[chimerax-users] saving PDB

[Elaine Meng]

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 at 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 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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> > 
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