Re: [PyMOL] attach_amino_acid

Kirk, Just FYI, you are outside the realm of what PyMOL has been designed to do (so far). Regardless, editor.attach_amino_acid("junk/94/C","trp") seems to work with current versions (0.99rev8 and the latest 1.00 beta code). Cheers, Warren _ From: pymol-users-boun...@lists.sourc

[PyMOL] attach_amino_acid

I'm having some trouble getting this function to work correctly. My pdb is called junk and residue 94 is the c-terminus, and I want to add a tryptophan to it- here's my input editor.attach_amino_acid('junk & resi 94 & name c', 'trp') The result is that the tryptophan is built, but it's not bonde

Re: [PyMOL] 1letter code by default

From: Warren DeLano > Andrea, > > What do you mean exactly? Hi all, sorry i realized that i didn't explain clearly my question. I was wondering if there was a possibility to put the residue labels by default in 1-letter code,let's say Q65 instead of GLN-65..doing the selection with the left but

Re: [PyMOL] selecting Na+ in pymol

Hi Warren, Actually, I tried to use select .., r. na\+ as the second option, but that didn't work for me (Pymol 0.99b on Suse 9.2). Oh, and I owe you an elaborate answer still on the mail from a while ago. But that got a bit buried.. sorry ;) Tsjerk On 2/2/07, DeLano Scientific wrote: Tsjer

[PyMOL] comparing proteins structures

Hi all! Does anyone know how to overlay two proteins structures? thanks! best Filo

Re: [PyMOL] selecting Na+ in pymol

Tsjerk & Abhinav, > Actually, it was a bit surprising to me to see you're right. + is the default list separator in selections. For example: select posi, ARG+HIS+LYS/ select backbone, n. N+CA+C+O That is why it needs to be escaped with a backslash. Commas can also be used, but only within p

Re: [PyMOL] mesure line width

Hi Andrea, * andrea carotti [2007-02-02 14:13] wrote: > Hi all, > is there the possibility to change the line width of the distance > measure between two atoms? set dash_width, 3 If you like using a white background like I do, you can also change the dash color using the "Setting... -> Color.

Re: [PyMOL] OSx X11 Pymol Clicking problem

Scott, > I have had this problem for the past few weeks, and it has been > difficult to diagnose the cause. The problem is that in the X11 version of pymol run on my mactel osx laptop does not interpret my three button mouse click properly. When I click on a given atom in the UI, it selects some

[PyMOL] mesure line width

Hi all, is there the possibility to change the line width of the distance measure between two atoms? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161

Re: [PyMOL] selecting Na+ in pymol

Hi Abhi, Actually, it was a bit surprising to me to see you're right. Now, for showing/hiding, it has been dealt with in the code, by allowing the "+" to be left out. However, for selecting (and alter_ing) that doesn't go, apparently. A workaround is to use cmd.select("selectionname","r. na\+")

[PyMOL] selecting Na+ in pymol

Hallo, I have an annoying problem. I have pdb file with Na+ atoms defined as ATOM 1 Na+ Na+53 -1.106 7.854 52.244 1.00 0.00 Na ATOM 2 Na+ Na+54 -0.106 3.854 27.244 1.00 0.00 Na ATOM 3 Na+ Na+55 1.894 -6.146 62.244 1.00 0.00 Na ATOM