Dear Chimera developers,

I'm using Chimera to estimate molecular weight from cryo-em map through volume viewer/tools/measure volume and area/
The value of the volume I got is in e3 unit. What dies this e3 mean. This e3 unit is used for area as well, which confused me. 
The version I'm using is 1.12. 
It seems that the e3 equals nm3, but I'm not sure. It would be a great appreciated if you could help me to make it clear. Thanks

Best regards

Qian



On 7 September 2017 at 16:44, <chimera-users-request@cgl.ucsf.edu> wrote:
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Today's Topics:

   1. COX inhibitor demo discrepancy (simon chapman)
   2. longbond command documentation? (Oliver Clarke)
   3. Re: Batch mode for Chimera (Elaine Meng)
   4. Re: COX inhibitor demo discrepancy (Elaine Meng)
   5. Re: longbond command documentation? (Elaine Meng)
   6. Re: COX inhibitor demo discrepancy (simon chapman)


----------------------------------------------------------------------

Message: 1
Date: Wed, 6 Sep 2017 12:17:56 +0100
From: simon chapman <rowanlodge19@gmail.com>
To: chimera-users@cgl.ucsf.edu
Subject: [Chimera-users] COX inhibitor demo discrepancy
Message-ID:
        <CAJPu8_4y4xVjZiXnT3TRXOj7XDnAtg2D7T-VuOQ7BTV3NdVteQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi, I'm very impressed with Chimera as  a user of only 3 weeks so far

Trying out the various facilities has been a very useful exercise for
completing my Masters in MedChem.

However, when I emulated  the tutorial covering COX 1 and 2 inhibition,
inputting the molecules fluribrofen and SC558 I generated via DS Visualiser
bind at the outside edge of  the enzymes. Not centrally as displayed in the
video.

I also noted the molecular data in  ViewDock, ie: energies etc, is missing.
The table is blank other than the molecule number. Selecting 'Column' etc
has no effect. The 'H-bonds' option does display however.

I've probably done something  wrong, hey ho...but can you enlighten me?

Best wishes   Simon
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Message: 2
Date: Wed, 06 Sep 2017 11:45:18 -0400
From: Oliver Clarke <olibclarke@gmail.com>
To: chimera List <chimera-users@cgl.ucsf.edu>
Subject: [Chimera-users] longbond command documentation?
Message-ID: <29BB8924-AED7-44D3-BFE9-28DC159BC067@gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi,



I want to use the longbond command to clean up display of a PDB file which has some ugly bits ? missing TER cards etc - and which hence has unphysical bonds displayed.



According to the manual `longbond` should be the command to use, but it doesn?t seem to work ? it just displays and undisplays pseudobonds.



If I attempt to use arguments as described in the docs, I get a message saying that longbond no longer takes arguments. Is there an updated description of this command? Or another command that does what longbond used to do?



Cheers

Oli



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Message: 3
Date: Wed, 6 Sep 2017 09:34:51 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
To: James Starlight <jmsstarlight@gmail.com>
Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Batch mode for Chimera
Message-ID: <4A3C046E-DA20-434A-9F9A-623C1758991E@cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

Hi Gleb,
Yes, but then you don?t know which one of those commands might show the graphics driver problem!  I guess you can experiment with which parts will work.  The descriptions of the presets say what they include:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/preset.html>

Then you can identify individual commands to do those things. Most of the stuff is in the ?set? command, see
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html>

Publication preset 2 includes white background and silhouette edges, commands:

set bgcol white
set silhouette

It also turns off depth-cueing (mist):

~set depth

? and changes to ?licorice? style ribbons (which doesn?t show helix and strand differently):

ribscale licorice

You might also be interested in other ?set? options  (see link above), and ?lighting?:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/lighting.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 6, 2017, at 12:49 AM, James Starlight <jmsstarlight@gmail.com> wrote:
>
> Thank you, Elaine!
>
> Regarding presets
> Is it possible to define step-by-step some commands to obtain
> something like preset 2 visualization state?
>
> Gleb




------------------------------

Message: 4
Date: Wed, 6 Sep 2017 09:59:25 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
To: simon chapman <rowanlodge19@gmail.com>
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] COX inhibitor demo discrepancy
Message-ID: <DFA62C64-630F-4DE6-A8F5-7FD42A817CF6@cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

HI Simon,
We?re glad Chimera has been helpful in your studies!

The COX inhibitors demo (under Tools? Demos in the menu) just uses some structures from RCSB PDB that already have the small molecules in the correct locations relative to the protein structures.  It?s not really a tutorial (it doesn?t tell you how to do anything) but a series of actions in Chimera that show you parts of these existing structures.  The Credits panel of that demo says which PDB entries were used:  1cqe (COX-1 with flurbiprofen) and 6cox (COX-2 with SC-558).  So if you just start Chimera and use command ?open 1cqe? for example, it will show the COX-1 complex structure.  1cqe and 6cox each contain a homodimer (two copies of the protein+ligand), but for simplicity in the demos, only monomers were shown.

I don?t know where you got the structures you opened, so the coordinates might be completely different.  I.e., maybe what you see is where DSV put the small molecules.  Also ViewDock will only display energies if what you read in to ViewDock is (1) a format that VIewDock knows, and (2) actually includes those energies.  Chimera doesn?t calculate them for you.  I have no idea what you opened in ViewDock.  Its manual page lists the types of docking outputs that it knows how to read, like from the programs DOCK, Glide, AutoDock, GOLD, etc.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

There is a ViewDock tutorial that includes sample input from DOCK:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

If you meant you tried the Autodock Vina interface in Chimera and it didn?t put the small molecules in the right place, that is the way of docking calculations. There are a lot of docking parameters and setup options and sometimes adjusting those will get the right answer, or simply sampling more orientations.  Unfortunately the interface in Chimera uses a web service that doesn?t allow very much sampling.  To do a thorough docking study, you might have to obtain a docking program and run it separately from Chimera.

However, no need to do docking for these particular molecules because the structures of the complexes are already known and publicly available from the PDB!

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 6, 2017, at 4:17 AM, simon chapman <rowanlodge19@gmail.com> wrote:
>
> Hi, I'm very impressed with Chimera as  a user of only 3 weeks so far
>
> Trying out the various facilities has been a very useful exercise for completing my Masters in MedChem.
>
> However, when I emulated  the tutorial covering COX 1 and 2 inhibition, inputting the molecules fluribrofen and SC558 I generated via DS Visualiser bind at the outside edge of  the enzymes. Not centrally as displayed in the video.
>
> I also noted the molecular data in  ViewDock, ie: energies etc, is missing. The table is blank other than the molecule number. Selecting 'Column' etc has no effect. The 'H-bonds' option does display however.
>
> I've probably done something  wrong, hey ho...but can you enlighten me?
>
> Best wishes   Simon




------------------------------

Message: 5
Date: Wed, 6 Sep 2017 10:14:49 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
To: Oliver Clarke <olibclarke@gmail.com>
Cc: chimera List <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] longbond command documentation?
Message-ID: <D4814C99-18C0-4C26-9B73-3EC30A6C2ABE@cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

Hi Oli,
The longbond documentation is up to date ? namely, our expectation is that when TER cards are missing, then pseudobonds (not bonds) are generated and shown in Chimera.  However, there may be something specific about your structure, or another issue I?ve seen is that when I?ve hidden some backbone atoms (not missing in my case), the autochaining can make some ugly long bonds.  So besides

~longbond

to hide missing-segment pseudobonds, you might also try turning autochaining off for the model:

setattr m autochain 0

This molecule model attribute is also listed in the Selection Inspector GUI.  Other than that, the only other idea is to individually specify/delete the bonds you don?t want with the command ~bond or in the Build Structure GUI, Adjust Bonds "delete selected bonds" option.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 6, 2017, at 8:45 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
>
> Hi,
> I want to use the longbond command to clean up display of a PDB file which has some ugly bits ? missing TER cards etc - and which hence has unphysical bonds displayed.
>
> According to the manual `longbond` should be the command to use, but it doesn?t seem to work ? it just displays and undisplays pseudobonds.
>
> If I attempt to use arguments as described in the docs, I get a message saying that longbond no longer takes arguments. Is there an updated description of this command? Or another command that does what longbond used to do?
> Cheers
> Oli




------------------------------

Message: 6
Date: Thu, 7 Sep 2017 10:17:45 +0100
From: simon chapman <rowanlodge19@gmail.com>
To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] COX inhibitor demo discrepancy
Message-ID:
        <CAJPu8_4B=RaPhocqX6nVuGA5=egcMxUAeixBx2cu7sx80qRXVw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Very kind Elaine. Thank you. I'll follow up your comments. Hope I don't
have to bother you too much again, but there will probably be occasions
when I hit a brick wall...

It's all a part of the learning process!!

Best wishes    Simon

On 6 September 2017 at 17:59, Elaine Meng <meng@cgl.ucsf.edu> wrote:

> HI Simon,
> We?re glad Chimera has been helpful in your studies!
>
> The COX inhibitors demo (under Tools? Demos in the menu) just uses some
> structures from RCSB PDB that already have the small molecules in the
> correct locations relative to the protein structures.  It?s not really a
> tutorial (it doesn?t tell you how to do anything) but a series of actions
> in Chimera that show you parts of these existing structures.  The Credits
> panel of that demo says which PDB entries were used:  1cqe (COX-1 with
> flurbiprofen) and 6cox (COX-2 with SC-558).  So if you just start Chimera
> and use command ?open 1cqe? for example, it will show the COX-1 complex
> structure.  1cqe and 6cox each contain a homodimer (two copies of the
> protein+ligand), but for simplicity in the demos, only monomers were shown.
>
> I don?t know where you got the structures you opened, so the coordinates
> might be completely different.  I.e., maybe what you see is where DSV put
> the small molecules.  Also ViewDock will only display energies if what you
> read in to ViewDock is (1) a format that VIewDock knows, and (2) actually
> includes those energies.  Chimera doesn?t calculate them for you.  I have
> no idea what you opened in ViewDock.  Its manual page lists the types of
> docking outputs that it knows how to read, like from the programs DOCK,
> Glide, AutoDock, GOLD, etc.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/
> framevd.html>
>
> There is a ViewDock tutorial that includes sample input from DOCK:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>
>
> If you meant you tried the Autodock Vina interface in Chimera and it
> didn?t put the small molecules in the right place, that is the way of
> docking calculations. There are a lot of docking parameters and setup
> options and sometimes adjusting those will get the right answer, or simply
> sampling more orientations.  Unfortunately the interface in Chimera uses a
> web service that doesn?t allow very much sampling.  To do a thorough
> docking study, you might have to obtain a docking program and run it
> separately from Chimera.
>
> However, no need to do docking for these particular molecules because the
> structures of the complexes are already known and publicly available from
> the PDB!
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Sep 6, 2017, at 4:17 AM, simon chapman <rowanlodge19@gmail.com>
> wrote:
> >
> > Hi, I'm very impressed with Chimera as  a user of only 3 weeks so far
> >
> > Trying out the various facilities has been a very useful exercise for
> completing my Masters in MedChem.
> >
> > However, when I emulated  the tutorial covering COX 1 and 2 inhibition,
> inputting the molecules fluribrofen and SC558 I generated via DS Visualiser
> bind at the outside edge of  the enzymes. Not centrally as displayed in the
> video.
> >
> > I also noted the molecular data in  ViewDock, ie: energies etc, is
> missing. The table is blank other than the molecule number. Selecting
> 'Column' etc has no effect. The 'H-bonds' option does display however.
> >
> > I've probably done something  wrong, hey ho...but can you enlighten me?
> >
> > Best wishes   Simon
>
>
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