Removing lonbond links from pipes-and-planks representation
Hi,
I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them.
Any help would be appreciated.
Phil
Hi Phil, The pipes-and-planks uses the chain connectivity, i.e. even though the residues are not directly connected, it "knows" they are in the same chain even when you've hidden those pseudobonds. So it is both smart and dumb. The (unfortunately somewhat inconvenient) way I know to prevent this is to text-edit the PDB file to add TER where you want the chain to physically break.
So for example, when I text-edit the PDB file for 1www and search for "MISSING" in the header lines, it shows me that the missing residues are 61-66 and 116-120 of chains V and W. So after residue 60 of chain V I insert a line that starts with TER, and do the same in 3 other places I want to physically break the protein chains. Here's how it looks for the first break:
[... stuff...] ATOM 467 CG ASP V 60 29.107 14.379 9.122 1.00 68.51 C ATOM 468 OD1 ASP V 60 29.745 14.288 8.052 1.00 73.84 O ATOM 469 OD2 ASP V 60 28.553 15.428 9.514 1.00 72.86 O TER ATOM 470 N GLY V 67 34.579 5.809 0.953 1.00 34.66 N ATOM 471 CA GLY V 67 33.800 4.556 0.891 1.00 33.58 C ATOM 472 C GLY V 67 33.603 3.934 2.260 1.00 36.60 C [... more stuff...]
Then reopen the file that you just edited and then recalculate pipes and planks.
If it is mainly the cylindrical representation of the helices that you like, you might want to take a look at using ChimeraX instead of Chimera, where tube-style helices are integrated with ribbons and can be turned on easily -- my 1www example used above doesn't have helices but another example with both helices and missing segments is 1hzx. E.g. the following ChimeraX commands where #1.2 is the "missing structure" mode with the longbondsl. Unlike Chimera, ChimeraX actually lists this model in the model panel (if you expand #1 with disclosure triangle) so you can look in that panel to see what model number it is.
open 1hzx preset cylinders hide #1.2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2023, at 12:48 PM, philip.robinson--- via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them. Any help would be appreciated. Phil
Hi Elaine,
Many thanks for the workaround – that worked great for me.
Cheers, Phil
From: Elaine Meng meng@cgl.ucsf.edu Reply-To: "chimera-users@cgl.ucsf.edu List" chimera-users@cgl.ucsf.edu Date: Thursday, 29 June 2023 at 21:27 To: "Philip Robinson (Staff)" philip.robinson@bbk.ac.uk Cc: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Removing lonbond links from pipes-and-planks representation
Hi Phil, The pipes-and-planks uses the chain connectivity, i.e. even though the residues are not directly connected, it "knows" they are in the same chain even when you've hidden those pseudobonds. So it is both smart and dumb. The (unfortunately somewhat inconvenient) way I know to prevent this is to text-edit the PDB file to add TER where you want the chain to physically break.
So for example, when I text-edit the PDB file for 1www and search for "MISSING" in the header lines, it shows me that the missing residues are 61-66 and 116-120 of chains V and W. So after residue 60 of chain V I insert a line that starts with TER, and do the same in 3 other places I want to physically break the protein chains. Here's how it looks for the first break:
[... stuff...] ATOM 467 CG ASP V 60 29.107 14.379 9.122 1.00 68.51 C ATOM 468 OD1 ASP V 60 29.745 14.288 8.052 1.00 73.84 O ATOM 469 OD2 ASP V 60 28.553 15.428 9.514 1.00 72.86 O TER ATOM 470 N GLY V 67 34.579 5.809 0.953 1.00 34.66 N ATOM 471 CA GLY V 67 33.800 4.556 0.891 1.00 33.58 C ATOM 472 C GLY V 67 33.603 3.934 2.260 1.00 36.60 C [... more stuff...]
Then reopen the file that you just edited and then recalculate pipes and planks.
If it is mainly the cylindrical representation of the helices that you like, you might want to take a look at using ChimeraX instead of Chimera, where tube-style helices are integrated with ribbons and can be turned on easily -- my 1www example used above doesn't have helices but another example with both helices and missing segments is 1hzx. E.g. the following ChimeraX commands where #1.2 is the "missing structure" mode with the longbondsl. Unlike Chimera, ChimeraX actually lists this model in the model panel (if you expand #1 with disclosure triangle) so you can look in that panel to see what model number it is.
open 1hzx preset cylinders hide #1.2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2023, at 12:48 PM, philip.robinson--- via Chimera-users <chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu> wrote:
Hi, I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them. Any help would be appreciated. Phil
participants (3)
-
Elaine Meng -
Philip Robinson (Staff) -
philip.robinson＠bbk.ac.uk