another chain in the same model

- just like different chains, you can specify them independently in commands, rainbow-color to give each its own color, etc. In commands, the different models read from a single PDB file are specified as #0.1, #0.2, ... (and residues within them specified using something like #0.1:23,350-355 ) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarc...

- further, each model can include several of its own chains, and it is OK if another model in the same file also uses the same chain IDs, as they are still distinguishable (#0.1:23.a is different than #0.2:23.a)

Now I'm actually disappointed when a Web server gives me multiple models as different chains in a single model, because it is less convenient.

I do agree there may be situations in which you want the models as different chains, such as for input to another program, but currently Chimera does not include that type of editing. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

-- ----------------------------------- 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@aecom.yu.edu -----------------------------------

Hi Hernando, As mentioned you can't do it in Chimera. You would need to find some other program or server that does it (unfortunately I don't know of any ... other chimera-users, opinions?) or just write a script. Depending on how robust to different types of input it must be, the script could be fairly simple. I attach a little fortran program 'multichain.f' I just whipped up. If you are on some unix-type computer with a fortran compiler, you could just compile it with something like f77 multichain.f -o multichain then just enter multichain or whatever you called the executable at the command line, and it would prompt you for input and output file names. Disclaimers: This program worked fine on the one NMR ensemble I tested it on, but I did not test it comprehensively. It is pretty simple and does not change any atom or residue numbers, and does not add SEQRES, so if you need that stuff you would need to use something else. I only provided for up to 26 chains because I couldn't remember what IDs aresupposed be used after that, but it could easily be modified to accommodate more chains. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 31, 2008, at 6:54 AM, hsosa@aecom.yu.edu wrote:

Hi Elaine,

The problem I have is actually not whith chimera. itself. I can display all the models etc nicely within it. However, I want to make now a PDB file of a multi-protein complex in a format that can be deposited in the PDB database. Then I run into problems if the models are separated by Model ENDMDL lines or have chains with the same letter identifier. I was hoping to be able to generate a multi-protein PDB file from my chimera fitting without having to manually edit a lot of lines in the multimodel PDB file. Any suggestions on how to best do this would be appreciated.

Thanks

Hernando

Elaine Meng wrote:

...

Hi Hernando, Sorry, Chimera does not have an option for changing chain IDs.

However, in Chimera I find it more convenient to work with structures read as multiple models as opposed to multiple chains in a single model:

While it is likely a driver problem, it may be possible to avoid the issue in subsequent uses of Chimera by turning off the multisampling option. In "Effects" (under Tools... Viewing Controls) set "multisampling" to false and click Save. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects Then later uses of Chimera might not give the error. There is also a Chimera startup option --nomultisample but on Windows it is more work to use startup options... http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#multisample Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Sun, 31 Aug 2008, hsosa@aecom.yu.edu wrote:

...

I just installed the latest production release version of chimera on laptop running Vista and got the following message when starting chimera:

Unable to run multisampling. Graphics hardware support request, but cannot switch while maintaining display data

I can run the program after clicking the OK button in the above message but then I cannot exit chimera.

Any idea of what is going on ?

When you get a mysterious bug with chimera, we really wish that you would submit the bug with chimera's Report a Bug dialog (in the help menu). The bug report tells us more about the configuration of your computer and then we can tailor the response appropriately. So what follows is a generic answer.

Your bug appears to be an immature graphics driver. The best solution would be to upgrade your graphics driver. And ideally you would get a newer graphics driver from the laptop vendor's website, because they often customize the drivers for their hardware, but the laptop vendor's rarely update the drivers (unlike NVidia and ATI/AMD which update their desktop drivers every month), so you may need to get a newer one from the graphics manufacturer. In particular, if you have Intel graphics, get a newer driver from <http://downloadcenter.intel.com/>.

Greg Couch UCSF Computer Graphics Lab