Hello,
I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Hi Heather, It is hard to understand your message... it reads like Ulysses. But maybe I'm just tired.
First you say the structures aren't saved, but then you say they open how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained here... it doesn't have anything to do with matchmaker: https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Morning Heather
I am not apart of the chimera crew but sometimes I when files don't open (via the command line) its because the name contains spaces. change: why wont you open 2.pdb to whywontyouopen2.pdb
This could explain why you can both open (via the open>name.pdb in the menu) and not in the command line
Good luck.
Kako
----- Original Message -----
From: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu To: "Noriega, Heather" heather.noriega@bison.howard.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Date: 2021-11-11 11:33:47 Subject: Re: [chimerax-users] saving PDB
Hi Heather, It is hard to understand your message... it reads like Ulysses. But maybe I'm just tired.
First you say the structures aren't saved, but then you say they open how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained here... it doesn't have anything to do with matchmaker: https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hello Elaine,
I am sorry it came out like Ulysses. They do save, I was just trying to explain I have tried multiple saving options. The saved PDB do not open in ChimeraX. I have attached one of the saved PDB that will not open in ChimeraX. I would like it to open in ChimeraX.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021 at 9:33 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Heather, It is hard to understand your message... it reads like Ulysses. But maybe I'm just tired.
First you say the structures aren't saved, but then you say they open how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained here... it doesn't have anything to do with matchmaker: https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am going to attach my command line. OK, so I created a specific capsid
that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs"
format session
Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models
#2-61 displayedOnly true relModel #1
close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs"
format session
Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models
#2-61 selectedOnly true
close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format
pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Heather, There are no atomic coordinates in that PDB file. It has lines in it but they are just the information lines that are typically in the top part of a PDB file, no lines with ATOM in them. E.g. as if you chose "selected only" option while saving when there were no atoms selected. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 7:04 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Elaine,
I am sorry it came out like Ulysses. They do save, I was just trying to explain I have tried multiple saving options. The saved PDB do not open in ChimeraX. I have attached one of the saved PDB that will not open in ChimeraX. I would like it to open in ChimeraX.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021 at 9:33 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, It is hard to understand your message... it reads like Ulysses. But maybe I'm just tired.
First you say the structures aren't saved, but then you say they open how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained here... it doesn't have anything to do with matchmaker: https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<AAV 3B 1-1-8.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you Elaine. It does, I think I need rest too.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021, 10:10 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Heather, There are no atomic coordinates in that PDB file. It has lines in it but they are just the information lines that are typically in the top part of a PDB file, no lines with ATOM in them. E.g. as if you chose "selected only" option while saving when there were no atoms selected. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 7:04 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello Elaine,
I am sorry it came out like Ulysses. They do save, I was just trying to
explain I have tried multiple saving options. The saved PDB do not open in ChimeraX. I have attached one of the saved PDB that will not open in ChimeraX. I would like it to open in ChimeraX.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021 at 9:33 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, It is hard to understand your message... it reads like Ulysses. But
maybe I'm just tired.
First you say the structures aren't saved, but then you say they open
how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained here...
it doesn't have anything to do with matchmaker:
https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are
hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am going to attach my command line. OK, so I created a specific
capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights
reserved.
open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs"
format session
Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models
#2-61 displayedOnly true relModel #1
close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format
pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights
reserved.
open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs"
format session
Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models
#2-61 selectedOnly true
close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format
pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<AAV 3B 1-1-8.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
A few more thoughts:
(1) when using "sym" make sure to use the "copies true" option so that the copies will actually have atoms, as suggested in our previous answers to you: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002862.html https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002873.html
(2) the "selected only" and "displayed only" save options allow omitting some of the atoms from the PDB file output. If you don't want to omit any atoms, do not use these options.
(3) If the atoms are already present in your ChimeraX session, you don't really need to save a PDB file, you could just use "molmap" on them directly, as in Tom's example: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002873.html
Best, Elaine
On Nov 10, 2021, at 7:20 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thank you Elaine. It does, I think I need rest too.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021, 10:10 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, There are no atomic coordinates in that PDB file. It has lines in it but they are just the information lines that are typically in the top part of a PDB file, no lines with ATOM in them. E.g. as if you chose "selected only" option while saving when there were no atoms selected. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 7:04 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Elaine,
I am sorry it came out like Ulysses. They do save, I was just trying to explain I have tried multiple saving options. The saved PDB do not open in ChimeraX. I have attached one of the saved PDB that will not open in ChimeraX. I would like it to open in ChimeraX.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021 at 9:33 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, It is hard to understand your message... it reads like Ulysses. But maybe I'm just tired.
First you say the structures aren't saved, but then you say they open how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained here... it doesn't have anything to do with matchmaker: https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<AAV 3B 1-1-8.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Ok, I appreciate it.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Thu, Nov 11, 2021, 1:37 PM Elaine Meng meng@cgl.ucsf.edu wrote:
A few more thoughts:
(1) when using "sym" make sure to use the "copies true" option so that the copies will actually have atoms, as suggested in our previous answers to you: < https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002862.html
< https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002873.html
(2) the "selected only" and "displayed only" save options allow omitting some of the atoms from the PDB file output. If you don't want to omit any atoms, do not use these options.
(3) If the atoms are already present in your ChimeraX session, you don't really need to save a PDB file, you could just use "molmap" on them directly, as in Tom's example: < https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002873.html
Best, Elaine
On Nov 10, 2021, at 7:20 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine. It does, I think I need rest too.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021, 10:10 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, There are no atomic coordinates in that PDB file. It has lines in it
but they are just the information lines that are typically in the top part of a PDB file, no lines with ATOM in them. E.g. as if you chose "selected only" option while saving when there were no atoms selected.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 7:04 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello Elaine,
I am sorry it came out like Ulysses. They do save, I was just trying
to explain I have tried multiple saving options. The saved PDB do not open in ChimeraX. I have attached one of the saved PDB that will not open in ChimeraX. I would like it to open in ChimeraX.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Wed, Nov 10, 2021 at 9:33 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, It is hard to understand your message... it reads like Ulysses. But
maybe I'm just tired.
First you say the structures aren't saved, but then you say they open
how you want them to in Chimera, which suggests the atomic coordinates are actually saved. It is impossible to tell without having the PDB file to examine. Even if you did send that file, I may not be able to tell whether it contains what you wanted it to contain.
Selection is what is shown with a green outline and is explained
here... it doesn't have anything to do with matchmaker:
https://rbvi.ucsf.edu/chimerax/docs/user/selection.html
Displayed means that the atoms are displayed. So if some atoms are
hidden and you choose "displayed only" to be saved, the hidden atoms will not be saved.
Sorry, that's all I can think of to say. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 10, 2021, at 6:13 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am going to attach my command line. OK, so I created a specific
capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night.
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights
reserved.
open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs"
format session
Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models
#2-61 displayedOnly true relModel #1
close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format
pdb
UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights
reserved.
open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs"
format session
Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb"
models #2-61 selectedOnly true
close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb"
format pdb
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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participants (3)
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Elaine Meng -
Noriega, Heather -
Stapleton kevin2017/4/3