[PyMOL] naming of chain id

I have a protein which contains 32 chains. By using A-Z can only name 26 chains. Can I use expression containing two character such as A1, AB, etc. to as chain id? Will this change the format of the pdb files? Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -

[PyMOL] cartoon and line representation

Dear all I want to display structures which contains numerous chains such as viruses in pymol. I find these sturctures can be displayed normally as line representation. However, when I show them as cartoon, usually only one chain can be displayed, and usually it is cartoon loop rather than the n

Re: [PyMOL] Installation problem

Hi Peter, we haven't seen this problem before, can you give us some details about your setup? Is this on Windows 8? Thanks, Thomas On 29 Aug 2014, at 14:11, Peter Kahn wrote: > Dear All: > > Help! > Re-installing Pymol 1.7.0.5 after uninstalling failed with the following > error: > "Pymol

Re: [PyMOL] cartoon and line representation

Hi Yeping - I’m unable to reproduce the behavior you’re seeing—using your commands in Open Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon. What version of PyMOL are you using? You could also try using the `all_states` setting instead: fetch 3j2v, type=pdb1, async

[PyMOL] python script to define an extra pymol function and then use it during the same session

Dear Pymol mailing list, I am facing a problem with some python scripting involving pymol... I have a python script which adds a new function to pymol (align_all_to_all.py that I found on pymolwiki). I added some features to it so that it can load pdbs and thus automate the calculations. Whene

Re: [PyMOL] python script to define an extra pymol function and then use it during the same session

Hi, When you call cmd.extend(), it does not add the function to pymol.cmd. Just call it directly: Change pymol.cmd.align_all_to_all() to align_all_to_all() You may need to import it if you haven't already (and make sure it is in the PYTHONPATH). HTH, Matt Baumgartner On 09/02/2014 10:38 AM

[PyMOL] re： cartoon and line representation

Dear Jared,I am using  Open Source PyMOL 1.6.0.0. If you save the whole virus structure as a single pdb file, and reload it into pymol and then show it as cartoon, can you still display the whole structure? As for me, it can display only one chain shown as cartoon_loop.Best regards. Yeping Sun

Re: [PyMOL] re： cartoon and line representation

Hi Yeping - Yes, I can. But there is one additional requirement: to save all the states, you must add a `state=0` keyword argument to the save command to include all states. Otherwise, the default is `state=-1`, which includes only the current state. http://www.pymolwiki.org/index.php/Save