[Chimera-users] Chimera-users Digest, Vol 173, Issue 3

Pu Qian p.qian at sheffield.ac.uk
Fri Sep 8 01:01:22 PDT 2017


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 at 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 at gmail.com>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] COX inhibitor demo discrepancy
> Message-ID:
>         <CAJPu8_4y4xVjZiXnT3TRXOj7XDnAtg2D7T-VuOQ7BTV3NdVteQ at 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 at gmail.com>
> To: chimera List <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] longbond command documentation?
> Message-ID: <29BB8924-AED7-44D3-BFE9-28DC159BC067 at 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 at cgl.ucsf.edu>
> To: James Starlight <jmsstarlight at gmail.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Batch mode for Chimera
> Message-ID: <4A3C046E-DA20-434A-9F9A-623C1758991E at 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 at 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 at cgl.ucsf.edu>
> To: simon chapman <rowanlodge19 at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] COX inhibitor demo discrepancy
> Message-ID: <DFA62C64-630F-4DE6-A8F5-7FD42A817CF6 at 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 at 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 at cgl.ucsf.edu>
> To: Oliver Clarke <olibclarke at gmail.com>
> Cc: chimera List <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] longbond command documentation?
> Message-ID: <D4814C99-18C0-4C26-9B73-3EC30A6C2ABE at 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 at 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 at gmail.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] COX inhibitor demo discrepancy
> Message-ID:
>         <CAJPu8_4B=RaPhocqX6nVuGA5=egcMxUAeixBx2cu7sx80qRXVw at mail.gm
> ail.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 at 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 at 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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