[chimerax-users] saving PDB

[Noriega, Heather]

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 at bison.howard.edu
520-203-1883

On Wed, Nov 10, 2021, 10:10 PM Elaine Meng <meng at 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 at 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 at bison.howard.edu
> > 520-203-1883
> >
> >
> > On Wed, Nov 10, 2021 at 9:33 PM Elaine Meng <meng at 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 at 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 at bison.howard.edu
> > > 520-203-1883
> > > _______________________________________________
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> >
> > <AAV 3B 1-1-8.pdb>_______________________________________________
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