From yasser.almeida at gmail.com  Thu Oct  1 01:21:28 2015
From: yasser.almeida at gmail.com (=?UTF-8?Q?Yasser_Almeida_Hern=c3=a1ndez?=)
Date: Thu, 1 Oct 2015 10:21:28 +0200
Subject: [Chimera-users] Angle between pseudobond and principal axis
Message-ID: <560CED08.2010201@gmail.com>

Hi all,

I want to measure the angle between a pseudobond and the X, Y, Z axis. 
How can I do so?

Best

Yasser


From olibclarke at gmail.com  Thu Oct  1 06:35:34 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 1 Oct 2015 09:35:34 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
Message-ID: <CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>

Just tried out the new daily build and the command line history
autofiltering works great, thanks Eric! This makes it much easier to cycle
through previous selection commands, or to remember syntax for previous vop
commands.

Cheers,
Oliver.

On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> That sounds great, thanks Eric! I look forward to trying it out, think
> it'll be a real timesaver!
>
> Cheers,
> Oli.
>
> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Oliver,
>>         This seems like a useful suggestion.  I have implemented it in a
>> slightly different form.  If you use the shift key while navigating the
>> command history (i.e. shift up/down arrow or control-N/P), then it will
>> jump to the next history entry that matches the current command name.
>> Available in the next daily build.
>>
>> ?Eric
>>
>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com>
>> wrote:
>> >
>> > Hi all,
>> >
>> > Just a suggestion (I guess for chimera 2) - would it be possible to
>> autofilter the command history based on the typed substring?
>> >
>> > That is if I have typed ?sel? and hit the up arrow, to only cycle
>> through those commands in the history that start with ?sel?.
>> >
>> > This would be particularly handy for scrolling quickly through recent
>> ?sel? and ?color? commands - a similar mechanism is implemented in several
>> shells and it works well.
>> >
>> > Cheers,
>> > Oliver.
>> > _______________________________________________
>> > Chimera-users mailing list
>> > Chimera-users at cgl.ucsf.edu
>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> >
>>
>>
>
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From meng at cgl.ucsf.edu  Thu Oct  1 10:09:33 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 1 Oct 2015 10:09:33 -0700
Subject: [Chimera-users] Angle between pseudobond and principal axis
In-Reply-To: <560CED08.2010201@gmail.com>
References: <560CED08.2010201@gmail.com>
Message-ID: <CAE08533-B626-41EF-8140-E8092DD210E7@cgl.ucsf.edu>

Hi Yasser,
You could use Axes/Planes/Centroids (or command ?define?) to define axes and then measure angles between them.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

For example, 
(1) select the two atoms on the end of the pseudobond and then use the Axes/Planes/Centroids tool (in menu under Tools? Structure Analysis) to define an axis from the selected atoms (remember to uncheck ?Replace existing axes? if you want to keep any axes you already have).  Or, instead use the command:

define axis sel

Either way, the Axis/Planes/Centroids table of objects will then list the axis and it will be shown as a cylinder in the main window.

(2) define other axes that you want to measure angles with.  If you really mean just the X, Y, Z coordinate axes, I?ve attached a little PDB file ?axes.pdb? of fake atoms for which you could define these axes with commands after you opened that file:

define axis name X @x1,x2
define axis name Y @x1,x3
define axis name Z @x1,x4

(3) then choose with the mouse (click, Ctrl-click) any pair of axes in the table of objects, and the crossing angle will be reported at the bottom of the dialog.  You could also use the ?angle? command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

If you instead meant the principal axes of some other set of atoms, you could use Axes/Planes/Centroids or the ?define? command to define a measurement-friendly first eigenvector (major axis) for that set of atoms.  However, this approach does not give second or third principal axes, only the first.

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

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> On Oct 1, 2015, at 1:21 AM, Yasser Almeida Hern?ndez <yasser.almeida at gmail.com> wrote:
> 
> Hi all,
> 
> I want to measure the angle between a pseudobond and the X, Y, Z axis. How can I do so?
> 
> Best
> 
> Yasser
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


From pett at cgl.ucsf.edu  Thu Oct  1 12:31:45 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 1 Oct 2015 12:31:45 -0700
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
Message-ID: <1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>

I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
> 
> Cheers,
> Oliver.
> 
> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
> 
> Cheers,
> Oli.
> 
> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi Oliver,
>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
> 
> ?Eric
> 
> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
> >
> > Hi all,
> >
> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
> >
> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
> >
> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
> >
> > Cheers,
> > Oliver.
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> >
> 
> 
> 

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From olibclarke at gmail.com  Thu Oct  1 14:37:37 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 1 Oct 2015 17:37:37 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
	<1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
Message-ID: <431439B0-E8A9-4C0D-A683-F0CB49DDB3DA@gmail.com>

That sounds great Eric, those two modifications combined will make finding and repeating old commands much easier!

Oliver.
> On Oct 1, 2015, at 3:31 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
>> 
>> Cheers,
>> Oliver.
>> 
>> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
>> 
>> Cheers,
>> Oli.
>> 
>> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> Hi Oliver,
>>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
>> 
>> ?Eric
>> 
>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> >
>> > Hi all,
>> >
>> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
>> >
>> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
>> >
>> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
>> >
>> > Cheers,
>> > Oliver.
>> > _______________________________________________
>> > Chimera-users mailing list
>> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> >
>> 
>> 
>> 
> 

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From skere at lf1.cuni.cz  Fri Oct  2 06:21:20 2015
From: skere at lf1.cuni.cz (Dr Kereiche)
Date: Fri, 2 Oct 2015 15:21:20 +0200
Subject: [Chimera-users] Morphs
In-Reply-To: <8FFC6CAE-784A-446D-833E-C8A982255366@cgl.ucsf.edu>
References: <564BCC60-7853-45CC-9C35-37CF5B548C65@lf1.cuni.cz>
	<8FFC6CAE-784A-446D-833E-C8A982255366@cgl.ucsf.edu>
Message-ID: <6F1B60DB-B48B-409A-AA3C-5D1758147AAA@lf1.cuni.cz>

Dear Elaine,

thank you for your quick reply. 
I had a bit of struggle and some points are still unclear to me but it works finally. Thus I could make the movie.

Again thank you 

have nice week end

Sami 

On Sep 30, 2015, at 7:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Sami,
> Yes, you can play a map morph and molecule morph at the same time, and you can play them both back and forth as you wish.  It requires using Chimera commands instead of the GUIs, however.  For more information please see this previous post and links therein:
> 
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008752.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Sep 29, 2015, at 11:54 PM, Dr Kereiche <skere at lf1.cuni.cz> wrote:
> 
>> Dear Chimera team,
>> 
>> lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. 
>> To make it clearer, I  hope, 
>> I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly.
>> I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) ,  using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command.
>> Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. 
>> Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth?
>> 
>> Thank you in advance, 
>> Sincerely 
>> Sami
> 




From anfelvas at gmail.com  Fri Oct  2 07:49:23 2015
From: anfelvas at gmail.com (Felipe Vasquez)
Date: Fri, 2 Oct 2015 09:49:23 -0500
Subject: [Chimera-users] Problems detecting h-bonds
Message-ID: <CAPGHGYNd9wjfp4nCsr=XzcaTsVFXjiawzDOZSHQPTArm5tdQaA@mail.gmail.com>

Hi,

I have recently obtained some docking results (I have a complex) and I am
trying to detect any protein-ligand h-bonds. Soon, I faced a first problem
when I obtain this error message: "More than 2 coplanar positions
specified!", and I think I solved it once my ligand was selected and I
enter into the command line: "setattr a idatmType sel". However, I obtained
later an entire panel (with a big list in it) asking me to indicate the
expetd geometries and number of substituents for a large list of atoms,
from both ligand and protein. How could I overcome this issue knowing that
there is several expected h-bonds to be detected in my complex?

Thanks in advance for your help.

Best regards,


*Andr?s Felipe V?squez J., BSc, MSc.*
Profesional - Grupo de Fisiolog?a Molecular
Subdirecci?n de Investigaci?n Cient?fica y Tecnol?gica
Direcci?n de Investigaci?n en Salud P?blica
Instituto Nacional de Salud
Avenida calle 26 No. 51-20 - Zona 6 CAN
Bogot?, D.C., Colombia
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From meng at cgl.ucsf.edu  Fri Oct  2 09:30:53 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 2 Oct 2015 09:30:53 -0700
Subject: [Chimera-users] Problems detecting h-bonds
In-Reply-To: <CAPGHGYNd9wjfp4nCsr=XzcaTsVFXjiawzDOZSHQPTArm5tdQaA@mail.gmail.com>
References: <CAPGHGYNd9wjfp4nCsr=XzcaTsVFXjiawzDOZSHQPTArm5tdQaA@mail.gmail.com>
Message-ID: <3E86E9FC-E82C-4249-B111-ACE696E9C661@cgl.ucsf.edu>

Hi, 
It may be that the coordinates are weird somehow (strained, or multiple conformations of same atoms), or the structure input format was wrong.   Check the input carefully for format or other problems ? it is not possible to tell specifically what is wrong without looking at your data.

Your setattr command doesn?t make sense because it doesn?t specify any type.  Maybe it erased all the types, which would certainly make everything worse!  A correct setattr command would be something like ?setattr a idatmType C3 sel? to change the selected atom to type C3.  However, Chimera generally figures out the atom types itself and you would not need to change them (e.g. with setattr). Atom types:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

You could try ?Help? Report a Bug? and attach the structure (or session) and describe exactly what to do to get that error in FindHBond.  Don?t change the atom types before sending us the data, since that is expected to really mess things up.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 2, 2015, at 7:49 AM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi, 
> I have recently obtained some docking results (I have a complex) and I am trying to detect any protein-ligand h-bonds. Soon, I faced a first problem when I obtain this error message: "More than 2 coplanar positions specified!", and I think I solved it once my ligand was selected and I enter into the command line: "setattr a idatmType sel". However, I obtained later an entire panel (with a big list in it) asking me to indicate the expetd geometries and number of substituents for a large list of atoms, from both ligand and protein. How could I overcome this issue knowing that there is several expected h-bonds to be detected in my complex?
> 
> Thanks in advance for your help.
> 
> Best regards,
> 
> Andr?s Felipe V?squez J., BSc, MSc.
> Profesional - Grupo de Fisiolog?a Molecular
> Subdirecci?n de Investigaci?n Cient?fica y Tecnol?gica
> Direcci?n de Investigaci?n en Salud P?blica
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> Bogot?, D.C., Colombia 




From meng at cgl.ucsf.edu  Fri Oct  2 09:59:44 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 2 Oct 2015 09:59:44 -0700
Subject: [Chimera-users] 3D-visualization of protein chain and mutation
References: <1005E736-577A-4818-9E9A-90F52D8EB261@cgl.ucsf.edu>
Message-ID: <88806AC9-0E99-4118-8EB5-6C6BB7225D17@cgl.ucsf.edu>


> From: "Coci, Emanuele" <Emanuele.Coci at akh-celle.de<mailto:Emanuele.Coci at akh-celle.de>>
> Date: Friday, October 2, 2015 at 8:54 AM
> Subject: 3D-visualization of protein chain
> 
> Deat Chimera team,
> my name is Emanuele Coci, MD PhD.
> 
> I would kindly ask you for help about Chimera software in solving the following technical issue. I want to visualize the 3D-structure of a mutated protein chain.
> 
> Which of the chimera tools is more indicated to visualize the 3D structure?
> Is the toll open source?
> Which software do I need to download the tool on my PC : JAVA, ??
> 
> Best regards and many thanks in advance?
> Emanuele Coci

Dear Emanuele Coci,
Chimera is a free download for any noncommercial use (research, education, ?) and is available for Windows, Mac, and Linux.  You should not have to download any other software to use it.  All you need is a reasonably modern computer. See Chimera homepage and download links:
<http://www.rbvi.ucsf.edu/chimera/index.html>
<http://www.rbvi.ucsf.edu/chimera/download.html>

I?ve CC?d chimera-users at cgl.ucsf.edu ? that is the proper address for user questions.

There are many possible styles of displaying a protein, and you have to use your own judgement and artistic taste to decide which style is best for what you want to see for yourself or show to others.  There are several step-by-step tutorials for learning how to use Chimera, including ?getting started? for beginners and some example image tutorials:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

For showing a mutation, the first thing you could do is just show the location of that amino acid on the structure (without mutating it), for example coloring it differently than the rest of the structure.  It may be helpful to show the sequence of the protein so that you can identify the correct position (Chimera menu: Favorites? Sequence).  You can choose a residue with the mouse in the sequence window, which will automatically select-highlight it in the structure.

Secondly, you could try ?mutating? that residue computationally.  This could be done with the Rotamers tool (in menu under Tools? Structure Editing) or the ?swapaa? command.  There is an example of using the Rotamers tool in the ?Structure Analysis and Comparison? tutorial:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

However, Chimera will not predict any larger-scale changes in the structure from the mutation or calculate changes in stability or affinity. It will only change the sidechain and not move anything else.  You can use Rotamers to analyze the H-bonds and clashes (bad contacts) of different conformations of the sidechain, which may allow you to hypothesize whether the mutation would be disruptive to the stability or interactions of the protein.

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

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From goddard at sonic.net  Fri Oct  2 14:45:46 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 2 Oct 2015 14:45:46 -0700
Subject: [Chimera-users] Saving images of all scenes in session?
In-Reply-To: <3AB8BDC8-57D3-4009-B8BF-9DAF20549FF5@gmail.com>
References: <FE625C86-2B23-427D-9DE0-CB41116A4C15@gmail.com>
	<3AB8BDC8-57D3-4009-B8BF-9DAF20549FF5@gmail.com>
Message-ID: <749F5477-6F5E-402E-AAAF-1A34AB6A9042@sonic.net>

Saving an image of each scene would be a nice feature.  The scene support in Chimera 1 is limited, not everything gets saved in a scene.  In Chimera 2 scenes will be handled with the same code that saves sessions so they should handle everything that session saving will handle.  And we will add your suggestion to save images for each scene in Chimera 2.  But we won?t have scene support in our initial Chimera 2 release at the end of this year though.

	Tom


> On Sep 28, 2015, at 7:30 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> OK, sort of figured out the second part of this - here is a basic extension that will iterate over each scene and take an image at each with the defined parameters - I still think it would be very handy if something similar were to be incorporated into the image saving part of the GUI though:
> 
> from Midas.midas_text import addCommand
> def cmd_scenesnap(scenesnap,args):
>  from Midas.midas_text import doExtensionFunc
>  def scenesnap(rootname):
>    from chimera import runCommand
>    from Animate import Scenes
>    scene_list=Scenes.scenes.dispnames()
>    mkdir_cmd="cd ~; system mkdir chimera_tmp; cd chimera_tmp; system mkdir {0}; cd {0}".format(rootname)
>    runCommand(mkdir_cmd)
>    for scene in scene_list:
>      runCommand("scene {} reset".format(scene))
>      img_name=str(rootname)+"_"+str(scene)
>      runCommand("copy file {} png width 2000 supersample 4".format(img_name))
>  doExtensionFunc(scenesnap,args)
> addCommand("scenesnap", cmd_scenesnap, help=False)
> 
> 
>> On Sep 27, 2015, at 11:01 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> Apologies for yet another post and thank you for your patience! :-)
>> 
>> Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc).
>> 
>> This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say ?Fig1.py?, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for ?save images for all scenes in session?, or something similar.
>> 
>> It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel.
>> 
>> I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can?t quite figure it out - any tips much appreciated.
>> 
>> Cheers,
>> Oli.
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From olibclarke at gmail.com  Mon Oct  5 20:28:26 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 5 Oct 2015 23:28:26 -0400
Subject: [Chimera-users] solid rendering color voxel by voxel?
Message-ID: <409A2089-36B6-4D5F-8B75-840F8D48D70F@gmail.com>

Hi all,

I don?t think this is possible right now, but i just wanted to check and maybe put in a request for addition to Chimera 2 at some point if you think it would be a useful feature.

I like generating looping maximum intensity projection movies like the following (using EMDB 2807 as an example):

https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0 <https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0>

https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0 <https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0>

Command used to generate representation:
#Makes a pseudoprojection style view of the given volume
#Usage: volume_project #map_id
alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0 color white sdlevel 20,1 color white style solid projectionMode 3d maximumIntensityProjection true btCorrection true linearInterpolation true; unset depthCue

I feel like even at small sizes, this gives a good idea of the overall quality of the electron density, in both mobile and well-ordered regions, due to the non-thresholded nature of the representation. 

It seems to me that this would be a natural fit for Resmap coloring to color a map by local resolution, as one of the issues I have with the application of Resmap in surface representation is that if you contour the map at a sufficiently low threshold to see the less well ordered parts of the structure, you can?t see the voxels that have the best local resolution (necessitating slabbing of the map).

This would also be handy for using Color Zone to color different regions of the map based on the model.

Would it be possible to add per-voxel coloring in solid representation at some point, similar to scolor for surface representation, to make this kind of thing possible?

Cheers,
Oliver.
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From matej.repic at epfl.ch  Tue Oct  6 07:54:29 2015
From: matej.repic at epfl.ch (Repic Matej)
Date: Tue, 6 Oct 2015 14:54:29 +0000
Subject: [Chimera-users] Newlines in labelopt string
Message-ID: <D239AD44.12A90%matej.repic@epfl.ch>

Hi everyone,

I have pretty long atom labels and it would be nice if I could split them
with newlines. I set labels with labelopt info %(name)s %(ee).2f %(ea).2f
%(er).2f

# what I have
C3 0.41 0.22 0.14

# what I want
C3
0.41
0.22
0.14

The obvious \n does not work. Any ideas?

Thank you,

------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------




From pett at cgl.ucsf.edu  Tue Oct  6 12:10:48 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 6 Oct 2015 12:10:48 -0700
Subject: [Chimera-users] Newlines in labelopt string
In-Reply-To: <D239AD44.12A90%matej.repic@epfl.ch>
References: <D239AD44.12A90%matej.repic@epfl.ch>
Message-ID: <E00B6D84-DA83-4BE7-92DB-94F1FA39386F@cgl.ucsf.edu>

Hi Matej,
	I think you?re out of luck.  Even if you manage to get a literal newline (or its Unicode equivalent) into an atom label, it doesn?t produce a newline, it just shows a boxed question mark instead.
	There?s a horrible workaround that I barely want to mention.  You could open 4 copies of the structure and have each one show a different part of the label, with a different label offset for each.  You would have to change the labelopt before labeling each structure.  Like I said, horrible!

?Eric


	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 6, 2015, at 7:54 AM, Repic Matej <matej.repic at epfl.ch> wrote:
> 
> Hi everyone,
> 
> I have pretty long atom labels and it would be nice if I could split them
> with newlines. I set labels with labelopt info %(name)s %(ee).2f %(ea).2f
> %(er).2f
> 
> # what I have
> C3 0.41 0.22 0.14
> 
> # what I want
> C3
> 0.41
> 0.22
> 0.14
> 
> The obvious \n does not work. Any ideas?
> 
> Thank you,
> 
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique F?d?rale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC ? LCBC
> BCH 4108
> CH - 1015 Lausanne
> ------------------------------------------------------
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From hamish.todd1 at googlemail.com  Tue Oct  6 02:33:47 2015
From: hamish.todd1 at googlemail.com (Hamish Todd)
Date: Tue, 6 Oct 2015 10:33:47 +0100
Subject: [Chimera-users] Exporting coarse-grained models of proteins
Message-ID: <CAJi-=J5VP3mTqT_Bv=093PpB=snxw9osuS8ypRb2hvHeRPMZ8g@mail.gmail.com>

Hello all,

So sorry to bother you all but I've tried googling a lot of things and not
found out how to create a coarse grained protein surface like this one
<http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/capsid.png>.
Creating a *surface* is easy of course, but where does that nice,
intuitive, bulbous STMV protein come from? And when I get it, can I export
the vertex and polygon data?

Hamish

-- 
Hamish Todd
07722 400 806
Personal Website <http://www.musicofthespheresgame.com/?page_id=21>
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From francesco.papi at unifi.it  Tue Oct  6 02:47:21 2015
From: francesco.papi at unifi.it (Francesco Papi)
Date: Tue, 06 Oct 2015 11:47:21 +0200
Subject: [Chimera-users] Problem on Nucleic Acid Ribbon
In-Reply-To: <4cb82a4028ef53a71ce16918b5d8de48@proxy-imap.sf-int.unifi.it>
References: <4cb82a4028ef53a71ce16918b5d8de48@proxy-imap.sf-int.unifi.it>
Message-ID: <c738253d5c1f625328a9c0b8ea7f956d@proxy-imap.sf-int.unifi.it>

Good morning,

I'm working on a DNA X-ray structure. The problem I have observed is 
that the terminal nucleotide of the DNA sequence is excluded from the 
backbone ribbon, in other terms the backbone ribbon is shown and it is 
ok, but it is made of all the residues except the terminal one, which is 
linked to the ribbon by a long phosphodiester bond (see the attached 
image). Moreover, if I put the representation "Show side (sugar/base)", 
from the option "Nucleotides", to be "fill/slab", the terminal residue 
still features an "Atom & Bonds" style. The PDB file seems to be ok, as 
confirmed by a colleague. Do you how to solve this problem?

Best regards

Francesco Papi
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From carlos.gonzalezoliver at mail.mcgill.ca  Tue Oct  6 13:49:13 2015
From: carlos.gonzalezoliver at mail.mcgill.ca (Carlos Gonzalez Oliver, Mr)
Date: Tue, 6 Oct 2015 20:49:13 +0000
Subject: [Chimera-users] Joining Models + Avoiding Steric Clashes
Message-ID: <ADCA6E73-C080-480C-B0EB-8C93B0E61D5A@mail.mcgill.ca>

Dear Chimera,

I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD.

However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated.

Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works.

So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes.

But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond)

Thanks!


--
Carlos G. Oliver
M.Sc. Student

Vogel Lab
Department of Biology
McGill University
Montr?al, QC, Canada






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From goddard at sonic.net  Tue Oct  6 14:22:02 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 6 Oct 2015 14:22:02 -0700
Subject: [Chimera-users] solid rendering color voxel by voxel?
In-Reply-To: <409A2089-36B6-4D5F-8B75-840F8D48D70F@gmail.com>
References: <409A2089-36B6-4D5F-8B75-840F8D48D70F@gmail.com>
Message-ID: <F5485F6A-8F08-4110-A9B7-EBD6ABCD4A98@sonic.net>

Hi Oliver,

  I have played with coloring volumetric (?solid? style) rendering in Chimera.  Attached is an image of segmented bacteria in termite gut with the first, second and fourth panels showing colored volumetric rendering.  This is from a project 5 years ago with Manfred Auer at LBL ? here?s a poster that I took these images from

	http://www.cgl.ucsf.edu/chimera/data/termitegut.pdf <http://www.cgl.ucsf.edu/chimera/data/termitegut.pdf>

That capability didn?t make it into Chimera though (I thought it was a secret command called vmask, but in fact that is so secret it only resides on my machine).  If you are into hacking Chimera Python code the underlying support to color volumetric rendering is there.  If v is your Volume object you set v.mask_colors = a function that can modulate the colors for grid points.  I?ll attach the code called I used to make the image below as an example.  It uses a segmentation integer array the same size as the density map where different integer values correspond to different segmentation regions ? then it assigns random colors to each region (preserving the transparency).

	Tom






> On Oct 5, 2015, at 8:28 PM, Oliver Clarke wrote:
> 
> Hi all,
> 
> I don?t think this is possible right now, but i just wanted to check and maybe put in a request for addition to Chimera 2 at some point if you think it would be a useful feature.
> 
> I like generating looping maximum intensity projection movies like the following (using EMDB 2807 as an example):
> 
> https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0 <https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0>
> 
> https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0 <https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0>
> 
> Command used to generate representation:
> #Makes a pseudoprojection style view of the given volume
> #Usage: volume_project #map_id
> alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0 color white sdlevel 20,1 color white style solid projectionMode 3d maximumIntensityProjection true btCorrection true linearInterpolation true; unset depthCue
> 
> I feel like even at small sizes, this gives a good idea of the overall quality of the electron density, in both mobile and well-ordered regions, due to the non-thresholded nature of the representation. 
> 
> It seems to me that this would be a natural fit for Resmap coloring to color a map by local resolution, as one of the issues I have with the application of Resmap in surface representation is that if you contour the map at a sufficiently low threshold to see the less well ordered parts of the structure, you can?t see the voxels that have the best local resolution (necessitating slabbing of the map).
> 
> This would also be handy for using Color Zone to color different regions of the map based on the model.
> 
> Would it be possible to add per-voxel coloring in solid representation at some point, similar to scolor for surface representation, to make this kind of thing possible?
> 
> Cheers,
> Oliver.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From meng at cgl.ucsf.edu  Tue Oct  6 14:33:41 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 6 Oct 2015 14:33:41 -0700
Subject: [Chimera-users] Exporting coarse-grained models of proteins
In-Reply-To: <CAJi-=J5VP3mTqT_Bv=093PpB=snxw9osuS8ypRb2hvHeRPMZ8g@mail.gmail.com>
References: <CAJi-=J5VP3mTqT_Bv=093PpB=snxw9osuS8ypRb2hvHeRPMZ8g@mail.gmail.com>
Message-ID: <7A3771B0-1056-4F81-AD5A-E8EA9AA058A7@cgl.ucsf.edu>

Hello Hamish,
Those low-res surfaces can be made with the Multiscale Models tool (in Chimera menu under Tools? Higher-Order Structure) or the command ?sym? with the ?surfaces true? option; both of those can use symmetry information to generate the symmetry copies as low-res surfaces (optionally) from a single copy of the atomic coordinates (the asymmetric unit). 

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

the Multiscale Models dialog has a resolution option, and can also be used to generate one surface per chain for structures for which all the chains already have atomic coordinates loaded (for example, open the 4-chain structure 4HHB and use Multiscale Models on it).

You can export surfaces with File? Export Scene in main Chimera menu.  There are several format options, see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>

An alternative way of making a low-res surface for any arbitrary (user-specified) set of atoms is to use the ?molmap? command to simulate a density map from the atoms and then in the Volume Viewer dialog (which automatically appears) adjust the density isosurface level.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

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


> On Oct 6, 2015, at 2:33 AM, Hamish Todd <hamish.todd1 at googlemail.com> wrote:
> 
> Hello all,
> So sorry to bother you all but I've tried googling a lot of things and not found out how to create a coarse grained protein surface like this one. Creating a *surface* is easy of course, but where does that nice, intuitive, bulbous STMV protein come from? And when I get it, can I export the vertex and polygon data?
> Hamish




From olibclarke at gmail.com  Tue Oct  6 14:48:33 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 6 Oct 2015 17:48:33 -0400
Subject: [Chimera-users] solid rendering color voxel by voxel?
In-Reply-To: <F5485F6A-8F08-4110-A9B7-EBD6ABCD4A98@sonic.net>
References: <409A2089-36B6-4D5F-8B75-840F8D48D70F@gmail.com>
	<F5485F6A-8F08-4110-A9B7-EBD6ABCD4A98@sonic.net>
Message-ID: <CAPghYOqRfdCoXKbpE4JFrJ3Yik29FKf3fwDs2eX1hP7X_jNZhg@mail.gmail.com>

Thanks Tom!

I'll have a play with your code when I have some time and see if I can
repurpose it to color by volume data value of another map rather than with
a mask - might be beyond my python abilities but will give it a try!

Cheers,
Oliver.



On Tue, Oct 6, 2015 at 5:22 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>
>   I have played with coloring volumetric (?solid? style) rendering in
> Chimera.  Attached is an image of segmented bacteria in termite gut with
> the first, second and fourth panels showing colored volumetric rendering.
> This is from a project 5 years ago with Manfred Auer at LBL ? here?s a
> poster that I took these images from
>
> http://www.cgl.ucsf.edu/chimera/data/termitegut.pdf
>
> That capability didn?t make it into Chimera though (I thought it was a
> secret command called vmask, but in fact that is so secret it only resides
> on my machine).  If you are into hacking Chimera Python code the underlying
> support to color volumetric rendering is there.  If v is your Volume object
> you set v.mask_colors = a function that can modulate the colors for grid
> points.  I?ll attach the code called I used to make the image below as an
> example.  It uses a segmentation integer array the same size as the density
> map where different integer values correspond to different segmentation
> regions ? then it assigns random colors to each region (preserving the
> transparency).
>
> Tom
>
>
>
>
>
>
> On Oct 5, 2015, at 8:28 PM, Oliver Clarke wrote:
>
> Hi all,
>
> I don?t think this is possible right now, but i just wanted to check and
> maybe put in a request for addition to Chimera 2 at some point if you think
> it would be a useful feature.
>
> I like generating looping maximum intensity projection movies like the
> following (using EMDB 2807 as an example):
>
> https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0
>
> https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0
>
> Command used to generate representation:
> #Makes a pseudoprojection style view of the given volume
> #Usage: volume_project #map_id
> alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0
> color white sdlevel 20,1 color white style solid projectionMode 3d
> maximumIntensityProjection true btCorrection true linearInterpolation true;
> unset depthCue
>
> I feel like even at small sizes, this gives a good idea of the overall
> quality of the electron density, in both mobile and well-ordered regions,
> due to the non-thresholded nature of the representation.
>
> It seems to me that this would be a natural fit for Resmap coloring to
> color a map by local resolution, as one of the issues I have with the
> application of Resmap in surface representation is that if you contour the
> map at a sufficiently low threshold to see the less well ordered parts of
> the structure, you can?t see the voxels that have the best local resolution
> (necessitating slabbing of the map).
>
> This would also be handy for using Color Zone to color different regions
> of the map based on the model.
>
> Would it be possible to add per-voxel coloring in solid representation at
> some point, similar to scolor for surface representation, to make this kind
> of thing possible?
>
> Cheers,
> Oliver.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
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From meng at cgl.ucsf.edu  Tue Oct  6 15:10:00 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 6 Oct 2015 15:10:00 -0700
Subject: [Chimera-users] Problem on Nucleic Acid Ribbon
In-Reply-To: <c738253d5c1f625328a9c0b8ea7f956d@proxy-imap.sf-int.unifi.it>
References: <4cb82a4028ef53a71ce16918b5d8de48@proxy-imap.sf-int.unifi.it>
	<c738253d5c1f625328a9c0b8ea7f956d@proxy-imap.sf-int.unifi.it>
Message-ID: <3B8301E5-5041-4F91-A664-12257C4D8602@cgl.ucsf.edu>

Good morning (or afternoon for us!),

One issue is that the default ribbon path is smoothed, and the smoothing has the following side effects:

(A) being a bit shorter at the end so the last base is hanging out beyond it
(B) being farther from the real backbone atom positions, so that when a connecting stick is drawn between the backbone and sidechain atoms, it can be obviously too long or short compared to the real bond

It?s discussed further here, 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

?. but the short answer is to fix it, you could use a different ribbon spline that is guaranteed to follow the real backbone atom positions (for nucleic acids, the P atoms).  For example, command:

ribspline cardinal

Then the ribbon will not be as smooth, but the connections to the sidechain atoms will look better.  There are some options to the command for tweaking the result, see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

However, I don?t know what is causing the problem of not showing that residue as fill and slab like the others.  I did not have that problem with my test PDB file (1BNA), and I don?t recall seeing the problem with other structures either.  If the structure is not private, you could try using menu: Help? Report a Bug and attaching the file and including a short description and your email address.  It might be not be a bug, but instead something with the atom names in the file or whether that last residue is missing any atoms, but no way to tell without looking at it.  Or if it is private but you don?t mind sharing it with just the Chimera team, you can mail it to just me (meng at cgl.ucsf.edu).

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


> On Oct 6, 2015, at 2:47 AM, Francesco Papi <francesco.papi at unifi.it> wrote:
> 
> Good morning,
> 
> I'm working on a DNA X-ray structure. The problem I have observed is that the terminal nucleotide of the DNA sequence is excluded from the backbone ribbon, in other terms the backbone ribbon is shown and it is ok, but it is made of all the residues except the terminal one, which is linked to the ribbon by a long phosphodiester bond (see the attached image). Moreover, if I put the representation "Show side (sugar/base)", from the option "Nucleotides", to be "fill/slab", the terminal residue still features an "Atom & Bonds" style. The PDB file seems to be ok, as confirmed by a colleague. Do you how to solve this problem?
> 
> Best regards
> 
> Francesco Papi<image.png>



From pett at cgl.ucsf.edu  Tue Oct  6 16:22:28 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 6 Oct 2015 16:22:28 -0700
Subject: [Chimera-users] Joining Models + Avoiding Steric Clashes
In-Reply-To: <ADCA6E73-C080-480C-B0EB-8C93B0E61D5A@mail.mcgill.ca>
References: <ADCA6E73-C080-480C-B0EB-8C93B0E61D5A@mail.mcgill.ca>
Message-ID: <1BC42BA5-E0B5-4FC1-AD0F-83A7ADE44126@cgl.ucsf.edu>

Hi Carlos,
	I think you are going to have to resort to Python here.  First, look at this page for a basic example of how to loop over some files and do something with them in Chimera/Python:

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

	You form the C-N peptide bond using the cnPeptideBond function from the BuildStructure module.  Here?s a pseudocode fragment to form the bond:

	runCommand(?sel atom-spec-to-select-the-N-and-the-C?)
	from chimera.selection import currentAtoms
	n, c = currentAtoms()
	if n.element.name != ?N?:
		# the atoms were in the other order, swap them
		n, c = c, n
	from BuildStructure import cnPeptideBond
	cnPeptideBond(c, n, c, 1.33, 180.0, phi=-120.0)

You might want to put the above in yet another loop so that you could try various phi angles.  Naturally you would have to break the bond before trying another value, probably with the ~bond command.
	You might also want to directly measure the clashes in the script rather than write them out to a file.  You do that with the detectClash function in the DetectClash module.  Here?s more pseudocode:

	runCommand(?sel atom-spec to select the C-terminal tail?)
	from chimera.selection import currentAtoms
	from DetectClash import detectClash
	num_clashing_atoms = len(detectClash(currentAtoms()))

Good luck!

?Eric
	
	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 6, 2015, at 1:49 PM, Carlos Gonzalez Oliver, Mr <carlos.gonzalezoliver at mail.mcgill.ca> wrote:
> 
> Dear Chimera,
> 
> I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD.
> 
> However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated.
> 
> Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works.
> 
> So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes.
> 
> But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond)
> 
> Thanks!
> 
> 
> --
> Carlos G. Oliver
> M.Sc. Student
> 
> Vogel Lab
> Department of Biology
> McGill University
> Montr?al, QC, Canada
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From matej.repic at epfl.ch  Wed Oct  7 00:35:48 2015
From: matej.repic at epfl.ch (Repic Matej)
Date: Wed, 7 Oct 2015 07:35:48 +0000
Subject: [Chimera-users] Newlines in labelopt string
In-Reply-To: <E00B6D84-DA83-4BE7-92DB-94F1FA39386F@cgl.ucsf.edu>
References: <D239AD44.12A90%matej.repic@epfl.ch>
	<E00B6D84-DA83-4BE7-92DB-94F1FA39386F@cgl.ucsf.edu>
Message-ID: <D23A9710.12AB2%matej.repic@epfl.ch>

Hi Eric,

Thanks for the suggestion. I might just leave it as is, since getting the right label offset is probably more trouble than it is worth.

Best,
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------

From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Date: Tuesday, October 6, 2015 at 21:10
To: Matej Repic <matej.repic at epfl.ch<mailto:matej.repic at epfl.ch>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Newlines in labelopt string

Hi Matej,
I think you?re out of luck.  Even if you manage to get a literal newline (or its Unicode equivalent) into an atom label, it doesn?t produce a newline, it just shows a boxed question mark instead.
There?s a horrible workaround that I barely want to mention.  You could open 4 copies of the structure and have each one show a different part of the label, with a different label offset for each.  You would have to change the labelopt before labeling each structure.  Like I said, horrible!

?Eric


Eric Pettersen
UCSF Computer Graphics Lab


On Oct 6, 2015, at 7:54 AM, Repic Matej <matej.repic at epfl.ch<mailto:matej.repic at epfl.ch>> wrote:

Hi everyone,

I have pretty long atom labels and it would be nice if I could split them
with newlines. I set labels with labelopt info %(name)s %(ee).2f %(ea).2f
%(er).2f

# what I have
C3 0.41 0.22 0.14

# what I want
C3
0.41
0.22
0.14

The obvious \n does not work. Any ideas?

Thank you,

------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------


_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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From byrdra at mail.nih.gov  Thu Oct  8 14:20:38 2015
From: byrdra at mail.nih.gov (Byrd, Robert A. (NIH/NCI) [E])
Date: Thu, 8 Oct 2015 21:20:38 +0000
Subject: [Chimera-users] display a coordinate system in view
Message-ID: <D23C5664.252C8%byrdra@mail.nih.gov>

I would like to represent a xyz coordinate system by the unit vectors on the display with a molecule. Ideally, for a two domain protein, I would like to have two coordinate systems, one for each domain. In an ensemble of structures where one domain changes orientation with respect to the other, one coordinate system would move to the new position. It would be nice to then morph from one position to the next. This is straightforward with a set of structures and the morph utility in CHIMERA. The ability to add the two coordinate systems to the display, and have them ?move? or morph from one position to the other, would highlight the geometrical averaging that takes place.

Is this possible in CHIMERA?

Thanks
Andy Byrd

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From meng at cgl.ucsf.edu  Thu Oct  8 16:36:39 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 8 Oct 2015 16:36:39 -0700
Subject: [Chimera-users] display a coordinate system in view
In-Reply-To: <D23C5664.252C8%byrdra@mail.nih.gov>
References: <D23C5664.252C8%byrdra@mail.nih.gov>
Message-ID: <54FF89C0-7D66-41E4-BF9F-76FA05C2B8A2@cgl.ucsf.edu>

Hi Andy,
Well, you could open the attached BILD file (simple text format) to show coordinate axes. Scale, colors and origin can be edited, and you could open multiple copies. See BILD format description:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>

However, the difficult part would be calculating the desired transformation from the domain movement to apply to these models at each step of your morph trajectory. It could be done within a per-frame script in the MD Movie tool (the tool that plays back the morph trajectory).  I haven?t tried it, but I imagine something like having an additional invisible copy of the structure with fixed coordinates, calculating the transformation that would be required to match some set of atoms in each domain from that fixed invisible model to their current position in the trajectory, and applying those transformations to the respective axis-object models.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

Per-frame scripts can be in Chimera commands or in Python (often needed if there aren?t commands to do what you need).  I tried using the ?match? command with ?move? specifying only the relevant axis-object model.  Unfortunately in a small test this didn?t work? I guess the ?move? model has to be an atomic model, not an object (argh, so close and yet so far!).  Another thought is to actually move the the invisible model with ?match" and then use the command ?matrixcopy? to apply the same transformation to the  object model.  Then the per-frame script would also need to put the invisible model back to its original position, say with ?reset? with its ?move? option to move only the invisible model.  

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>

I think this would work but I only did small tests of the various parts of my suggestion.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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> On Oct 8, 2015, at 2:20 PM, Byrd, Robert A. (NIH/NCI) [E] <byrdra at mail.nih.gov> wrote:
> 
> I would like to represent a xyz coordinate system by the unit vectors on the display with a molecule. Ideally, for a two domain protein, I would like to have two coordinate systems, one for each domain. In an ensemble of structures where one domain changes orientation with respect to the other, one coordinate system would move to the new position. It would be nice to then morph from one position to the next. This is straightforward with a set of structures and the morph utility in CHIMERA. The ability to add the two coordinate systems to the display, and have them ?move? or morph from one position to the other, would highlight the geometrical averaging that takes place.
> 
> Is this possible in CHIMERA?
> 
> Thanks
> Andy Byrd


From smith_liu123 at 163.com  Thu Oct  8 18:08:54 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Fri, 9 Oct 2015 09:08:54 +0800 (CST)
Subject: [Chimera-users] on command scripts related to movie by chimera
Message-ID: <1f0f41fa.253a.1504a24c19b.Coremail.smith_liu123@163.com>

Dear All,


I want to learn several commands on chimera movie preparation. Only read the on-line material I find I still meet some difficulty.


Suppose I have 2 scripts? each for 1 movie. Will you please tell me by which command in the script I can link the 2 scripts so that the 2 movie will change into 1 movie?


Suppose in Chimera I have opened 2 PDB files. Will you please show me the commands to view the structure in the first PDB, then change to view the structure of the second PDB ?different from the purpose of morph?? And how about if then we see the 2 structures together, all in a single movie?


Best regards.


Smith
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From saluja.raag at gmail.com  Thu Oct  8 23:54:42 2015
From: saluja.raag at gmail.com (Raag Saluja)
Date: Fri, 9 Oct 2015 12:24:42 +0530
Subject: [Chimera-users] Chimera crashes when I try to open a .gro file
Message-ID: <EAF2EDD8-97B8-4220-85E5-78F6A26B38B5@gmail.com>

Hi!

Chimera crashes when I try to open a .gro file (created through GROMACS). 

I wanted to open the .gro file and then superimpose it on a .pdb file. 

Can you please guide? Thank you!

Regards,
Raag



From matej.repic at epfl.ch  Fri Oct  9 00:29:48 2015
From: matej.repic at epfl.ch (Repic Matej)
Date: Fri, 9 Oct 2015 07:29:48 +0000
Subject: [Chimera-users] Chimera crashes when I try to open a .gro file
In-Reply-To: <EAF2EDD8-97B8-4220-85E5-78F6A26B38B5@gmail.com>
References: <EAF2EDD8-97B8-4220-85E5-78F6A26B38B5@gmail.com>
Message-ID: <D23D35AB.12BC1%matej.repic@epfl.ch>

Hi Raag,

Chimera is not really efficient with big files (many atoms), but you can
try a few of these:

1) run on a machine with lots of ram
2) avoid as many atoms as possible
3) match as few atoms as possible
4) avoid rendering the file
5) if you want to have it rendered, disable smart display (Chimera pref >
New Molecules > Smart Initial Display)

Ad 4) Write a command line chimera script (run with "chimera --nogui
script.cmd"), for example:
-----script.cmd------
open file1.gro file2.pdb
match #0:res #1:res
write format pdb relative 1 0 aligned.pdb
---------------------

Best,




------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------







On 10/9/15, 08:54, "chimera-users-bounces at cgl.ucsf.edu on behalf of Raag
Saluja" <chimera-users-bounces at cgl.ucsf.edu on behalf of
saluja.raag at gmail.com> wrote:

>Hi!
>
>Chimera crashes when I try to open a .gro file (created through GROMACS).
>
>I wanted to open the .gro file and then superimpose it on a .pdb file.
>
>Can you please guide? Thank you!
>
>Regards,
>Raag
>
>_______________________________________________
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu
>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Fri Oct  9 09:22:20 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 Oct 2015 09:22:20 -0700
Subject: [Chimera-users] on command scripts related to movie by chimera
In-Reply-To: <1f0f41fa.253a.1504a24c19b.Coremail.smith_liu123@163.com>
References: <1f0f41fa.253a.1504a24c19b.Coremail.smith_liu123@163.com>
Message-ID: <F3638F86-EA6E-4EFB-B0CC-7C0B032EE1F4@cgl.ucsf.edu>

Hi Smith,
(1) Combine the scripts into one script file (or open the second script from the first with the ?open? command).  If they are Chimera command scripts, there should be a total of one ?movie record [options]? (start recording) before it starts showing what you want in the movie and one ?movie encode [options]? (create movie file) after all the stuff you want in the movie is done. In other words, you will probably need to edit the files so that they don?t record twice and save twice, or otherwise overlap or conflict with each other.  It makes sense if you actually look in the scripts and understand what the commands are doing and in what order; scripts are in plain text, so you can just use your favorite text editor.  You can?t just treat them as black boxes and stick them together without any modification. 

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#content>

If for some reason (like you have to stop recording and do something manually in between) they must remain as two separate script files, it is possible but more complicated.  Then in the first script you have to record with a specific filename pattern and stop recording at the end, but without encoding a movie file.  Then in the second script you have to resume recording with the same filename pattern.  These are options to the movie command (see its manual page).  If you are not in this special case, it is generally simpler to put everything in one script and record only once.

(2) how to display and undisplay multiple structures is basic Chimera use, regardless of whether you are making a movie.  You just need to know which model is which so that you can specify it correctly with commands: display, ribbon, surface, modeldisplay,
for example ?~modeldisp #1? to hide model 1, ?modeldisp #2-4? to show models 2-4.  See the individual manual pages of those commands for explanations of what they do.  You might also want to take a look at the ?getting started: commands? tutorial.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 8, 2015, at 6:08 PM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> I want to learn several commands on chimera movie preparation. Only read the on-line material I find I still meet some difficulty.
> 
> Suppose I have 2 scripts? each for 1 movie. Will you please tell me by which command in the script I can link the 2 scripts so that the 2 movie will change into 1 movie?
> 
> Suppose in Chimera I have opened 2 PDB files. Will you please show me the commands to view the structure in the first PDB, then change to view the structure of the second PDB ?different from the purpose of morph?? And how about if then we see the 2 structures together, all in a single movie?
> 
> Best regards.
> 
> Smith




From Thomas.Marlovits at imba.oeaw.ac.at  Fri Oct  9 00:15:10 2015
From: Thomas.Marlovits at imba.oeaw.ac.at (Marlovits,Thomas)
Date: Fri, 9 Oct 2015 07:15:10 +0000
Subject: [Chimera-users] bootstrap wanted boxsize
Message-ID: <5A60773F-8E6D-4ED5-A8A3-A2C778094834@imp.ac.at>

Hi Chimera-developers, 
I am wondering, whether there is a command to generate a new (empty) volume box from scratch? This would be a great help.
Many thanks,
-Thomas




From Emanuele.Coci at akh-celle.de  Fri Oct  9 04:46:06 2015
From: Emanuele.Coci at akh-celle.de (Coci, Emanuele)
Date: Fri, 9 Oct 2015 11:46:06 +0000
Subject: [Chimera-users] 3D-visualization of protein chain and mutation
In-Reply-To: <88806AC9-0E99-4118-8EB5-6C6BB7225D17@cgl.ucsf.edu>
References: <1005E736-577A-4818-9E9A-90F52D8EB261@cgl.ucsf.edu>
	<88806AC9-0E99-4118-8EB5-6C6BB7225D17@cgl.ucsf.edu>
Message-ID: <C09DB4FED0F8BF42942D7612031C3090056672@vmexchange.akh-celle.de>

Dear Elaine,

many thanks for your detailed information and sorry for my delayed answer- I was out of duties.

Since I will need soon to use properly the software, I have looked in details the links you sent me; nevertheless I think I will come back to you for some specific question in the near future.

Best regards

Emanuele

________________________________
Von: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Gesendet: Freitag, 2. Oktober 2015 19:00
An: Coci, Emanuele
Cc: chimera-users at cgl.ucsf.edu List
Betreff: 3D-visualization of protein chain and mutation


From: "Coci, Emanuele" <Emanuele.Coci at akh-celle.de<mailto:Emanuele.Coci at akh-celle.de><mailto:Emanuele.Coci at akh-celle.de>>
Date: Friday, October 2, 2015 at 8:54 AM
Subject: 3D-visualization of protein chain

Deat Chimera team,
my name is Emanuele Coci, MD PhD.

I would kindly ask you for help about Chimera software in solving the following technical issue. I want to visualize the 3D-structure of a mutated protein chain.

Which of the chimera tools is more indicated to visualize the 3D structure?
Is the toll open source?
Which software do I need to download the tool on my PC : JAVA, ...?

Best regards and many thanks in advance?
Emanuele Coci

Dear Emanuele Coci,
Chimera is a free download for any noncommercial use (research, education, ...) and is available for Windows, Mac, and Linux.  You should not have to download any other software to use it.  All you need is a reasonably modern computer. See Chimera homepage and download links:
<http://www.rbvi.ucsf.edu/chimera/index.html>
<http://www.rbvi.ucsf.edu/chimera/download.html>

I've CC'd chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> - that is the proper address for user questions.

There are many possible styles of displaying a protein, and you have to use your own judgement and artistic taste to decide which style is best for what you want to see for yourself or show to others.  There are several step-by-step tutorials for learning how to use Chimera, including "getting started" for beginners and some example image tutorials:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

For showing a mutation, the first thing you could do is just show the location of that amino acid on the structure (without mutating it), for example coloring it differently than the rest of the structure.  It may be helpful to show the sequence of the protein so that you can identify the correct position (Chimera menu: Favorites... Sequence).  You can choose a residue with the mouse in the sequence window, which will automatically select-highlight it in the structure.

Secondly, you could try "mutating" that residue computationally.  This could be done with the Rotamers tool (in menu under Tools... Structure Editing) or the "swapaa" command.  There is an example of using the Rotamers tool in the "Structure Analysis and Comparison" tutorial:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

However, Chimera will not predict any larger-scale changes in the structure from the mutation or calculate changes in stability or affinity. It will only change the sidechain and not move anything else.  You can use Rotamers to analyze the H-bonds and clashes (bad contacts) of different conformations of the sidechain, which may allow you to hypothesize whether the mutation would be disruptive to the stability or interactions of the protein.

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

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From meng at cgl.ucsf.edu  Fri Oct  9 09:54:44 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 Oct 2015 09:54:44 -0700
Subject: [Chimera-users] display a coordinate system in view
In-Reply-To: <54FF89C0-7D66-41E4-BF9F-76FA05C2B8A2@cgl.ucsf.edu>
References: <D23C5664.252C8%byrdra@mail.nih.gov>
	<54FF89C0-7D66-41E4-BF9F-76FA05C2B8A2@cgl.ucsf.edu>
Message-ID: <81E32BE7-B929-411B-BAFC-A60FA1F4533C@cgl.ucsf.edu>

Now I?m thinking that the origin offsets and/or different centers of rotation of the invisible structure and the arrow-model might cause problems. I?m not sure, just trying to picture what might happen? if it looks wrong, that might be the reason.  If so, it might work to apply only the rotation part of the transformation to the arrow-model, but that would require a Python per-frame script (beyond my skill set, sorry).
Elaine

On Oct 8, 2015, at 4:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Andy,
> Well, you could open the attached BILD file (simple text format) to show coordinate axes. Scale, colors and origin can be edited, and you could open multiple copies. See BILD format description:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
> 
> However, the difficult part would be calculating the desired transformation from the domain movement to apply to these models at each step of your morph trajectory. It could be done within a per-frame script in the MD Movie tool (the tool that plays back the morph trajectory).  I haven?t tried it, but I imagine something like having an additional invisible copy of the structure with fixed coordinates, calculating the transformation that would be required to match some set of atoms in each domain from that fixed invisible model to their current position in the trajectory, and applying those transformations to the respective axis-object models.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
> 
> Per-frame scripts can be in Chimera commands or in Python (often needed if there aren?t commands to do what you need).  I tried using the ?match? command with ?move? specifying only the relevant axis-object model.  Unfortunately in a small test this didn?t work? I guess the ?move? model has to be an atomic model, not an object (argh, so close and yet so far!).  Another thought is to actually move the the invisible model with ?match" and then use the command ?matrixcopy? to apply the same transformation to the  object model.  Then the per-frame script would also need to put the invisible model back to its original position, say with ?reset? with its ?move? option to move only the invisible model.  
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
> 
> I think this would work but I only did small tests of the various parts of my suggestion.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <XYZ-axes.bild>
>> On Oct 8, 2015, at 2:20 PM, Byrd, Robert A. (NIH/NCI) [E] <byrdra at mail.nih.gov> wrote:
>> 
>> I would like to represent a xyz coordinate system by the unit vectors on the display with a molecule. Ideally, for a two domain protein, I would like to have two coordinate systems, one for each domain. In an ensemble of structures where one domain changes orientation with respect to the other, one coordinate system would move to the new position. It would be nice to then morph from one position to the next. This is straightforward with a set of structures and the morph utility in CHIMERA. The ability to add the two coordinate systems to the display, and have them ?move? or morph from one position to the other, would highlight the geometrical averaging that takes place.
>> 
>> Is this possible in CHIMERA?
>> 
>> Thanks
>> Andy Byrd
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From pett at cgl.ucsf.edu  Fri Oct  9 10:13:18 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 9 Oct 2015 10:13:18 -0700
Subject: [Chimera-users] display a coordinate system in view
In-Reply-To: <81E32BE7-B929-411B-BAFC-A60FA1F4533C@cgl.ucsf.edu>
References: <D23C5664.252C8%byrdra@mail.nih.gov>
	<54FF89C0-7D66-41E4-BF9F-76FA05C2B8A2@cgl.ucsf.edu>
	<81E32BE7-B929-411B-BAFC-A60FA1F4533C@cgl.ucsf.edu>
Message-ID: <C5B5E4BA-BE9B-434B-8932-DCC2D2AB3A40@cgl.ucsf.edu>

I?m not 1000% sure this would work completely right, but you could edit your structure files to add a fake 4-atom residue to ?depict? the axes, one atom at the origin and the other three on the axes.  You might have to add CONECT records to get Chimera to bond them right, or you could use bond/~bond commands in Chimera afterward to set up the bonding.  I think Chimera would morph the ?axes? along with the domains?

?Eric

> On Oct 9, 2015, at 9:54 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Now I?m thinking that the origin offsets and/or different centers of rotation of the invisible structure and the arrow-model might cause problems. I?m not sure, just trying to picture what might happen? if it looks wrong, that might be the reason.  If so, it might work to apply only the rotation part of the transformation to the arrow-model, but that would require a Python per-frame script (beyond my skill set, sorry).
> Elaine
> 
> On Oct 8, 2015, at 4:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
>> Hi Andy,
>> Well, you could open the attached BILD file (simple text format) to show coordinate axes. Scale, colors and origin can be edited, and you could open multiple copies. See BILD format description:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
>> 
>> However, the difficult part would be calculating the desired transformation from the domain movement to apply to these models at each step of your morph trajectory. It could be done within a per-frame script in the MD Movie tool (the tool that plays back the morph trajectory).  I haven?t tried it, but I imagine something like having an additional invisible copy of the structure with fixed coordinates, calculating the transformation that would be required to match some set of atoms in each domain from that fixed invisible model to their current position in the trajectory, and applying those transformations to the respective axis-object models.
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
>> 
>> Per-frame scripts can be in Chimera commands or in Python (often needed if there aren?t commands to do what you need).  I tried using the ?match? command with ?move? specifying only the relevant axis-object model.  Unfortunately in a small test this didn?t work? I guess the ?move? model has to be an atomic model, not an object (argh, so close and yet so far!).  Another thought is to actually move the the invisible model with ?match" and then use the command ?matrixcopy? to apply the same transformation to the  object model.  Then the per-frame script would also need to put the invisible model back to its original position, say with ?reset? with its ?move? option to move only the invisible model.  
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
>> 
>> I think this would work but I only did small tests of the various parts of my suggestion.
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> <XYZ-axes.bild>
>>> On Oct 8, 2015, at 2:20 PM, Byrd, Robert A. (NIH/NCI) [E] <byrdra at mail.nih.gov> wrote:
>>> 
>>> I would like to represent a xyz coordinate system by the unit vectors on the display with a molecule. Ideally, for a two domain protein, I would like to have two coordinate systems, one for each domain. In an ensemble of structures where one domain changes orientation with respect to the other, one coordinate system would move to the new position. It would be nice to then morph from one position to the next. This is straightforward with a set of structures and the morph utility in CHIMERA. The ability to add the two coordinate systems to the display, and have them ?move? or morph from one position to the other, would highlight the geometrical averaging that takes place.
>>> 
>>> Is this possible in CHIMERA?
>>> 
>>> Thanks
>>> Andy Byrd
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Fri Oct  9 11:10:51 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 9 Oct 2015 11:10:51 -0700
Subject: [Chimera-users] Chimera crashes when I try to open a .gro file
In-Reply-To: <D23D35AB.12BC1%matej.repic@epfl.ch>
References: <EAF2EDD8-97B8-4220-85E5-78F6A26B38B5@gmail.com>
	<D23D35AB.12BC1%matej.repic@epfl.ch>
Message-ID: <8994F7BD-3604-4220-81E5-EF53941FA445@cgl.ucsf.edu>

Hi Raag,
	All Matej?s suggestions are excellent.  In addition, there are two more things I can think of.  One, you might consider using Chimera?s ?Report A Bug? entry in the Help menu to send us a bug report (and attach the .gro file) ? there may be something I can do about it.  The other thing is to make sure your are using the 64-bit version of Chimera ? it can handle larger systems than the 32-bit version.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 9, 2015, at 12:29 AM, Repic Matej <matej.repic at epfl.ch> wrote:
> 
> Hi Raag,
> 
> Chimera is not really efficient with big files (many atoms), but you can
> try a few of these:
> 
> 1) run on a machine with lots of ram
> 2) avoid as many atoms as possible
> 3) match as few atoms as possible
> 4) avoid rendering the file
> 5) if you want to have it rendered, disable smart display (Chimera pref >
> New Molecules > Smart Initial Display)
> 
> Ad 4) Write a command line chimera script (run with "chimera --nogui
> script.cmd"), for example:
> -----script.cmd------
> open file1.gro file2.pdb
> match #0:res #1:res
> write format pdb relative 1 0 aligned.pdb
> ---------------------
> 
> Best,
> 
> 
> 
> 
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique F?d?rale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC ? LCBC
> BCH 4108
> CH - 1015 Lausanne
> ------------------------------------------------------
> 
> 
> 
> 
> 
> 
> 
> On 10/9/15, 08:54, "chimera-users-bounces at cgl.ucsf.edu on behalf of Raag
> Saluja" <chimera-users-bounces at cgl.ucsf.edu on behalf of
> saluja.raag at gmail.com> wrote:
> 
>> Hi!
>> 
>> Chimera crashes when I try to open a .gro file (created through GROMACS).
>> 
>> I wanted to open the .gro file and then superimpose it on a .pdb file.
>> 
>> Can you please guide? Thank you!
>> 
>> Regards,
>> Raag
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From goddard at sonic.net  Fri Oct  9 11:11:15 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 9 Oct 2015 11:11:15 -0700
Subject: [Chimera-users] bootstrap wanted boxsize
In-Reply-To: <5A60773F-8E6D-4ED5-A8A3-A2C778094834@imp.ac.at>
References: <5A60773F-8E6D-4ED5-A8A3-A2C778094834@imp.ac.at>
Message-ID: <96BB0D17-3444-4681-A350-C0E48642185A@sonic.net>

Hi Thomas,

  There is not a command to do this, but I just added one in tonight's daily build, that you can  use like

	vop new "my new map" size 10,20,30 gridSpacing .15 modelId #5

The mask command can also create a new map bounding a surface with ones inside the surface, for example,

	mask ones #3

  Tom


> On Oct 9, 2015, at 12:15 AM, Marlovits,Thomas <Thomas.Marlovits at imba.oeaw.ac.at> wrote:
> 
> Hi Chimera-developers, 
> I am wondering, whether there is a command to generate a new (empty) volume box from scratch? This would be a great help.
> Many thanks,
> -Thomas
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From goddard at sonic.net  Fri Oct  9 12:20:52 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 9 Oct 2015 12:20:52 -0700
Subject: [Chimera-users] pipes & planks
In-Reply-To: <9330EBBF-59D6-4907-992F-94B8564C84C5@scripps.edu>
References: <9330EBBF-59D6-4907-992F-94B8564C84C5@scripps.edu>
Message-ID: <323C89B5-4DCC-45AF-B097-534552F97289@sonic.net>

Hi Gabe,

  I've added a "pipes" command to tonight's Chimera daily build, for example,

	pipes #0 helixColor pink strandColor salmon

and to delete the pipes and planks

	~pipes #0

Other command options with default values are:

       helixColor = None,
       helixEdgeColor = None,
       helixArrow = True,
       helixFixedRadius = True,
       helixRadius = 1.25,
       helixSplit = False,
       helixSplitRatio = 2.5,
       strandColor = None,
       strandEdgeColor = None,
       strandArrow = True,
       strandFixedWidth = True,
       strandWidth = 2.5,
       strandFixedThickness = True,
       strandThickness = 1.0,
       strandSplit = False,
       strandSplitRatio = 2.5,
       displayCoils = True,
       displayTurns = True,
       turnColor = None,
       turnEdgeColor = None,
       turnResolution = 10,
       turnWidth = 0.25,
       turnThickness = 0.25

Colors by default match the ribbon color, or molecule color.

  Tom


> On Oct 9, 2015, at 1:12 AM, Gabriel Lander wrote:
> 
> Hi Tom,
> 2 quick questions:
> 
> 1) is there a way to turn generate a pipes & planks model from the command line?
> 2) Can the coils in the pipes & planks be depicted as rounded instead of edged?
> 
> Thanks as always,
> -gabe
> 
> 




From matthewd at bcm.edu  Fri Oct  9 13:34:20 2015
From: matthewd at bcm.edu (Dougherty, Matthew T)
Date: Fri, 9 Oct 2015 20:34:20 +0000
Subject: [Chimera-users] python/model panel
Message-ID: <BLUPR0601MB1682AA4A5E28FDCE69B41334DE340@BLUPR0601MB1682.namprd06.prod.outlook.com>

I would like to print out the model ID, name and input files as they are listed in the model panel.


Can you point me in the direction of how to loop over the model panel ?

Such as elevant variables, and what would be a block of code in chimera that I should study.



Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
=================================================
=================================================
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From pett at cgl.ucsf.edu  Fri Oct  9 15:37:58 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 9 Oct 2015 15:37:58 -0700
Subject: [Chimera-users] python/model panel
In-Reply-To: <BLUPR0601MB1682AA4A5E28FDCE69B41334DE340@BLUPR0601MB1682.namprd06.prod.outlook.com>
References: <BLUPR0601MB1682AA4A5E28FDCE69B41334DE340@BLUPR0601MB1682.namprd06.prod.outlook.com>
Message-ID: <1AD0742A-1914-4DB4-9394-E1B15E319DEE@cgl.ucsf.edu>


> On Oct 9, 2015, at 1:34 PM, Dougherty, Matthew T <matthewd at bcm.edu> wrote:
> 
> I would like to print out the model ID, name and input files as they are listed in the model panel.
> 
> Can you point me in the direction of how to loop over the model panel ?
> Such as elevant variables, and what would be a block of code in chimera that I should study. 

Hi Matt,
	I don?t know that you need to go through the Model Panel per se, you could just go through Chimera?s open models list:

chimera.openModels.list()


Each model in the list has:

id			ID number
subid		Sub-ID number (None if it doesn?t have a sub-ID)
name		Name
openedAs	If it came from a file, a 4-tuple of stuff you mostly don?t care about, but the first element is the file name

Since some models don?t come from files (e.g. on-the-fly VRML models), you may want to use the model panel?s ?inputPath? function to always get a usable/readable string:

from ModelPanel import inputPath
path = inputPath(model)

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

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From matthewd at bcm.edu  Fri Oct  9 17:42:00 2015
From: matthewd at bcm.edu (Dougherty, Matthew T)
Date: Sat, 10 Oct 2015 00:42:00 +0000
Subject: [Chimera-users] python/model panel
In-Reply-To: <1AD0742A-1914-4DB4-9394-E1B15E319DEE@cgl.ucsf.edu>
References: <BLUPR0601MB1682AA4A5E28FDCE69B41334DE340@BLUPR0601MB1682.namprd06.prod.outlook.com>,
	<1AD0742A-1914-4DB4-9394-E1B15E319DEE@cgl.ucsf.edu>
Message-ID: <CY1PR0601MB1692A6CCEA2619068C1B4889DE330@CY1PR0601MB1692.namprd06.prod.outlook.com>

thanks.

suggestion on feature


when exiting session, chimera auto writes out a csv file of model id, name and path. file name equals session name with csv extension. The file could be incorporated into a database.


Would make organizing assets & archiving session files easier.


Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
=================================================
=================================================


________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Friday, October 9, 2015 5:37 PM
To: Dougherty, Matthew T
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] python/model panel


On Oct 9, 2015, at 1:34 PM, Dougherty, Matthew T <matthewd at bcm.edu<mailto:matthewd at bcm.edu>> wrote:

I would like to print out the model ID, name and input files as they are listed in the model panel.

Can you point me in the direction of how to loop over the model panel ?
Such as elevant variables, and what would be a block of code in chimera that I should study.

Hi Matt,
I don't know that you need to go through the Model Panel per se, you could just go through Chimera's open models list:

chimera.openModels.list()


Each model in the list has:

id ID number
subid Sub-ID number (None if it doesn't have a sub-ID)
name Name
openedAs If it came from a file, a 4-tuple of stuff you mostly don't care about, but the first element is the file name

Since some models don't come from files (e.g. on-the-fly VRML models), you may want to use the model panel's "inputPath" function to always get a usable/readable string:

from ModelPanel import inputPath
path = inputPath(model)

-Eric

Eric Pettersen
UCSF Computer Graphics Lab

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From olibclarke at gmail.com  Mon Oct 12 05:59:07 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Mon, 12 Oct 2015 08:59:07 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
	<1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
Message-ID: <5CAB86B8-241A-4755-94BE-87AA85055743@gmail.com>

Hi Eric, I have been using the alterations you made to history navigation in Chimera and I like them a lot - they make it much easier to locate old commands.

I have one suggestion for a slight tweak? at the moment, scrolling up through the history (with Shift+Up) seems to update the string to filter on as I scroll. There is a (very) minor issue with this approach. It means the process is not reversible and the results depend on the contents and ordering of the history.

For example, lets say I?m looking for a command I typed a while back, i know it started with ?bond? but can?t remember the exact name of the command. If I type ?bond? and then hit Shift+Up, I will only find the first matching command - if I had both bondrepr and bondzone in my command history, for example, I will only see the first one. I think it would be more intuitive if history filtering paid attention to only the initially typed string, if that is possible - so if I type ?bond?, I will scroll up through bondrepr, bond zone, bonddisplay etc, and will obtain the same results heading back ?down? through the command history.

Cheers,
Oli.


> On Oct 1, 2015, at 3:31 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
>> 
>> Cheers,
>> Oliver.
>> 
>> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
>> 
>> Cheers,
>> Oli.
>> 
>> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> Hi Oliver,
>>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
>> 
>> ?Eric
>> 
>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> >
>> > Hi all,
>> >
>> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
>> >
>> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
>> >
>> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
>> >
>> > Cheers,
>> > Oliver.
>> > _______________________________________________
>> > Chimera-users mailing list
>> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> >
>> 
>> 
>> 
> 

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From chiendarret at gmail.com  Mon Oct 12 10:12:12 2015
From: chiendarret at gmail.com (Francesco Pietra)
Date: Mon, 12 Oct 2015 19:12:12 +0200
Subject: [Chimera-users] rmsd overlay
Message-ID: <CAEv0nmvimgxN3NzQXOM7C-P5wN6uwgBgMUJiXK3PDwD4m_W+cQ@mail.gmail.com>

Hello;

Ho to superimpose a fake atom (pdb file available) to a coordiated metal in
a protein? I could change the name of the fake atom to that of the metal,
but then I need an rmsd overlay.

hope it is clear. thanks

francesco pietra
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From meng at cgl.ucsf.edu  Mon Oct 12 12:06:10 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Oct 2015 12:06:10 -0700
Subject: [Chimera-users] rmsd overlay
In-Reply-To: <CAEv0nmvimgxN3NzQXOM7C-P5wN6uwgBgMUJiXK3PDwD4m_W+cQ@mail.gmail.com>
References: <CAEv0nmvimgxN3NzQXOM7C-P5wN6uwgBgMUJiXK3PDwD4m_W+cQ@mail.gmail.com>
Message-ID: <2F2CBEDF-9A40-417F-BC37-A4E8CA73E025@cgl.ucsf.edu>

Hi Francesco,
You would use the ?match? command.  The atoms don?t need to have the same names since they are specified in the command.  Of course, if you are matching fewer than 3 pairs of atoms, the superposition will not be unique.  It will still work, but there will be a warning.

If you are only superimposing one pair of atoms (one atom in one model, another in a different model), an easy way is to just select the two atoms (ctrl-click, Shift-ctrl-click) and then use command: match sel

That will move the model containing the atom you selected first.  Otherwise you could specify atoms in the normal command-line way by model number, residue number or name, chain ID, and atom name.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic>

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


> On Oct 12, 2015, at 10:12 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> Hello;
> 
> Ho to superimpose a fake atom (pdb file available) to a coordiated metal in a protein? I could change the name of the fake atom to that of the metal, but then I need an rmsd overlay.
> 
> hope it is clear. thanks
> 
> francesco pietra




From chiendarret at gmail.com  Mon Oct 12 14:10:55 2015
From: chiendarret at gmail.com (Francesco Pietra)
Date: Mon, 12 Oct 2015 23:10:55 +0200
Subject: [Chimera-users] rmsd overlay
In-Reply-To: <2F2CBEDF-9A40-417F-BC37-A4E8CA73E025@cgl.ucsf.edu>
References: <CAEv0nmvimgxN3NzQXOM7C-P5wN6uwgBgMUJiXK3PDwD4m_W+cQ@mail.gmail.com>
	<2F2CBEDF-9A40-417F-BC37-A4E8CA73E025@cgl.ucsf.edu>
Message-ID: <CAEv0nmva8PkxJ0VOo6W=f_-S3MappD+YB5ft6P3oaO9EhaSGKA@mail.gmail.com>

Elaine:

> If you are only superimposing one pair of atoms (one atom in one model,
> another in a different model), an easy way is to just select the two atoms
> (ctrl-click, Shift-ctrl-click) and then use command: match sel
>

That worked nicely, the fake atom brought all its connections with. I had
only to combine the generated models (on saving pdb), deleting the original
metal atoms.

Thanks
francesco

On Mon, Oct 12, 2015 at 9:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> You would use the ?match? command.  The atoms don?t need to have the same
> names since they are specified in the command.  Of course, if you are
> matching fewer than 3 pairs of atoms, the superposition will not be
> unique.  It will still work, but there will be a warning.
>
> If you are only superimposing one pair of atoms (one atom in one model,
> another in a different model), an easy way is to just select the two atoms
> (ctrl-click, Shift-ctrl-click) and then use command: match sel
>
> That will move the model containing the atom you selected first.
> Otherwise you could specify atoms in the normal command-line way by model
> number, residue number or name, chain ID, and atom name.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic
> >
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Oct 12, 2015, at 10:12 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >
> > Hello;
> >
> > Ho to superimpose a fake atom (pdb file available) to a coordiated metal
> in a protein? I could change the name of the fake atom to that of the
> metal, but then I need an rmsd overlay.
> >
> > hope it is clear. thanks
> >
> > francesco pietra
>
>
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From smith_liu123 at 163.com  Tue Oct 13 08:22:54 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Tue, 13 Oct 2015 23:22:54 +0800 (CST)
Subject: [Chimera-users] on 2d label related movie command
Message-ID: <3a9b3dfa.fb42.15061cc102d.Coremail.smith_liu123@163.com>

Dear All,


By chimera is any method we label a residue in a protein after scaling-up around that residue in a movie?


Best regards.


Smith
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From meng at cgl.ucsf.edu  Tue Oct 13 09:27:19 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 13 Oct 2015 09:27:19 -0700
Subject: [Chimera-users] on 2d label related movie command
In-Reply-To: <3a9b3dfa.fb42.15061cc102d.Coremail.smith_liu123@163.com>
References: <3a9b3dfa.fb42.15061cc102d.Coremail.smith_liu123@163.com>
Message-ID: <9FBD534B-C985-4556-BCB2-E7B01D3C6109@cgl.ucsf.edu>

Dear Smith,
Your two choices are 

(1) The regular 3D labels (flat but located in 3D space and move along with associated atoms), such as shown with the command ?rlabel?, ?label? or menu: Actions? Label.  For example, to label model 0 residue 50 in chain A, command: rlabel #0:50.a

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rlabel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/label.html>

(2) 2D labels (flat, located in 2D space and do not move along with atoms) such as created with the command ?2dlabels? or 2D Labels graphical interface

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>

The 2D labels are generally more attractive and there is more flexibility: you can have multiple labels of different colors and sizes, with arbitrary contents including symbols.  You can create, hide, show, fade-in, fade-out, and move these completely with the command.  Or, you can pre-make several labels with the graphical interface and save them along with your session.  Later (e.g. after restarting the session) you can hide and show the already created 2D labels with the command.

Example scripts with 2D labels?

This one is pretty short, just open in Chimera to see it execute, view text to see commands:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com>

This one is a morphing movie in our Animation Gallery, links to both the movie and the script file:
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>

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


> On Oct 13, 2015, at 8:22 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
> Dear All,
> 
> By chimera is any method we label a residue in a protein after scaling-up around that residue in a movie?
> 
> Best regards.
> 
> Smith
> 



From gijsschot at gmail.com  Mon Oct 12 19:26:53 2015
From: gijsschot at gmail.com (gijs)
Date: Tue, 13 Oct 2015 11:26:53 +0900
Subject: [Chimera-users] output hdf5
Message-ID: <CC06534F-689A-4DFC-8DE1-C1BFFDABBB6D@gmail.com>

Dear Sir/Madam.

First of all I want to complement the chimera team for writing a fantastic package for view macromolecular complexes. 

I am a researcher from the coherent X-ray diffraction community and we are also producing 3D models using our software [1]. However, we write data in a hdf5 format. Would you be interested to incorporate our file system into your package, or, and I think this is for now the better solution, could you provide a way I can write my hdf5 file to a chimera readable format and visa versa? For instance, I am trying to open a .map file from the EM databank, but do not know to exactly how to convert it. Are there tools? What file tree in hdf5 do I need?

With kind regards,
Gijs van der Schot

[1]  http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098102


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From goddard at sonic.net  Tue Oct 13 14:35:57 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 13 Oct 2015 14:35:57 -0700
Subject: [Chimera-users] output hdf5
In-Reply-To: <CC06534F-689A-4DFC-8DE1-C1BFFDABBB6D@gmail.com>
References: <CC06534F-689A-4DFC-8DE1-C1BFFDABBB6D@gmail.com>
Message-ID: <2817B39B-92B8-4222-9559-BFCCC71FF6B9@sonic.net>

Hi Gijs,

  Chimera can probably directly read your HDF density map if you have it read it using Chimera map format.  If you use File / Open? in Chimera and choose File Type: All (ask type) and specify Chimera map.  It won?t get the grid spacing but it will look in the HDF5 file for any 3d arrays and show them.  The format of this Chimera specific density map is briefly described at the top of the Python code

	http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/cmap/cmap_format.py

which is included in your Chimera distribution in

	chimera/share/VolumeData/cmap/cmap_format.py

or on Mac

	Chimera.app/Contents/Resources/share/VolumeData/cmap/cmap_format.py

If you wanted other software to read your files you might instead use the format used by EMDB, namely CCP4 or MRC:

	http://www.emdatabank.org/mapformat.html <http://www.emdatabank.org/mapformat.html>

For an example of Python code that reads and writes that format you can look in Chimera

	chimera/share/VolumeData/mrc/mrc_format.py

	chimera/share/VolumeData/mrc/writemrc.py

  Tom



> On Oct 12, 2015, at 7:26 PM, gijs wrote:
> 
> Dear Sir/Madam.
> 
> First of all I want to complement the chimera team for writing a fantastic package for view macromolecular complexes. 
> 
> I am a researcher from the coherent X-ray diffraction community and we are also producing 3D models using our software [1]. However, we write data in a hdf5 format. Would you be interested to incorporate our file system into your package, or, and I think this is for now the better solution, could you provide a way I can write my hdf5 file to a chimera readable format and visa versa? For instance, I am trying to open a .map file from the EM databank, but do not know to exactly how to convert it. Are there tools? What file tree in hdf5 do I need?
> 
> With kind regards,
> Gijs van der Schot
> 
> [1]  http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098102 <http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098102>
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From Melanie.Sanders at ARS.USDA.GOV  Tue Oct 13 14:11:02 2015
From: Melanie.Sanders at ARS.USDA.GOV (Sanders, Melanie - ARS)
Date: Tue, 13 Oct 2015 21:11:02 +0000
Subject: [Chimera-users] drawing single stranded dna
Message-ID: <C2166A1968B31D4DBD730CA792E5087D6EF11D@001FSN2MPN1-014.001f.mgd2.msft.net>

Dear,

Is it possible to draw a single stranded dna. I always get a double stranded one if I enter the nucleic acids.

Best regards,

Melanie Sanders, PhD.
Mycotoxin Prevention and Applied Microbiology
USDA-ARS
1815 North University Street
Peoria, Illinois 61604-3999
Phone: 309-681-6208
e-mail: melanie.sanders at ars.usda.gov<mailto:melanie.sanders at ars.usda.gov>

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From meng at cgl.ucsf.edu  Tue Oct 13 15:28:54 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 13 Oct 2015 15:28:54 -0700
Subject: [Chimera-users] drawing single stranded dna
In-Reply-To: <C2166A1968B31D4DBD730CA792E5087D6EF11D@001FSN2MPN1-014.001f.mgd2.msft.net>
References: <C2166A1968B31D4DBD730CA792E5087D6EF11D@001FSN2MPN1-014.001f.mgd2.msft.net>
Message-ID: <19EE6E00-61CB-4D56-9AF3-558D1CE5D9CA@cgl.ucsf.edu>

Hi Melanie,
I guess you are referring to building DNA with the Build Structure tool.  You can only build double-stranded nucleic acids in Chimera, not single-stranded.  However, regardless of how you got a double-stranded structure (e.g. from the Protein Data Bank structure repository), you could always delete or hide one strand.  Of course, the remaining strand will still be in the original conformation.  Single-stranded nucleic acids are less regular in structure in reality, and Chimera does not have anything to predict reasonable coordinates in that situation.

If you built it with Chimera, one strand is chain A and the other is chain B.  You could select one chain (for example, menu: Select? Chain? B)

? then hide the selection (for example, menu: Actions? Atoms/Bonds? hide, menu: Actions? Ribbon? hide)

? or delete the selection (Actions? Atoms/Bonds? delete) which is irreversible.

There are also lots of options for how to display it.  For example, see the Getting Started tutorial part 2 (menu: Help? Tutorials).

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

> On Oct 13, 2015, at 2:11 PM, Sanders, Melanie - ARS <Melanie.Sanders at ARS.USDA.GOV> wrote:
> 
> Dear,
>  
> Is it possible to draw a single stranded dna. I always get a double stranded one if I enter the nucleic acids.
>  
> Best regards,
>  
> Melanie Sanders, PhD.
> Mycotoxin Prevention and Applied Microbiology
> USDA-ARS
> 1815 North University Street
> Peoria, Illinois 61604-3999
> Phone: 309-681-6208
> e-mail: melanie.sanders at ars.usda.gov




From pett at cgl.ucsf.edu  Tue Oct 13 16:59:01 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 13 Oct 2015 16:59:01 -0700
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <5CAB86B8-241A-4755-94BE-87AA85055743@gmail.com>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
	<1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
	<5CAB86B8-241A-4755-94BE-87AA85055743@gmail.com>
Message-ID: <C89F4601-ACFC-4488-8899-09DC8C4C72FF@cgl.ucsf.edu>

Hi Oliver,
	Certainly a useful suggestion, though it will require some implementation effort.  Right now, the command line has no ?state? ? when you type something, it doesn?t need to know what keys were typed before, whereas with your suggestion when someone types up/down arrow the behavior depends on whether the preceding typed key was an up/down arrow or was some other key.  Also, nothing in the code monitors every keystroke; only some keystrokes (e.g. up/down arrow, Return) are handled as they occur.
	Consequently, this is getting on my to-do list but may be awhile before anything materializes.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Oct 12, 2015, at 5:59 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi Eric, I have been using the alterations you made to history navigation in Chimera and I like them a lot - they make it much easier to locate old commands.
> 
> I have one suggestion for a slight tweak? at the moment, scrolling up through the history (with Shift+Up) seems to update the string to filter on as I scroll. There is a (very) minor issue with this approach. It means the process is not reversible and the results depend on the contents and ordering of the history.
> 
> For example, lets say I?m looking for a command I typed a while back, i know it started with ?bond? but can?t remember the exact name of the command. If I type ?bond? and then hit Shift+Up, I will only find the first matching command - if I had both bondrepr and bondzone in my command history, for example, I will only see the first one. I think it would be more intuitive if history filtering paid attention to only the initially typed string, if that is possible - so if I type ?bond?, I will scroll up through bondrepr, bond zone, bonddisplay etc, and will obtain the same results heading back ?down? through the command history.
> 
> Cheers,
> Oli.
> 
> 
>> On Oct 1, 2015, at 3:31 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> 
>> I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?
>> 
>> ?Eric
>> 
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>>> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> 
>>> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
>>> 
>>> Cheers,
>>> Oliver.
>>> 
>>> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
>>> 
>>> Cheers,
>>> Oli.
>>> 
>>> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>> Hi Oliver,
>>>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
>>> 
>>> ?Eric
>>> 
>>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> >
>>> > Hi all,
>>> >
>>> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
>>> >
>>> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
>>> >
>>> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
>>> >
>>> > Cheers,
>>> > Oliver.
>>> > _______________________________________________
>>> > Chimera-users mailing list
>>> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>> >
>>> 
>>> 
>>> 
>> 
> 

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From olibclarke at gmail.com  Tue Oct 13 17:00:39 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 13 Oct 2015 20:00:39 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <C89F4601-ACFC-4488-8899-09DC8C4C72FF@cgl.ucsf.edu>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
	<1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
	<5CAB86B8-241A-4755-94BE-87AA85055743@gmail.com>
	<C89F4601-ACFC-4488-8899-09DC8C4C72FF@cgl.ucsf.edu>
Message-ID: <66E0CCC1-8265-4FAF-93C0-57BB2C852DC1@gmail.com>

Ah, makes perfect sense, thanks Eric! The current behaviour is much better than it was previously anyway - this was just a minor suggestion for improvement.

Cheers,
Oli.
> On Oct 13, 2015, at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Oliver,
> 	Certainly a useful suggestion, though it will require some implementation effort.  Right now, the command line has no ?state? ? when you type something, it doesn?t need to know what keys were typed before, whereas with your suggestion when someone types up/down arrow the behavior depends on whether the preceding typed key was an up/down arrow or was some other key.  Also, nothing in the code monitors every keystroke; only some keystrokes (e.g. up/down arrow, Return) are handled as they occur.
> 	Consequently, this is getting on my to-do list but may be awhile before anything materializes.
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Oct 12, 2015, at 5:59 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Hi Eric, I have been using the alterations you made to history navigation in Chimera and I like them a lot - they make it much easier to locate old commands.
>> 
>> I have one suggestion for a slight tweak? at the moment, scrolling up through the history (with Shift+Up) seems to update the string to filter on as I scroll. There is a (very) minor issue with this approach. It means the process is not reversible and the results depend on the contents and ordering of the history.
>> 
>> For example, lets say I?m looking for a command I typed a while back, i know it started with ?bond? but can?t remember the exact name of the command. If I type ?bond? and then hit Shift+Up, I will only find the first matching command - if I had both bondrepr and bondzone in my command history, for example, I will only see the first one. I think it would be more intuitive if history filtering paid attention to only the initially typed string, if that is possible - so if I type ?bond?, I will scroll up through bondrepr, bond zone, bonddisplay etc, and will obtain the same results heading back ?down? through the command history.
>> 
>> Cheers,
>> Oli.
>> 
>> 
>>> On Oct 1, 2015, at 3:31 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>> 
>>> I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?
>>> 
>>> ?Eric
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>>> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>> 
>>>> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
>>>> 
>>>> Cheers,
>>>> Oliver.
>>>> 
>>>> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
>>>> 
>>>> Cheers,
>>>> Oli.
>>>> 
>>>> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>>> Hi Oliver,
>>>>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
>>>> 
>>>> ?Eric
>>>> 
>>>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>> >
>>>> > Hi all,
>>>> >
>>>> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
>>>> >
>>>> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
>>>> >
>>>> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
>>>> >
>>>> > Cheers,
>>>> > Oliver.
>>>> > _______________________________________________
>>>> > Chimera-users mailing list
>>>> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>> >
>>>> 
>>>> 
>>>> 
>>> 
>> 
> 

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From olibclarke at gmail.com  Tue Oct 13 17:13:37 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 13 Oct 2015 20:13:37 -0400
Subject: [Chimera-users] Show symmetry axis?
Message-ID: <5DBFD175-0F48-4731-9E7E-C3F635BC571D@gmail.com>

Hi all,

Is there any way to easily generate an axis (of the type created by define axis, not a BILD file) corresponding to the z-axis of a map? Or of the symmetry axis of a map as identified by measure symmetry (which should be the same thing I guess)?

I would like to be able to align Cn symmetric maps,  which in general have the Cn symmetry axis coincident with z, while strictly obeying the Cn symmetry of the map. 

There is no built-in way to do this in chimera that I know of, but if I could create an axis corresponding to z for both maps, I could measure correlation between the two maps about that axis, after first aligning the symmetry axes of the two maps and approximately matching their translations along that axis (incidentally, for the same purpose it would be handy to have an additional option for "measure correlation rotationaxis", to measure correlation in a distance range corresponding to +/- x ? from the current position along the specified axis - angleRange is currently present, ?distanceRange? seems like it could be a useful extension).

The closest I have come so far is the following alias:

alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define axis sel; ~disp sel; reset tmp

This will generate an axis perpendicular to and in the center of the screen, but this seems like a bit of a hack? also when I use measure correlation with this axis ("measure correlation #2 #0 rotationAxis a1?, where #2 and #0 are the two maps and the axis is a1),  I get the attached error - is this a bug or did I make a stupid mistake somewhere?

Cheers,
Oliver.




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From olibclarke at gmail.com  Tue Oct 13 18:26:52 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 13 Oct 2015 21:26:52 -0400
Subject: [Chimera-users] Show symmetry axis?
In-Reply-To: <mailman.21.1444781644.28391.chimera-users@cgl.ucsf.edu>
References: <mailman.21.1444781644.28391.chimera-users@cgl.ucsf.edu>
Message-ID: <2DFC9B4F-1940-4FCE-B626-E136D833461E@gmail.com>

Actually never mind? just realized I have requested similar previously and there is already a ticket open (http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829>). 

Nevertheless, consider this another vote for constraining fitmap to the symmetry of the input maps (or models) - would be very very helpful when dealing with ion channels.

Cheers,
Oliver.
> 
> Message: 1
> Date: Tue, 13 Oct 2015 20:13:37 -0400
> From: Oliver Clarke <olibclarke at gmail.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Show symmetry axis?
> Message-ID: <5DBFD175-0F48-4731-9E7E-C3F635BC571D at gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> Is there any way to easily generate an axis (of the type created by define axis, not a BILD file) corresponding to the z-axis of a map? Or of the symmetry axis of a map as identified by measure symmetry (which should be the same thing I guess)?
> 
> I would like to be able to align Cn symmetric maps,  which in general have the Cn symmetry axis coincident with z, while strictly obeying the Cn symmetry of the map. 
> 
> There is no built-in way to do this in chimera that I know of, but if I could create an axis corresponding to z for both maps, I could measure correlation between the two maps about that axis, after first aligning the symmetry axes of the two maps and approximately matching their translations along that axis (incidentally, for the same purpose it would be handy to have an additional option for "measure correlation rotationaxis", to measure correlation in a distance range corresponding to +/- x ? from the current position along the specified axis - angleRange is currently present, ?distanceRange? seems like it could be a useful extension).
> 
> The closest I have come so far is the following alias:
> 
> alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define axis sel; ~disp sel; reset tmp
> 
> This will generate an axis perpendicular to and in the center of the screen, but this seems like a bit of a hack? also when I use measure correlation with this axis ("measure correlation #2 #0 rotationAxis a1?, where #2 and #0 are the two maps and the axis is a1),  I get the attached error - is this a bug or did I make a stupid mistake somewhere?
> 
> Cheers,
> Oliver.
> 
> 
> 
> 
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> 
> ------------------------------
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> End of Chimera-users Digest, Vol 150, Issue 18
> **********************************************

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From goddard at sonic.net  Tue Oct 13 18:30:23 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 13 Oct 2015 18:30:23 -0700
Subject: [Chimera-users] Show symmetry axis?
In-Reply-To: <5DBFD175-0F48-4731-9E7E-C3F635BC571D@gmail.com>
References: <5DBFD175-0F48-4731-9E7E-C3F635BC571D@gmail.com>
Message-ID: <497ABFA6-0CD8-4529-8D4B-FF2273824EB7@sonic.net>

Hi Oliver,

Sounds like your goal is to align to maps with Cn symmetry such that the symmetry axes exactly match.  The closest to that is to align the maps and use the Fit Map dialog or fitmap command.  But that doesn?t guarantee the symmetry axes exactly match.  Since you want to exactly match the axes it seems you need two things, first to define the axis.  That sounds like "measure symmetry? because you need a point on the axis that measure symmetry figures out.  But that command doesn?t have any option to create an axis. It wouldn?t be too hard to add such an option.  Then to optimize the fit you want to allow only translations along the axis and rotations around the axis.  Chimera can?t do that.  The underlying fitmap code could do it but it would require modifications to the algorithmic code, and command options.  All the above things would be nice, but it is too much work to do on Chimera 1 when we are working on Chimera 2.

The error with your ?measure correlation? command is that the rotationAxis option does not recognize axes defined by ?define axis?.  Should give a nice error message explaining that ? the traceback instead of a readable error message is a bug.

	Tom


> On Oct 13, 2015, at 5:13 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all,
> 
> Is there any way to easily generate an axis (of the type created by define axis, not a BILD file) corresponding to the z-axis of a map? Or of the symmetry axis of a map as identified by measure symmetry (which should be the same thing I guess)?
> 
> I would like to be able to align Cn symmetric maps,  which in general have the Cn symmetry axis coincident with z, while strictly obeying the Cn symmetry of the map. 
> 
> There is no built-in way to do this in chimera that I know of, but if I could create an axis corresponding to z for both maps, I could measure correlation between the two maps about that axis, after first aligning the symmetry axes of the two maps and approximately matching their translations along that axis (incidentally, for the same purpose it would be handy to have an additional option for "measure correlation rotationaxis", to measure correlation in a distance range corresponding to +/- x ? from the current position along the specified axis - angleRange is currently present, ?distanceRange? seems like it could be a useful extension).
> 
> The closest I have come so far is the following alias:
> 
> alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define axis sel; ~disp sel; reset tmp
> 
> This will generate an axis perpendicular to and in the center of the screen, but this seems like a bit of a hack? also when I use measure correlation with this axis ("measure correlation #2 #0 rotationAxis a1?, where #2 and #0 are the two maps and the axis is a1),  I get the attached error - is this a bug or did I make a stupid mistake somewhere?
> 
> Cheers,
> Oliver.
> 
> <PastedGraphic-1.png>
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From olibclarke at gmail.com  Tue Oct 13 19:02:00 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Tue, 13 Oct 2015 22:02:00 -0400
Subject: [Chimera-users] Show symmetry axis?
In-Reply-To: <497ABFA6-0CD8-4529-8D4B-FF2273824EB7@sonic.net>
References: <5DBFD175-0F48-4731-9E7E-C3F635BC571D@gmail.com>
	<497ABFA6-0CD8-4529-8D4B-FF2273824EB7@sonic.net>
Message-ID: <CAPghYOqSja6n7Z+qOqy7jQvsCZ3Trbae0ugshQ857cQR+hSjyw@mail.gmail.com>

Got it, thanks Tom, yep that's exactly what I want to do... I use fitmap at
the moment, and it is close, but I can tell the match is not symmetric
because the difference map is asymmetric. My apologies for bothering you, I
realized after posting I had asked a similar question previously. Looking
forward to seeing Chimera 2 when it's ready!

Cheers,
Oliver.

On Tue, Oct 13, 2015 at 9:30 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>
> Sounds like your goal is to align to maps with Cn symmetry such that the
> symmetry axes exactly match.  The closest to that is to align the maps and
> use the Fit Map dialog or fitmap command.  But that doesn?t guarantee the
> symmetry axes exactly match.  Since you want to exactly match the axes it
> seems you need two things, first to define the axis.  That sounds like
> "measure symmetry? because you need a point on the axis that measure
> symmetry figures out.  But that command doesn?t have any option to create
> an axis. It wouldn?t be too hard to add such an option.  Then to optimize
> the fit you want to allow only translations along the axis and rotations
> around the axis.  Chimera can?t do that.  The underlying fitmap code could
> do it but it would require modifications to the algorithmic code, and
> command options.  All the above things would be nice, but it is too much
> work to do on Chimera 1 when we are working on Chimera 2.
>
> The error with your ?measure correlation? command is that the rotationAxis
> option does not recognize axes defined by ?define axis?.  Should give a
> nice error message explaining that ? the traceback instead of a readable
> error message is a bug.
>
>         Tom
>
>
> > On Oct 13, 2015, at 5:13 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> >
> > Hi all,
> >
> > Is there any way to easily generate an axis (of the type created by
> define axis, not a BILD file) corresponding to the z-axis of a map? Or of
> the symmetry axis of a map as identified by measure symmetry (which should
> be the same thing I guess)?
> >
> > I would like to be able to align Cn symmetric maps,  which in general
> have the Cn symmetry axis coincident with z, while strictly obeying the Cn
> symmetry of the map.
> >
> > There is no built-in way to do this in chimera that I know of, but if I
> could create an axis corresponding to z for both maps, I could measure
> correlation between the two maps about that axis, after first aligning the
> symmetry axes of the two maps and approximately matching their translations
> along that axis (incidentally, for the same purpose it would be handy to
> have an additional option for "measure correlation rotationaxis", to
> measure correlation in a distance range corresponding to +/- x ? from the
> current position along the specified axis - angleRange is currently
> present, ?distanceRange? seems like it could be a useful extension).
> >
> > The closest I have come so far is the following alias:
> >
> > alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip
> hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define
> axis sel; ~disp sel; reset tmp
> >
> > This will generate an axis perpendicular to and in the center of the
> screen, but this seems like a bit of a hack? also when I use measure
> correlation with this axis ("measure correlation #2 #0 rotationAxis a1?,
> where #2 and #0 are the two maps and the axis is a1),  I get the attached
> error - is this a bug or did I make a stupid mistake somewhere?
> >
> > Cheers,
> > Oliver.
> >
> > <PastedGraphic-1.png>
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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From cathy.lawson at rutgers.edu  Wed Oct 14 09:22:56 2015
From: cathy.lawson at rutgers.edu (Cathy Lawson)
Date: Wed, 14 Oct 2015 12:22:56 -0400
Subject: [Chimera-users] Announcing the 2015/2016 EMDataBank Model Challenge
Message-ID: <6503AC33-9930-46E7-9DF3-C2AAB60A0675@rutgers.edu>

Dear Chimera User List Members,
EMDataBank is pleased to announce the 2015/2016 Model Challenge.

All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.

Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 ?. 

Challengers are sought to create and validate models from challenge target maps in four different categories (1. optimize current cryoEM model, 2. fit known related cryoEM, crystallographic, or comparative models, 3. ab initio model building, 4. any other method of map interpretation), and upload their results with associated details.

Assessors are sought to participate in evaluating submitted models.

Registration is now open for all interested participants. Challengers may submit their models between November and April.  Before submissions open, all are encouraged to provide feedback on submission requirements.  An open assessment period will commence in late 2016.

To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MODEL CHALLENGE" in the menu bar.

This is the second of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.  The first challenge is focused on creating reconstructions from raw 2D image data and is currently in progress (click on "MAP CHALLENGE" in the menu bar).


Sincerely,

Cathy Lawson on behalf of the EMDataBank Team and the Model Challenge Committee
emdatabank.org 
www.facebook.com/emdatabank3dem
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From meng at cgl.ucsf.edu  Wed Oct 14 09:57:32 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Oct 2015 09:57:32 -0700
Subject: [Chimera-users] Interactive Protein Structure and Sequence
	Alignment?
In-Reply-To: <CAFnT6q_D4-LeSFCSQsXXw_gP+otEJgVNhoXQgVGnfPOZA8GTsA@mail.gmail.com>
References: <CAFnT6q_D4-LeSFCSQsXXw_gP+otEJgVNhoXQgVGnfPOZA8GTsA@mail.gmail.com>
Message-ID: <9EBB3589-9EA1-4461-A600-092E713C0118@cgl.ucsf.edu>


On Oct 13, 2015, at 6:44 PM, Abba Leffler <aleffler at alumni.princeton.edu> wrote:

> Dear Professor Meng,
> I'm a frequent user of Chimera, mostly for visualization of homology models of large complexes. There's one feature I've search for in Chimera and not found. I wonder if you can help me.
> 
> I would like to do two things, which are related.
> 
> First, I would like to be able to visualize where inserts, deletions, and mutations are on the template structure relative to the target sequence. Is there any way to do that? I haven't found one.
> 
> In a related question, I'd like to be able to interactively edit the sequence alignment (i.e. move indels that are in secondary structure elements) and then recompute the homology model to see if the DOPE score gets better or worse. Is that a possibility?
> 
> I've found that many people have told me that alignments have to be "manually corrected", but there don't seem to be many tools out there for doing that in a sane way. If there are any you could recommend, I would sincerely appreciate it.
> 
> All best,
> -Abba

Dear Abba,

(1) Any time you have a structure open in Chimera and associated with some sequence in MultAlign Viewer (Chimera?s sequence viewer), you can easily  map between the sequence and structure.  It can be an individual sequence or one within a multiple sequence alignment. You can just highlight an area of interest on the sequence with the mouse and it will be highlighted on the structure.  

See the Sequences and Structures tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>

? and/or the Multalign Viewer documentation, especially the part about sequence-structure association:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association>

If you used the Modeller interface in Chimera, you already have the target-template sequence alignment open in Chimera.  Then you could just use the mouse to highlight where in the sequence there is a mutation or insertion to have it highlighted on the structure(s).  Actually this does selection.  Then you can use the Actions menu to do something (e.g. coloring) to the current structure selection.  While you can?t highlight something in the sequence that isn?t there (a deletion), you could certainly highlight the positions around it.

(2) Multalign Viewer does allow for some small amount of manual editing, but it is not optimized for this purpose and other programs should be more suitable for any serious amount of editing.  However, I don?t do this myself so I cannot advise... maybe JalView?  Here are the instructions for manual editing in Multalign Viewer:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing>

I hope this helps.  I?ve CC?d this reply to chimera-users, which is the address we recommend for asking Chimera questions. Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco






From pett at cgl.ucsf.edu  Wed Oct 14 14:11:51 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 14 Oct 2015 14:11:51 -0700
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <66E0CCC1-8265-4FAF-93C0-57BB2C852DC1@gmail.com>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
	<1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
	<5CAB86B8-241A-4755-94BE-87AA85055743@gmail.com>
	<C89F4601-ACFC-4488-8899-09DC8C4C72FF@cgl.ucsf.edu>
	<66E0CCC1-8265-4FAF-93C0-57BB2C852DC1@gmail.com>
Message-ID: <FECD3823-E0E0-40E9-932A-4BD9FAEF33B4@cgl.ucsf.edu>

Well, got to this sooner than I thought I would.  Will be in the next daily build.

?Eric

> On Oct 13, 2015, at 5:00 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Ah, makes perfect sense, thanks Eric! The current behaviour is much better than it was previously anyway - this was just a minor suggestion for improvement.
> 
> Cheers,
> Oli.
>> On Oct 13, 2015, at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> 
>> Hi Oliver,
>> 	Certainly a useful suggestion, though it will require some implementation effort.  Right now, the command line has no ?state? ? when you type something, it doesn?t need to know what keys were typed before, whereas with your suggestion when someone types up/down arrow the behavior depends on whether the preceding typed key was an up/down arrow or was some other key.  Also, nothing in the code monitors every keystroke; only some keystrokes (e.g. up/down arrow, Return) are handled as they occur.
>> 	Consequently, this is getting on my to-do list but may be awhile before anything materializes.
>> 
>> ?Eric
>> 
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>>> On Oct 12, 2015, at 5:59 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> 
>>> Hi Eric, I have been using the alterations you made to history navigation in Chimera and I like them a lot - they make it much easier to locate old commands.
>>> 
>>> I have one suggestion for a slight tweak? at the moment, scrolling up through the history (with Shift+Up) seems to update the string to filter on as I scroll. There is a (very) minor issue with this approach. It means the process is not reversible and the results depend on the contents and ordering of the history.
>>> 
>>> For example, lets say I?m looking for a command I typed a while back, i know it started with ?bond? but can?t remember the exact name of the command. If I type ?bond? and then hit Shift+Up, I will only find the first matching command - if I had both bondrepr and bondzone in my command history, for example, I will only see the first one. I think it would be more intuitive if history filtering paid attention to only the initially typed string, if that is possible - so if I type ?bond?, I will scroll up through bondrepr, bond zone, bonddisplay etc, and will obtain the same results heading back ?down? through the command history.
>>> 
>>> Cheers,
>>> Oli.
>>> 
>>> 
>>>> On Oct 1, 2015, at 3:31 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>>> 
>>>> I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?
>>>> 
>>>> ?Eric
>>>> 
>>>> 	Eric Pettersen
>>>> 	UCSF Computer Graphics Lab
>>>> 
>>>>> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>> 
>>>>> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
>>>>> 
>>>>> Cheers,
>>>>> Oliver.
>>>>> 
>>>>> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
>>>>> 
>>>>> Cheers,
>>>>> Oli.
>>>>> 
>>>>> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>>>> Hi Oliver,
>>>>>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
>>>>> 
>>>>> ?Eric
>>>>> 
>>>>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>> >
>>>>> > Hi all,
>>>>> >
>>>>> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
>>>>> >
>>>>> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
>>>>> >
>>>>> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
>>>>> >
>>>>> > Cheers,
>>>>> > Oliver.
>>>>> > _______________________________________________
>>>>> > Chimera-users mailing list
>>>>> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>>>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>>> >
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 

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From olibclarke at gmail.com  Wed Oct 14 15:01:53 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 14 Oct 2015 18:01:53 -0400
Subject: [Chimera-users] Suggestion - autofilter history by typed
	substring?
In-Reply-To: <FECD3823-E0E0-40E9-932A-4BD9FAEF33B4@cgl.ucsf.edu>
References: <312B2BD2-BFD6-42D1-8F29-6CB96BFE0878@gmail.com>
	<F79C06E2-52BA-4CDC-A7A8-97AA03561FEB@cgl.ucsf.edu>
	<CAPghYOrU6twhkEHAseKRBA4CWOj4v=52LRdzu0apWwQ-=YfrSg@mail.gmail.com>
	<CAPghYOqT=mFD+FqdfnJ8Q_bsVw8-EfcFEUhCP=WQDheEugbFrg@mail.gmail.com>
	<1D385337-EBB8-4CBE-B0B9-6552FBE62B2D@cgl.ucsf.edu>
	<5CAB86B8-241A-4755-94BE-87AA85055743@gmail.com>
	<C89F4601-ACFC-4488-8899-09DC8C4C72FF@cgl.ucsf.edu>
	<66E0CCC1-8265-4FAF-93C0-57BB2C852DC1@gmail.com>
	<FECD3823-E0E0-40E9-932A-4BD9FAEF33B4@cgl.ucsf.edu>
Message-ID: <44E5196D-5CE6-4501-9967-59CDBE65F6ED@gmail.com>

Wow, that was quick! Thanks Eric!

Oli.
> On Oct 14, 2015, at 5:11 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Well, got to this sooner than I thought I would.  Will be in the next daily build.
> 
> ?Eric
> 
>> On Oct 13, 2015, at 5:00 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Ah, makes perfect sense, thanks Eric! The current behaviour is much better than it was previously anyway - this was just a minor suggestion for improvement.
>> 
>> Cheers,
>> Oli.
>>> On Oct 13, 2015, at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>> 
>>> Hi Oliver,
>>> 	Certainly a useful suggestion, though it will require some implementation effort.  Right now, the command line has no ?state? ? when you type something, it doesn?t need to know what keys were typed before, whereas with your suggestion when someone types up/down arrow the behavior depends on whether the preceding typed key was an up/down arrow or was some other key.  Also, nothing in the code monitors every keystroke; only some keystrokes (e.g. up/down arrow, Return) are handled as they occur.
>>> 	Consequently, this is getting on my to-do list but may be awhile before anything materializes.
>>> 
>>> ?Eric
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>>> On Oct 12, 2015, at 5:59 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>> 
>>>> Hi Eric, I have been using the alterations you made to history navigation in Chimera and I like them a lot - they make it much easier to locate old commands.
>>>> 
>>>> I have one suggestion for a slight tweak? at the moment, scrolling up through the history (with Shift+Up) seems to update the string to filter on as I scroll. There is a (very) minor issue with this approach. It means the process is not reversible and the results depend on the contents and ordering of the history.
>>>> 
>>>> For example, lets say I?m looking for a command I typed a while back, i know it started with ?bond? but can?t remember the exact name of the command. If I type ?bond? and then hit Shift+Up, I will only find the first matching command - if I had both bondrepr and bondzone in my command history, for example, I will only see the first one. I think it would be more intuitive if history filtering paid attention to only the initially typed string, if that is possible - so if I type ?bond?, I will scroll up through bondrepr, bond zone, bonddisplay etc, and will obtain the same results heading back ?down? through the command history.
>>>> 
>>>> Cheers,
>>>> Oli.
>>>> 
>>>> 
>>>>> On Oct 1, 2015, at 3:31 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>>>> 
>>>>> I also just tweaked the up/down history navigation so that if the navigation would produce a result identical to whatever is currently in the command line, it ?keeps going? until it yields a results that isn?t identical.  This applies to both normal up/down and shifted up/down.  So, if you have several consecutive identical entries in your command history, this effectively treats them as one entry and therefore may reduce the need for a preference to not record consecutive identical entries in the command history?
>>>>> 
>>>>> ?Eric
>>>>> 
>>>>> 	Eric Pettersen
>>>>> 	UCSF Computer Graphics Lab
>>>>> 
>>>>>> On Oct 1, 2015, at 6:35 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>>> 
>>>>>> Just tried out the new daily build and the command line history autofiltering works great, thanks Eric! This makes it much easier to cycle through previous selection commands, or to remember syntax for previous vop commands.
>>>>>> 
>>>>>> Cheers,
>>>>>> Oliver.
>>>>>> 
>>>>>> On Wed, Sep 30, 2015 at 2:46 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>>> That sounds great, thanks Eric! I look forward to trying it out, think it'll be a real timesaver!
>>>>>> 
>>>>>> Cheers,
>>>>>> Oli.
>>>>>> 
>>>>>> On Wed, Sep 30, 2015 at 2:19 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>>>>> Hi Oliver,
>>>>>>         This seems like a useful suggestion.  I have implemented it in a slightly different form.  If you use the shift key while navigating the command history (i.e. shift up/down arrow or control-N/P), then it will jump to the next history entry that matches the current command name.  Available in the next daily build.
>>>>>> 
>>>>>> ?Eric
>>>>>> 
>>>>>> > On Sep 23, 2015, at 2:42 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>>>>> >
>>>>>> > Hi all,
>>>>>> >
>>>>>> > Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring?
>>>>>> >
>>>>>> > That is if I have typed ?sel? and hit the up arrow, to only cycle through those commands in the history that start with ?sel?.
>>>>>> >
>>>>>> > This would be particularly handy for scrolling quickly through recent ?sel? and ?color? commands - a similar mechanism is implemented in several shells and it works well.
>>>>>> >
>>>>>> > Cheers,
>>>>>> > Oliver.
>>>>>> > _______________________________________________
>>>>>> > Chimera-users mailing list
>>>>>> > Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>>>>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>>>> >
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 

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From smith_liu123 at 163.com  Thu Oct 15 07:17:14 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Thu, 15 Oct 2015 22:17:14 +0800 (CST)
Subject: [Chimera-users] on scale command
Message-ID: <63804b9a.19cd2.1506bdca779.Coremail.smith_liu123@163.com>

Dear All,


If I have used "scale 1.04" to scale up, will you please tell me the factor x in "scale x" by which I can return to the original size before I used "scale 1.04" ?


Best regards.




Smith
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From boris.steipe at utoronto.ca  Thu Oct 15 07:36:40 2015
From: boris.steipe at utoronto.ca (Boris Steipe)
Date: Thu, 15 Oct 2015 10:36:40 -0400
Subject: [Chimera-users] on scale command
In-Reply-To: <63804b9a.19cd2.1506bdca779.Coremail.smith_liu123@163.com>
References: <63804b9a.19cd2.1506bdca779.Coremail.smith_liu123@163.com>
Message-ID: <EDED95D4-7D4C-444C-98F5-1D4D62CEDD14@utoronto.ca>

Without much further thought I would try (1/1.04) = 0.9615385
B.


On Oct 15, 2015, at 10:17 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> 
> If I have used "scale 1.04" to scale up, will you please tell me the factor x in "scale x" by which I can return to the original size before I used "scale 1.04" ?
> 
> Best regards.
> 
> 
> Smith
> 
> 
>  
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Thu Oct 15 09:14:32 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 15 Oct 2015 09:14:32 -0700
Subject: [Chimera-users] on scale command
In-Reply-To: <EDED95D4-7D4C-444C-98F5-1D4D62CEDD14@utoronto.ca>
References: <63804b9a.19cd2.1506bdca779.Coremail.smith_liu123@163.com>
	<EDED95D4-7D4C-444C-98F5-1D4D62CEDD14@utoronto.ca>
Message-ID: <12E7ABA2-39E8-40E8-8FA7-60516DD005B3@cgl.ucsf.edu>

Boris has the direct answer!

My indirect answer is more of a general suggestion: use command ?savepos? to save a position if you might want to restore it (with command ?reset?).  Of course, you have to do this before making the changes (scaling, rotation, translation?).  Use commands ?help savepos? and ?help reset? to see their manual pages.

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 15, 2015, at 7:36 AM, Boris Steipe <boris.steipe at utoronto.ca> wrote:
> 
> Without much further thought I would try (1/1.04) = 0.9615385
> B.
> 
> On Oct 15, 2015, at 10:17 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
>> Dear All,
>> If I have used "scale 1.04" to scale up, will you please tell me the factor x in "scale x" by which I can return to the original size before I used "scale 1.04" ?
>> Best regards.
>> Smith



From smith_liu123 at 163.com  Fri Oct 16 05:44:28 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Fri, 16 Oct 2015 20:44:28 +0800 (CST)
Subject: [Chimera-users] on mrz file
Message-ID: <7b87c81.129db.15070ae1485.Coremail.smith_liu123@163.com>

Dear All,


Suppose I have 2 mrc files which are similar on the same protein, we call one map A one map B, and suppose onece we open them by chimera, A was in the centre of the window and B was not. By mouse dragging we moved map B almost overlap with chain B, then we fit map B to map A by the chimera "Fit in map" function. Is any way we can save map B, so that when we open map A and the saved map B by chimera, both A and B were in the centre of the Windows and A and B fitted as just before we saved map B?


Best regards.


Smith

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From mailmd2011 at gmail.com  Fri Oct 16 06:41:53 2015
From: mailmd2011 at gmail.com (Albert)
Date: Fri, 16 Oct 2015 15:41:53 +0200
Subject: [Chimera-users] uneditable format
Message-ID: <5620FEA1.9030306@gmail.com>

Hello:

I've made a Chimera section which I would like to share with somebody 
else. However, I don't want the PDB within Chimera section to be 
exported by others. Is it possible for us to export some special file 
format so that other users can only visualize my file, but they cannot 
edit or export file into PDB coordinate?

Thanks a lot

Albert


From meng at cgl.ucsf.edu  Fri Oct 16 09:15:40 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 16 Oct 2015 09:15:40 -0700
Subject: [Chimera-users] on mrz file
In-Reply-To: <7b87c81.129db.15070ae1485.Coremail.smith_liu123@163.com>
References: <7b87c81.129db.15070ae1485.Coremail.smith_liu123@163.com>
Message-ID: <C5EF155A-DDC3-4C13-BCA8-2169899FAAA2@cgl.ucsf.edu>

Dear Smith,
Please see the ?Saving Maps after Fitting? section at the bottom of this page:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 16, 2015, at 5:44 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> Suppose I have 2 mrc files which are similar on the same protein, we call one map A one map B, and suppose onece we open them by chimera, A was in the centre of the window and B was not. By mouse dragging we moved map B almost overlap with chain B, then we fit map B to map A by the chimera "Fit in map" function. Is any way we can save map B, so that when we open map A and the saved map B by chimera, both A and B were in the centre of the Windows and A and B fitted as just before we saved map B?
> Best regards.
> Smith




From olibclarke at gmail.com  Fri Oct 16 09:20:18 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 16 Oct 2015 12:20:18 -0400
Subject: [Chimera-users] uneditable format
Message-ID: <CAPghYOpZhNwjP8X7Gg+gchenLE6Hd4puJc1P2dZXVSX5nFnJ_g@mail.gmail.com>

Hi Albert,


I'm pretty sure this doesn't exist at present, and I guess it would require
substantial changes to make it work - You'd need to make sure that chimera
couldn't write out anything after reading that session, and given that Chimera
is open source and has many different ways of writing data out that
might be tricky.

However, that said, I think having a read-only packaged session format would be
a very valuable addition (particularly if it incorporated support for
maps), because
it would solve a long standing issue in peer review of structural biology
results - how to provide raw data for inspection to reviewers without
providing maps
and models with no strings attached, which many PIs are disinclined to do.

Cheers,
Oliver.

>Hello:
>
>I've made a Chimera section which I would like to share with somebody
>else. However, I don't want the PDB within Chimera section to be
>exported by others. Is it possible for us to export some special file
>format so that other users can only visualize my file, but they cannot
>edit or export file into PDB coordinate?
>
>Thanks a lot
>
>Albert
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From pett at cgl.ucsf.edu  Fri Oct 16 10:00:18 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 16 Oct 2015 10:00:18 -0700
Subject: [Chimera-users] uneditable format
In-Reply-To: <5620FEA1.9030306@gmail.com>
References: <5620FEA1.9030306@gmail.com>
Message-ID: <BDDABFCC-83BF-43A9-A689-568A878BD55F@cgl.ucsf.edu>

Hi Albert,
	Look at the File->Export Scene menu.  That allows you to export to various file formats that your recipient may be able to view without any easy ability to save the result as a PDB file.  In particular the ?WebGL? export can be viewed as a web page in most modern browsers, with the ability to manipulate the structure interactively.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 16, 2015, at 6:41 AM, Albert <mailmd2011 at gmail.com> wrote:
> 
> Hello:
> 
> I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate?
> 
> Thanks a lot
> 
> Albert
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From gtzotzos at me.com  Fri Oct 16 09:14:11 2015
From: gtzotzos at me.com (George Tzotzos)
Date: Fri, 16 Oct 2015 19:14:11 +0300
Subject: [Chimera-users] Failure to reproduce complete Consurf output
Message-ID: <B0745348-31C1-4D22-9B55-F39AC18255E2@me.com>

Hi everybody,

I?m attaching a snapshot of the output of a Consurf job (snapshot1). Trying to save the file in EPS format produces only A PART of the right-hand-side pane of the output. No histogram is produced (see output.eps).

I?d appreciate any suggestions as to how to produce a complete output.

Thank you in advance

George

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From olibclarke at gmail.com  Fri Oct 16 10:35:24 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 16 Oct 2015 13:35:24 -0400
Subject: [Chimera-users] uneditable format
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
Message-ID: <35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>

Hi Eric,

I had no idea you could do this, it works great and could be very handy!! 

The colors and lighting (and positions) don?t seem to be preserved though and differ between firefox and safari  - see the attached screenshots and test webgl of 1BL* with EDS maps (WebGL link: https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0 <https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0>).

Oli.


> Hi Albert,
> 	Look at the File->Export Scene menu.  That allows you to export to various file formats that your recipient may be able to view without any easy ability to save the result as a PDB file.  In particular the ?WebGL? export can be viewed as a web page in most modern browsers, with the ability to manipulate the structure interactively.
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
> > On Oct 16, 2015, at 6:41 AM, Albert <mailmd2011 at gmail.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote:
> > 
> > Hello:
> > 
> > I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate?
> > 
> > Thanks a lot
> > 
> > Albert
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>


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From meng at cgl.ucsf.edu  Fri Oct 16 10:42:50 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 16 Oct 2015 10:42:50 -0700
Subject: [Chimera-users] uneditable format
In-Reply-To: <35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
Message-ID: <6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>

Hi Oliver,
The WebGL export is at least semi-experimental, and we are aware of several limitations in terms of differing appearance or omission of some things that are shown in the Chimera session.  So while we aren?t surprised at the differences you report, it may still be useful in various situations.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Oct 16, 2015, at 10:35 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi Eric,
> 
> I had no idea you could do this, it works great and could be very handy!! 
> 
> The colors and lighting (and positions) don?t seem to be preserved though and differ between firefox and safari  - see the attached screenshots and test webgl of 1BL* with EDS maps (WebGL link: https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0).
> 
> Oli.
> <Screenshot 2015-10-16 13.23.10.png><Screenshot 2015-10-16 13.23.02.png>
> <Screenshot 2015-10-16 13.28.31.png>
>> Hi Albert,
>> 	Look at the File->Export Scene menu.  That allows you to export to various file formats that your recipient may be able to view without any easy ability to save the result as a PDB file.  In particular the ?WebGL? export can be viewed as a web page in most modern browsers, with the ability to manipulate the structure interactively.
>> 
>> ?Eric
>> 
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>> 
>> >
>>  On Oct 16, 2015, at 6:41 AM, Albert <mailmd2011 at gmail.com
>> > wrote:
>> 
>> >
>>  
>> 
>> >
>>  Hello:
>> 
>> >
>>  
>> 
>> >
>>  I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate?
>> 
>> >
>>  
>> 
>> >
>>  Thanks a lot
>> 
>> >
>>  
>> 
>> >
>>  Albert
>> 
>> >
>>  _______________________________________________
>> 
>> >
>>  Chimera-users mailing list
>> 
>> > Chimera-users at cgl.ucsf.edu
>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From pett at cgl.ucsf.edu  Fri Oct 16 11:02:56 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 16 Oct 2015 11:02:56 -0700
Subject: [Chimera-users] Failure to reproduce complete Consurf output
In-Reply-To: <B0745348-31C1-4D22-9B55-F39AC18255E2@me.com>
References: <B0745348-31C1-4D22-9B55-F39AC18255E2@me.com>
Message-ID: <19163846-4AD0-4F2D-B667-C78F8B5786AB@cgl.ucsf.edu>

Hi George,
	In the Save EPS dialog you need to change the ?extent? setting from ?visible region? to ?entire alignment?.  Also, it is showing the histogram (at the top of the alignment).  I think you mean the dendrogram (on the left of the alignment)?  Anyway, when you save EPS in this situation it should actually produce two files, one that ends in ?-alignment.eps? (that contains the alignment) and one ending in ?-names.eps? (that contains the dendrogram and sequence names).  Unfortunately it is an implementation limitation that it cannot produce a combined file, though in some cases it is useful to have the ?-names? file available separately.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Oct 16, 2015, at 9:14 AM, George Tzotzos <gtzotzos at me.com> wrote:
> 
> Hi everybody,
> 
> I?m attaching a snapshot of the output of a Consurf job (snapshot1). Trying to save the file in EPS format produces only A PART of the right-hand-side pane of the output. No histogram is produced (see output.eps).
> 
> I?d appreciate any suggestions as to how to produce a complete output.
> 
> Thank you in advance
> 
> George
> 
> <snapshot1.tiff><output.eps>
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From goddard at sonic.net  Fri Oct 16 11:11:11 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 16 Oct 2015 11:11:11 -0700
Subject: [Chimera-users] uneditable format
In-Reply-To: <6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
	<6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
Message-ID: <EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>

One of the limitations that of WebGL export is that it doesn?t appear to display transparency correctly.  Also it doesn?t appear to handle lighting of meshes instead the mesh appears uniformly bright.  Both of these mess up the mesh in you example images.

	Tom


> On Oct 16, 2015, at 10:42 AM, Elaine Meng  wrote:
> 
> Hi Oliver,
> The WebGL export is at least semi-experimental, and we are aware of several limitations in terms of differing appearance or omission of some things that are shown in the Chimera session.  So while we aren?t surprised at the differences you report, it may still be useful in various situations.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> On Oct 16, 2015, at 10:35 AM, Oliver Clarke  wrote:
> 
>> Hi Eric,
>> 
>> I had no idea you could do this, it works great and could be very handy!! 
>> 
>> The colors and lighting (and positions) don?t seem to be preserved though and differ between firefox and safari  - see the attached screenshots and test webgl of 1BL* with EDS maps (WebGL link: https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0).
>> 
>> Oli.
>> <Screenshot 2015-10-16 13.23.10.png><Screenshot 2015-10-16 13.23.02.png>
>> <Screenshot 2015-10-16 13.28.31.png>
>>> Hi Albert,
>>> 	Look at the File->Export Scene menu.  That allows you to export to various file formats that your recipient may be able to view without any easy ability to save the result as a PDB file.  In particular the ?WebGL? export can be viewed as a web page in most modern browsers, with the ability to manipulate the structure interactively.
>>> 
>>> ?Eric
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>> 
>>>> 
>>> On Oct 16, 2015, at 6:41 AM, Albert <mailmd2011 at gmail.com
>>>> wrote:
>>> 
>>>> 
>>> 
>>> 
>>>> 
>>> Hello:
>>> 
>>>> 
>>> 
>>> 
>>>> 
>>> I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate?
>>> 
>>>> 
>>> 
>>> 
>>>> 
>>> Thanks a lot
>>> 
>>>> 
>>> 
>>> 
>>>> 
>>> Albert
>>> 
>>>> 
>>> _______________________________________________
>>> 
>>>> 
>>> Chimera-users mailing list
>>> 
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From goddard at sonic.net  Fri Oct 16 11:15:31 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 16 Oct 2015 11:15:31 -0700
Subject: [Chimera-users] uneditable format
In-Reply-To: <5620FEA1.9030306@gmail.com>
References: <5620FEA1.9030306@gmail.com>
Message-ID: <D2FAA265-C866-41A6-9299-AE9FFA28DEAA@sonic.net>

Hi Albert,

  The common approach to this is to provide a movie spinning the model around.  That isn?t as flexible for the viewer as using interactive 3d graphics, but the only 3d graphics viewer that everyone is likely to have is a web browser, and the WebGL export from Chimera is just a prototype (e.g. doesn?t handle transparency or lighting on mesh surfaces and other things).  Also if you were really concerned about someone getting your coordinates, those can be extracted from any 3d format including WebGL by someone dedicated willing to spend a day.  Probably that is safe enough and we hope to have WebGL output working in all cases in Chimera 2.

	Tom


> On Oct 16, 2015, at 6:41 AM, Albert wrote:
> 
> Hello:
> 
> I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate?
> 
> Thanks a lot
> 
> Albert
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From mailmd2011 at gmail.com  Fri Oct 16 11:45:23 2015
From: mailmd2011 at gmail.com (Albert)
Date: Fri, 16 Oct 2015 20:45:23 +0200
Subject: [Chimera-users] uneditable format
In-Reply-To: <EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
	<6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
	<EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>
Message-ID: <562145C3.1080608@gmail.com>

Thanks a lot for such helpful reply.

I found that there is some problem for both Firefox and Chrome under my 
Linux OS. It claimed that they didn't support webGL.

I am using Dell M3800 laptop which has Nvidia Quadra K1100 M plus Intel 
4600. I evoke the browser with command:

optirun /usr/bin/firefox

but the webGL still doesn't work....

Does anybody have any idea?

thx a lot


On 10/16/2015 08:11 PM, Tom Goddard wrote:
> One of the limitations that of WebGL export is that it doesn?t appear to display transparency correctly.  Also it doesn?t appear to handle lighting of meshes instead the mesh appears uniformly bright.  Both of these mess up the mesh in you example images.
>
> 	Tom



From goddard at sonic.net  Fri Oct 16 11:51:07 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 16 Oct 2015 11:51:07 -0700
Subject: [Chimera-users] uneditable format
In-Reply-To: <562145C3.1080608@gmail.com>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
	<6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
	<EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>
	<562145C3.1080608@gmail.com>
Message-ID: <38184DA6-07F8-4706-B956-52380703DBC5@sonic.net>

Essentially all current browsers support WebGL, so you perhaps have older browser versions.  Here is a web page describing which browser versions support WebGL and describing why some only partially support WebGL (usually video drivers are not up to date).

   http://caniuse.com/#feat=webgl

	Tom


> On Oct 16, 2015, at 11:45 AM, Albert <mailmd2011 at gmail.com> wrote:
> 
> Thanks a lot for such helpful reply.
> 
> I found that there is some problem for both Firefox and Chrome under my Linux OS. It claimed that they didn't support webGL.
> 
> I am using Dell M3800 laptop which has Nvidia Quadra K1100 M plus Intel 4600. I evoke the browser with command:
> 
> optirun /usr/bin/firefox
> 
> but the webGL still doesn't work....
> 
> Does anybody have any idea?
> 
> thx a lot
> 
> 
> On 10/16/2015 08:11 PM, Tom Goddard wrote:
>> One of the limitations that of WebGL export is that it doesn?t appear to display transparency correctly.  Also it doesn?t appear to handle lighting of meshes instead the mesh appears uniformly bright.  Both of these mess up the mesh in you example images.
>> 
>> 	Tom
> 




From mailmd2011 at gmail.com  Fri Oct 16 12:42:26 2015
From: mailmd2011 at gmail.com (Albert)
Date: Fri, 16 Oct 2015 21:42:26 +0200
Subject: [Chimera-users] uneditable format
In-Reply-To: <38184DA6-07F8-4706-B956-52380703DBC5@sonic.net>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
	<6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
	<EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>
	<562145C3.1080608@gmail.com>
	<38184DA6-07F8-4706-B956-52380703DBC5@sonic.net>
Message-ID: <56215322.4060900@gmail.com>

That's a little bit strange. I just check my browser version:

firefox: 40.0.3
Chrome: 45.0.2454.101

Thanks again

Albert


On 10/16/2015 08:51 PM, Tom Goddard wrote:
> Essentially all current browsers support WebGL, so you perhaps have older browser versions.  Here is a web page describing which browser versions support WebGL and describing why some only partially support WebGL (usually video drivers are not up to date).
>
>     http://caniuse.com/#feat=webgl
>
> 	Tom



From gregc at cgl.ucsf.edu  Fri Oct 16 13:13:46 2015
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 16 Oct 2015 13:13:46 -0700
Subject: [Chimera-users] uneditable format
In-Reply-To: <562145C3.1080608@gmail.com>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
	<6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
	<EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>
	<562145C3.1080608@gmail.com>
Message-ID: <56215A7A.5000406@cgl.ucsf.edu>

See https://www.khronos.org/webgl/wiki/BlacklistsAndWhitelists to see 
which graphics drivers are expected to work.  I see that for Chrome 
"WebGL is disabled on the dynamically switching NVIDIA+Intel GPUs", so 
you would need to turn off the Intel GPU in your BIOS for WebGL to work.

     HTH,

     Greg

On 10/16/2015 11:45 AM, Albert wrote:
> Thanks a lot for such helpful reply.
>
> I found that there is some problem for both Firefox and Chrome under 
> my Linux OS. It claimed that they didn't support webGL.
>
> I am using Dell M3800 laptop which has Nvidia Quadra K1100 M plus 
> Intel 4600. I evoke the browser with command:
>
> optirun /usr/bin/firefox
>
> but the webGL still doesn't work....
>
> Does anybody have any idea?
>
> thx a lot
>
>
> On 10/16/2015 08:11 PM, Tom Goddard wrote:
>> One of the limitations that of WebGL export is that it doesn?t appear 
>> to display transparency correctly.  Also it doesn?t appear to handle 
>> lighting of meshes instead the mesh appears uniformly bright.  Both 
>> of these mess up the mesh in you example images.
>>
>>     Tom
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>



From mailmd2011 at gmail.com  Fri Oct 16 14:13:38 2015
From: mailmd2011 at gmail.com (Albert)
Date: Fri, 16 Oct 2015 23:13:38 +0200
Subject: [Chimera-users] uneditable format
In-Reply-To: <56215A7A.5000406@cgl.ucsf.edu>
References: <7284EE19-E2EE-4B02-93E5-14E58431AE21@cumc.columbia.edu>
	<35E07469-CED6-421F-AF44-B75F77F21E04@gmail.com>
	<6E325BE8-62ED-45CA-97A8-3F5C3D443C01@cgl.ucsf.edu>
	<EDD2FC38-2030-4EF4-863E-15BB7303C417@sonic.net>
	<562145C3.1080608@gmail.com> <56215A7A.5000406@cgl.ucsf.edu>
Message-ID: <56216882.1090308@gmail.com>

thanks a lot. Finally it works in firefox after I change the config 
file. But still problem with chrome.





On 10/16/2015 10:13 PM, Greg Couch wrote:
> See https://www.khronos.org/webgl/wiki/BlacklistsAndWhitelists to see 
> which graphics drivers are expected to work.  I see that for Chrome 
> "WebGL is disabled on the dynamically switching NVIDIA+Intel GPUs", so 
> you would need to turn off the Intel GPU in your BIOS for WebGL to work.
>
>     HTH,
>
>     Greg 



From mailmd2011 at gmail.com  Fri Oct 16 14:16:18 2015
From: mailmd2011 at gmail.com (Albert)
Date: Fri, 16 Oct 2015 23:16:18 +0200
Subject: [Chimera-users] can you provide more opition for webGL?
Message-ID: <56216922.8070108@gmail.com>

Hello everybody:

I am just fascinated by the webGL function in Chimera and I am googling 
it today. Here I found something is even more interesting:

http://istar.cse.cuhk.edu.hk/iview/

As far as we can see, it provide much more options in the above link. I 
am just wondering, could the Chimera developer also consider provide 
more options for the exported webGL file? That's definitely would be 
very attractive for the users.

Thanks a lot

Albert


From mailmd2011 at gmail.com  Sat Oct 17 02:09:25 2015
From: mailmd2011 at gmail.com (Albert)
Date: Sat, 17 Oct 2015 11:09:25 +0200
Subject: [Chimera-users] label residues
Message-ID: <56221045.8050801@gmail.com>

Hello:

I got a question on label residues in Chimera. Is it possible to use a 
simple command line to label all protein residue name and number 
displayed in the workspace?

Thanks you very much

Albert


From meng at cgl.ucsf.edu  Sat Oct 17 09:07:02 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 17 Oct 2015 09:07:02 -0700
Subject: [Chimera-users] label residues
In-Reply-To: <56221045.8050801@gmail.com>
References: <56221045.8050801@gmail.com>
Message-ID: <7C23FD89-C394-4E50-9C2E-1AC1701A9A58@cgl.ucsf.edu>

Hello Albert,
You can use command ?rlabel?:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rlabel.html>

Note, however, that a limitation of webgl export is that it does not include labels.

To find out about Chimera features, you can search documentation, for example for ?label residue? with menu: Help? Search Documentation, or you could try one of the ?getting started? tutorials:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

You could also see the command index for short descriptions of all commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

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

On Oct 17, 2015, at 2:09 AM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
> I got a question on label residues in Chimera. Is it possible to use a simple command line to label all protein residue name and number displayed in the workspace?
> Thanks you very much
> Albert




From smith_liu123 at 163.com  Sun Oct 18 07:10:25 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Sun, 18 Oct 2015 22:10:25 +0800 (CST)
Subject: [Chimera-users] on movie command
Message-ID: <2b826e8.9967.1507b497dcb.Coremail.smith_liu123@163.com>

Dear All,


Suppose there is a 100-residue protein opened in chimera, and it was scaled to a windows which can hold 10 residues, for example residue 10-20. Is any good way we first center on residue 15, then smoothly center on residue 16 (window hold residue 11-21), then smoothly center on residue 17 (window hold residue 12-22),  then smoothly center on residue 18 (window hold residue 13-23), ......., until we center on residue 100? Here I emphasize "smoothly" so that the residue "move" was not too sudden to the eye.


Best regards.




Smith

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From meng at cgl.ucsf.edu  Sun Oct 18 10:02:02 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 18 Oct 2015 10:02:02 -0700
Subject: [Chimera-users] on movie command
In-Reply-To: <2b826e8.9967.1507b497dcb.Coremail.smith_liu123@163.com>
References: <2b826e8.9967.1507b497dcb.Coremail.smith_liu123@163.com>
Message-ID: <8BCF30EB-6E31-41E2-AA33-A6B1438397DF@cgl.ucsf.edu>

Dear Smith,
I would first create and save the positions (command ?savepos? including the position name) and save them in a session along with the protein.  Then,  you could re-open the session later several different times to work on creating the movie script and/or doing the recording, without having to re-make the positions each time.  For the movie, you could restore positions smoothly using ?reset? including the position name, or maybe even ?fly? for restoring multiple positions one after the other.

The hard part is creating the positions.  If you are willing to do it interactively (manually), moving the protein by hand to find each position before using ?savepos,? that will probably give the most attractive results.

Generating positions automatically is less tedious but much less effective, because there will usually be problems like something blocking the view of something else.

The following examples are for residues 10-20 in model 0 chain A. It is easy to use window or focus, but note they will change the scale (zoom) and clipping planes, and will not do any rotation, so that the residues might on top of each other.

window #0:10-20.A
(- or -)
focus #0:10-20.A

If you really want to avoid changing the scale, but allowing rotation is OK, you could try using align to stack the residues along Z followed by a 90-degree rotation to stack them along X instead of Z:

clip off
align #0:10-15.A #0:16-20.A
turn y 90

See the documentation for details/options of the various  commands.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#content>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

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

On Oct 18, 2015, at 7:10 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> Suppose there is a 100-residue protein opened in chimera, and it was scaled to a windows which can hold 10 residues, for example residue 10-20. Is any good way we first center on residue 15, then smoothly center on residue 16 (window hold residue 11-21), then smoothly center on residue 17 (window hold residue 12-22),  then smoothly center on residue 18 (window hold residue 13-23), ......., until we center on residue 100? Here I emphasize "smoothly" so that the residue "move" was not too sudden to the eye.
> Best regards.
> Smith




From jmeyerson at brandeis.edu  Sun Oct 18 10:39:02 2015
From: jmeyerson at brandeis.edu (Joel Meyerson)
Date: Sun, 18 Oct 2015 13:39:02 -0400
Subject: [Chimera-users] mouse selection not working
Message-ID: <CAEnYAiAx5PhrA1ybyW2tzw5gp66wz3tMgdvTZU665wyCohX12A@mail.gmail.com>

Hi,
I'm unable to click-and-drag to select objects in the latest version of
Chimera. Specifically, when I hold 'ctrl' and drag over an object, no
selection is made. This is something that worked just fine in previous
versions of the program. Any suggestions on how to fix the issue?

I'm using Chimera production version 1.10.2 (build 40686) and running Mac
OS X 10.10.4.

Thanks,
Joel
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From Petr.Brazda at seznam.cz  Mon Oct 19 02:07:46 2015
From: Petr.Brazda at seznam.cz (Petr.Brazda at seznam.cz)
Date: Mon, 19 Oct 2015 11:07:46 +0200 (CEST)
Subject: [Chimera-users] Color blobs automatically
Message-ID: <E3K.6pxB.6ubrZOTzDhi.1M9BBY@seznam.cz>

Hello,

I have both periodically distributed blobs and blobs, which are randomly 
distributed in my volume data. I know the translational vectors of the 
periodic net of blobs and I would like to automatically color them to 
distinguish them from the rest of the blobs. Is there a way to tell Chimera 
to color the blobs, which contain voxel with particular x, y, z coordinates?
Or is there some other way to do this job?

Best regards,

Petr
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From goddard at sonic.net  Mon Oct 19 10:23:40 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 19 Oct 2015 10:23:40 -0700
Subject: [Chimera-users] mouse drag selection not working
In-Reply-To: <CAEnYAiAx5PhrA1ybyW2tzw5gp66wz3tMgdvTZU665wyCohX12A@mail.gmail.com>
References: <CAEnYAiAx5PhrA1ybyW2tzw5gp66wz3tMgdvTZU665wyCohX12A@mail.gmail.com>
Message-ID: <74657CF4-09E2-4E7E-B735-924C7BBACCC9@sonic.net>

Hi Joel,

  Broken drag select is a bug in the Mac graphics drivers with Intel graphics.  I reported it to Apple about 14 months ago (Apple bug 18102609, the OpenGL  glPolygonMode() call does not work).  Nvidia graphics does work on the Mac.  Apple has not even commented on the bug.  They probably will not fix it because it is rarely used.  One ugly way to make drag select work is to display molecules in ?wire? style.  Here is the Chimera bug report for this issue:

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/13312

  Tom


> On Oct 18, 2015, at 10:39 AM, Joel Meyerson <jmeyerson at brandeis.edu> wrote:
> 
> Hi,
> I'm unable to click-and-drag to select objects in the latest version of Chimera. Specifically, when I hold 'ctrl' and drag over an object, no selection is made. This is something that worked just fine in previous versions of the program. Any suggestions on how to fix the issue?
> 
> I'm using Chimera production version 1.10.2 (build 40686) and running Mac OS X 10.10.4.
> 
> Thanks,
> Joel
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From goddard at sonic.net  Mon Oct 19 10:52:03 2015
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 19 Oct 2015 10:52:03 -0700
Subject: [Chimera-users] Color blobs automatically
In-Reply-To: <E3K.6pxB.6ubrZOTzDhi.1M9BBY@seznam.cz>
References: <E3K.6pxB.6ubrZOTzDhi.1M9BBY@seznam.cz>
Message-ID: <412BB4E4-C08B-4A3B-9770-F2AB04D93B15@sonic.net>

Hi Petr,

  How about you make a PDB file that contains an atom at each lattice position using whatever scripting language you like to use.  Open that PDB in Chimera, make sure the atoms overlap the density map blobs, then use the Color Zone tool (menu Tools / Volume Data / Color Zone) to color the density near those atoms to match the atoms.  Color zone colors a surface within a specified distance range of some selected atoms to match the colors of those atoms.

	Tom


> On Oct 19, 2015, at 2:07 AM, wrote:
> 
> Hello,
> 
> I have both periodically distributed blobs and blobs, which are randomly distributed in my volume data. I know the translational vectors of the periodic net of blobs and I would like to automatically color them to distinguish them from the rest of the blobs. Is there a way to tell Chimera to color the blobs, which contain voxel with particular x, y, z coordinates? Or is there some other way to do this job?
> 
> Best regards,
> 
> Petr
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From erik.laurini at di3.units.it  Tue Oct 20 06:32:44 2015
From: erik.laurini at di3.units.it (erik.laurini at di3.units.it)
Date: Tue, 20 Oct 2015 13:32:44 +0000
Subject: [Chimera-users] center of mass
Message-ID: <D7C7A15F67635A4F96017E1E0DFDEA7723274538@DI3-EXCH.ds.units.it>

Dear Chimera users,
I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the "MD plot" but it seems that it works only with atom selection. Do you have any advice?
Thanks in advance!

-erik-


Dr. Erik Laurini
Department of Engineering and Architecture
University of Trieste, Via Valerio 10, 34127, Trieste (Italy)
Tel. + 39 0405583440


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From goddard at sonic.net  Tue Oct 20 14:41:44 2015
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 20 Oct 2015 14:41:44 -0700
Subject: [Chimera-users] Change chain id of blank chain
In-Reply-To: <D5E3128D5233DE48A39ED4BF376E1C7D0105C096@SGWAEXM005.mc.cumc.columbia.edu>
References: <D5E3128D5233DE48A39ED4BF376E1C7D0105C096@SGWAEXM005.mc.cumc.columbia.edu>
Message-ID: <27F7F6FE-2C34-47ED-9208-87ADD86E5601@sonic.net>

Hi Joshua,

  Eric looked at the code and said the changechains command can?t change the blank chain id because it won?t accept a quoted space character as the chain letter.  It could be done with Python code, or as you mention you can do it with the change chain ids gui.

	Tom


> On Oct 20, 2015, at 2:07 PM, Broyde, Joshua E. <wrote:
> 
> Dear Tom,
> Hope you are well. I am having an issue with redefining the chains in a pdb open in Chimera. If a model has two chains (A and B) then it is easy to reassign the chain ids using:
> changechains A,B B,A
> 
> However, if one of the chains does not have a chain id already, (what Chimera calls, the "principle chain"), how do I assign a chain id? This is easy to do in the GUI, but I cannot find a command for doing so.
> 
> Sincerely,
> Joshua Broyde

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From meng at cgl.ucsf.edu  Tue Oct 20 16:08:25 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 20 Oct 2015 16:08:25 -0700
Subject: [Chimera-users] center of mass
In-Reply-To: <D7C7A15F67635A4F96017E1E0DFDEA7723274538@DI3-EXCH.ds.units.it>
References: <D7C7A15F67635A4F96017E1E0DFDEA7723274538@DI3-EXCH.ds.units.it>
Message-ID: <FCBD9BCF-17DD-465E-BB6A-5521AFAF9427@cgl.ucsf.edu>

Hi Erik,
Unfortunately I can?t think of a way to accomplish this with the built-in plotting in MD Movie, sorry.

The only idea I had (which may be more trouble than it?s worth) is to use the MD Movie per-frame scripting.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

  In the script, for each frame you could:

(1)  use ?define centroid? with mass-weighting to create a centroid object with a specified ID number at each of the centers of mass of interest. ( If the command-line specification of the biologic target portion is long and unwieldy, you can ?alias? it to a shorter name once beforehand.)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

(2) use ?distance? with the two centroid IDs to report distance to the Reply Log.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

(3) maybe echo frame number to Reply Log.

For example, a per-frame Chimera command script something like:
 
define centroid mass true number 1 ligand
define centroid mass true number 2 #0:54-85.a,99.a
dist c1 c2
echo <FRAME>

Then after going through your trajectory once start->end while running this script, you could save Reply Log contents, extract the data (maybe grep, awk, or other text processing) and use your own external plotting program of choice.

Sorry it is not a very convenient solution.  Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 20, 2015, at 6:32 AM, erik.laurini at di3.units.it wrote:
> 
> Dear Chimera users,
> I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the ?MD plot? but it seems that it works only with atom selection. Do you have any advice?
> Thanks in advance!
>  
> -erik-  




From rodrigogalindo at gmail.com  Wed Oct 21 11:03:11 2015
From: rodrigogalindo at gmail.com (ros)
Date: Wed, 21 Oct 2015 12:03:11 -0600
Subject: [Chimera-users] Calculating the total areaSAS from a series of PDB
	files
Message-ID: <CAEg5OQG-giVAHVJW50UR+sowRhQv1MiCoUH03tSXN8r3VzqtsA@mail.gmail.com>

Hello!

I would like to measure the SAS from a series of PDB files to see how
the surface value changes over time (the PDB files are from an MD
simulation).  I know that If I open a PDB file and calculate the
surface, I get the areaSAS value, but I do not want to do this 5000
times.

I am making progress on a python script to automate the process, which is:

--------------------------------------------
import os
from chimera import runCommand as rc
from chimera import replyobj

os.chdir("/home/tmp/pdb")

file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]

for fn in file_names:
    replyobj.status("Processing " + fn)
    rc("open " + fn)
    rc("surf")

    rc("sel :1-6")
    from chimera.selection import currentResidues
    residues = currentResidues()
    outf = open("/home/tmp/sas.dat", "w")
    for r in residues:
        print>>outf, r, r.areaSAS

rc("stop now")
--------------------------------------------

The PDB's consist of only 6 residues (DNA residues).  With this
script, I get the output:


#1 DA 1 320.8377808
#2 DC 3 277.614161432
#2 DG 4 323.883637217
#1 DC 3 284.934065707
#2 DT 6 221.04715555
#0 DA 1 321.883850728
#1 DC 5 345.231659889
#0 DC 2 179.379177183
#2 DC 5 350.455405176
#0 DC 3 285.785918236
#1 DT 6 245.048330456
#0 DG 4 303.501165912
#1 DG 4 314.409510799
#0 DC 5 352.639633257
#1 DC 2 193.509086639
#0 DT 6 214.883334659
#2 DC 2 183.766654447
#2 DA 1 344.369126737


using 3 test pdb's.

Is there a way to get the total value of areaSAS of each model and not
for each residue?  I am interested in having a file just like (using
for example 3 pdb's):

Model #     total areaSAS value
#0               123123.123122
#1                123123.12312
#3                123123.12312
...
etc.

I have tried deleting the residues loop, but I do not know how the
total areaSAS attribute is stored or how to assign it to a variable.

Thank you for your help!

Rodrigo.

PS.  The main goal is to be able to do this without the PDB files and
just reading an AMBER topology/trajectory...


From meng at cgl.ucsf.edu  Wed Oct 21 11:22:43 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 21 Oct 2015 11:22:43 -0700
Subject: [Chimera-users] Calculating the total areaSAS from a series of
	PDB files
In-Reply-To: <CAEg5OQG-giVAHVJW50UR+sowRhQv1MiCoUH03tSXN8r3VzqtsA@mail.gmail.com>
References: <CAEg5OQG-giVAHVJW50UR+sowRhQv1MiCoUH03tSXN8r3VzqtsA@mail.gmail.com>
Message-ID: <D5CB9178-410F-4204-8E2B-481336058041@cgl.ucsf.edu>

Hi Rodrigo,
One way without using attributes but involving more text processing would be to:

(1) open trajectory, show surface for first frame

(2) in MD Movie, define per-frame Chimera command script
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

echo <FRAME>

? to report the frame number into the Reply Log.  Start running that per-frame script.

(3) play through trajectory once without looping.  That will recalculate surface at each frame and report total area (along with a bunch of extra lines) in the Reply Log.  The per-frame script above will put the frame number in to help you parse the output.  Save Reply Log to text file and use your favorite text-editing approach to extract only the parts of interest. 

In my little test using NMR ensemble 1PLX as a trajectory, here?s what I get for the last two frames:
-----
79
/Users/meng/Desktop/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0
MSMSLIB 1.3 started on vpn-169-230-25-25.cgl.ucsf.edu
Copyright M.F. Sanner (March 2000)
Compilation flags  

Surface 1PLX.pdb, category main, probe radius 1.4, vertex density 2
  1 connected surface components
  Total solvent excluded surface area = 441.217
  Total solvent accessible surface area = 699.678
80
/Users/meng/Desktop/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0
MSMSLIB 1.3 started on vpn-169-230-25-25.cgl.ucsf.edu
Copyright M.F. Sanner (March 2000)
Compilation flags  

Surface 1PLX.pdb, category main, probe radius 1.4, vertex density 2
  1 connected surface components
  Total solvent excluded surface area = 445.855
  Total solvent accessible surface area = 713.182
-----

NOTE: The main problem is that the surface calculation will probably fail on some frames.  However, that would happen even if you did each one manually.

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

On Oct 21, 2015, at 11:03 AM, ros <rodrigogalindo at gmail.com> wrote:

> Hello!
> 
> I would like to measure the SAS from a series of PDB files to see how
> the surface value changes over time (the PDB files are from an MD
> simulation).  I know that If I open a PDB file and calculate the
> surface, I get the areaSAS value, but I do not want to do this 5000
> times.
> 
> I am making progress on a python script to automate the process, which is:
> 
> --------------------------------------------
> import os
> from chimera import runCommand as rc
> from chimera import replyobj
> 
> os.chdir("/home/tmp/pdb")
> 
> file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]
> 
> for fn in file_names:
>    replyobj.status("Processing " + fn)
>    rc("open " + fn)
>    rc("surf")
> 
>    rc("sel :1-6")
>    from chimera.selection import currentResidues
>    residues = currentResidues()
>    outf = open("/home/tmp/sas.dat", "w")
>    for r in residues:
>        print>>outf, r, r.areaSAS
> 
> rc("stop now")
> --------------------------------------------
> 
> The PDB's consist of only 6 residues (DNA residues).  With this
> script, I get the output:
> 
> 
> #1 DA 1 320.8377808
> #2 DC 3 277.614161432
> #2 DG 4 323.883637217
> #1 DC 3 284.934065707
> #2 DT 6 221.04715555
> #0 DA 1 321.883850728
> #1 DC 5 345.231659889
> #0 DC 2 179.379177183
> #2 DC 5 350.455405176
> #0 DC 3 285.785918236
> #1 DT 6 245.048330456
> #0 DG 4 303.501165912
> #1 DG 4 314.409510799
> #0 DC 5 352.639633257
> #1 DC 2 193.509086639
> #0 DT 6 214.883334659
> #2 DC 2 183.766654447
> #2 DA 1 344.369126737
> 
> 
> using 3 test pdb's.
> 
> Is there a way to get the total value of areaSAS of each model and not
> for each residue?  I am interested in having a file just like (using
> for example 3 pdb's):
> 
> Model #     total areaSAS value
> #0               123123.123122
> #1                123123.12312
> #3                123123.12312
> ...
> etc.
> 
> I have tried deleting the residues loop, but I do not know how the
> total areaSAS attribute is stored or how to assign it to a variable.
> 
> Thank you for your help!
> 
> Rodrigo.
> 
> PS.  The main goal is to be able to do this without the PDB files and
> just reading an AMBER topology/trajectory...




From rodrigogalindo at gmail.com  Wed Oct 21 12:36:57 2015
From: rodrigogalindo at gmail.com (ros)
Date: Wed, 21 Oct 2015 13:36:57 -0600
Subject: [Chimera-users] Calculating the total areaSAS from a series of
 PDB files
In-Reply-To: <D5CB9178-410F-4204-8E2B-481336058041@cgl.ucsf.edu>
References: <CAEg5OQG-giVAHVJW50UR+sowRhQv1MiCoUH03tSXN8r3VzqtsA@mail.gmail.com>
	<D5CB9178-410F-4204-8E2B-481336058041@cgl.ucsf.edu>
Message-ID: <CAEg5OQGbYYL+dJM-KAuxbwvSV3oBTdfLN4hUTCpNbeH2C-9_0A@mail.gmail.com>

Well! This did the trick perfectly.

All it took is:
grep 'accessible' reply.log

and I got a nice column with the areaSAS numbers for each frame.  Perfect!

Thank you very much!

Rodrigo.

On Wed, Oct 21, 2015 at 12:22 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Rodrigo,
> One way without using attributes but involving more text processing would be to:
>
> (1) open trajectory, show surface for first frame
>
> (2) in MD Movie, define per-frame Chimera command script
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
>
> echo <FRAME>
>
> ? to report the frame number into the Reply Log.  Start running that per-frame script.
>
> (3) play through trajectory once without looping.  That will recalculate surface at each frame and report total area (along with a bunch of extra lines) in the Reply Log.  The per-frame script above will put the frame number in to help you parse the output.  Save Reply Log to text file and use your favorite text-editing approach to extract only the parts of interest.
>
> In my little test using NMR ensemble 1PLX as a trajectory, here?s what I get for the last two frames:
> -----
> 79
> /Users/meng/Desktop/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0
> MSMSLIB 1.3 started on vpn-169-230-25-25.cgl.ucsf.edu
> Copyright M.F. Sanner (March 2000)
> Compilation flags
>
> Surface 1PLX.pdb, category main, probe radius 1.4, vertex density 2
>   1 connected surface components
>   Total solvent excluded surface area = 441.217
>   Total solvent accessible surface area = 699.678
> 80
> /Users/meng/Desktop/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0
> MSMSLIB 1.3 started on vpn-169-230-25-25.cgl.ucsf.edu
> Copyright M.F. Sanner (March 2000)
> Compilation flags
>
> Surface 1PLX.pdb, category main, probe radius 1.4, vertex density 2
>   1 connected surface components
>   Total solvent excluded surface area = 445.855
>   Total solvent accessible surface area = 713.182
> -----
>
> NOTE: The main problem is that the surface calculation will probably fail on some frames.  However, that would happen even if you did each one manually.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Oct 21, 2015, at 11:03 AM, ros <rodrigogalindo at gmail.com> wrote:
>
>> Hello!
>>
>> I would like to measure the SAS from a series of PDB files to see how
>> the surface value changes over time (the PDB files are from an MD
>> simulation).  I know that If I open a PDB file and calculate the
>> surface, I get the areaSAS value, but I do not want to do this 5000
>> times.
>>
>> I am making progress on a python script to automate the process, which is:
>>
>> --------------------------------------------
>> import os
>> from chimera import runCommand as rc
>> from chimera import replyobj
>>
>> os.chdir("/home/tmp/pdb")
>>
>> file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]
>>
>> for fn in file_names:
>>    replyobj.status("Processing " + fn)
>>    rc("open " + fn)
>>    rc("surf")
>>
>>    rc("sel :1-6")
>>    from chimera.selection import currentResidues
>>    residues = currentResidues()
>>    outf = open("/home/tmp/sas.dat", "w")
>>    for r in residues:
>>        print>>outf, r, r.areaSAS
>>
>> rc("stop now")
>> --------------------------------------------
>>
>> The PDB's consist of only 6 residues (DNA residues).  With this
>> script, I get the output:
>>
>>
>> #1 DA 1 320.8377808
>> #2 DC 3 277.614161432
>> #2 DG 4 323.883637217
>> #1 DC 3 284.934065707
>> #2 DT 6 221.04715555
>> #0 DA 1 321.883850728
>> #1 DC 5 345.231659889
>> #0 DC 2 179.379177183
>> #2 DC 5 350.455405176
>> #0 DC 3 285.785918236
>> #1 DT 6 245.048330456
>> #0 DG 4 303.501165912
>> #1 DG 4 314.409510799
>> #0 DC 5 352.639633257
>> #1 DC 2 193.509086639
>> #0 DT 6 214.883334659
>> #2 DC 2 183.766654447
>> #2 DA 1 344.369126737
>>
>>
>> using 3 test pdb's.
>>
>> Is there a way to get the total value of areaSAS of each model and not
>> for each residue?  I am interested in having a file just like (using
>> for example 3 pdb's):
>>
>> Model #     total areaSAS value
>> #0               123123.123122
>> #1                123123.12312
>> #3                123123.12312
>> ...
>> etc.
>>
>> I have tried deleting the residues loop, but I do not know how the
>> total areaSAS attribute is stored or how to assign it to a variable.
>>
>> Thank you for your help!
>>
>> Rodrigo.
>>
>> PS.  The main goal is to be able to do this without the PDB files and
>> just reading an AMBER topology/trajectory...
>



From pett at cgl.ucsf.edu  Wed Oct 21 15:40:17 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 21 Oct 2015 15:40:17 -0700
Subject: [Chimera-users] center of mass
In-Reply-To: <FCBD9BCF-17DD-465E-BB6A-5521AFAF9427@cgl.ucsf.edu>
References: <D7C7A15F67635A4F96017E1E0DFDEA7723274538@DI3-EXCH.ds.units.it>
	<FCBD9BCF-17DD-465E-BB6A-5521AFAF9427@cgl.ucsf.edu>
Message-ID: <C6C34001-2F90-4BCC-9DFD-8434B2B429B4@cgl.ucsf.edu>

And obviously this isn?t a truly correct answer but it is easy:  you could just plot the distance between atoms that are near the center of mass.  The plot can overlay multiple distances, so you could also plot distances from the ligand extremities to the other ?center of mass? and easily see what part of the ligand is closest at various frames.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 20, 2015, at 4:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Erik,
> Unfortunately I can?t think of a way to accomplish this with the built-in plotting in MD Movie, sorry.
> 
> The only idea I had (which may be more trouble than it?s worth) is to use the MD Movie per-frame scripting.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
> 
>  In the script, for each frame you could:
> 
> (1)  use ?define centroid? with mass-weighting to create a centroid object with a specified ID number at each of the centers of mass of interest. ( If the command-line specification of the biologic target portion is long and unwieldy, you can ?alias? it to a shorter name once beforehand.)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> 
> (2) use ?distance? with the two centroid IDs to report distance to the Reply Log.  
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> 
> (3) maybe echo frame number to Reply Log.
> 
> For example, a per-frame Chimera command script something like:
> 
> define centroid mass true number 1 ligand
> define centroid mass true number 2 #0:54-85.a,99.a
> dist c1 c2
> echo <FRAME>
> 
> Then after going through your trajectory once start->end while running this script, you could save Reply Log contents, extract the data (maybe grep, awk, or other text processing) and use your own external plotting program of choice.
> 
> Sorry it is not a very convenient solution.  Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Oct 20, 2015, at 6:32 AM, erik.laurini at di3.units.it wrote:
>> 
>> Dear Chimera users,
>> I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the ?MD plot? but it seems that it works only with atom selection. Do you have any advice?
>> Thanks in advance!
>> 
>> -erik-  
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From goddard at sonic.net  Thu Oct 22 11:49:16 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 22 Oct 2015 11:49:16 -0700
Subject: [Chimera-users] How to make a microtubule model
In-Reply-To: <E472A29C-F7F8-459B-8633-F7E9F2C2E0C4@exeter.ac.uk>
References: <E472A29C-F7F8-459B-8633-F7E9F2C2E0C4@exeter.ac.uk>
Message-ID: <29A65FEB-91DC-4E8C-ABC3-39ADA2393196@sonic.net>

  The following page shows a ?bent microtubule? model made with a Chimera Python script

	https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html <https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html>

The bend makes it more complicated than a straight microtubule.  Here is an explanation of how the Chimera ?sym? command can make a straight microtubule model.

  These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image.

	open 1jff
	sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5

The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble.  The trick is to find the right helical parameters.  I just did a few minutes trial and error to find the above.  The ?group? option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule).  This makes a single turn of the microtubule.  A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments.  So I just make one turn.  Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies.  The ?surf true? option says show the copies as surfaces.  Without that it will copy the atomic model and use a ton of memory.  The helix axis is x (just judged by eye after opening tubulin dimer 1jff.  The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm.  Here are the docs for the sym command:

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html>

  Here?s a web page where I did something more sensible to get better symmetry parameters ? I fit the tubulin dimer to an EM map of a microtubule.

	http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html <http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html>

    Tom





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From adi.uoh at gmail.com  Sat Oct 24 10:31:05 2015
From: adi.uoh at gmail.com (Aditya Padhi)
Date: Sat, 24 Oct 2015 13:31:05 -0400
Subject: [Chimera-users] Query on Cryo-EM map
Message-ID: <CABfSPKDd4-VRS3SmAr4B2VywDZirJRxtfrbmnKziydx5Q=2MEw@mail.gmail.com>

Dear Chimera Users,



I have a cryo-em map file and I would like to convert it into a PDB file.
How can I do that? I tried saving the .pdb file but it throws an error
saying ?No model chosen to save?.


Another question, If I open a .map file of a protein complex in Chimera,
how can I select a subregion (a particular chain) and colour the surface of
that part differently? I am not able to select the chain when I upload the
.map file.


Thank you,

Aditya
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From mpi566 at gmail.com  Sun Oct 25 07:38:28 2015
From: mpi566 at gmail.com (MPI)
Date: Sun, 25 Oct 2015 10:38:28 -0400
Subject: [Chimera-users] Non-alphanumeric character in keyword
Message-ID: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>

Dear users,

   In Chimera, I tried to run a vina docking in command line like

vina docking receptor #0 ligand #1 output mytest search_center 10,20,30


There is an error:

Non-alphanumeric character in keyword 'search_center'

I have tried tweaking  the keyword 'search_center' in  different ways
but  the error won't go.

Dose anyone know how to fix it ? or is this format correct ?

Many thanks,
Dwey


From meng at cgl.ucsf.edu  Sun Oct 25 09:36:32 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 25 Oct 2015 09:36:32 -0700
Subject: [Chimera-users] Query on Cryo-EM map
In-Reply-To: <CABfSPKDd4-VRS3SmAr4B2VywDZirJRxtfrbmnKziydx5Q=2MEw@mail.gmail.com>
References: <CABfSPKDd4-VRS3SmAr4B2VywDZirJRxtfrbmnKziydx5Q=2MEw@mail.gmail.com>
Message-ID: <D47300CF-140E-4577-9712-B001E228DDA8@cgl.ucsf.edu>

Dear Aditya,
A density map and an atomic structure (set of atomic coordinates) are two different things.  Only atomic coordinates, not a map, can be saved as a PDB file.  You can only save a map file in some map formats.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization>

The second question has a similar answer.  A map isn?t marked automatically as to which parts are which proteins or chains.  You would have to segment the map then save the map part inside the segment of interest, or if there is an atomic structure, you could open the atomic structure and then fit it into the map. After fitting, one approach would be to color the atomic structure so that different parts (like different chains) are different colors, then use Color Zone to color the map to match the atoms and then to split the map by colors.

See Chimera tools: Segment Map, Fit to Segments, Fit in Map, Color Zone
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/fitsegments.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

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

On Oct 24, 2015, at 10:31 AM, Aditya Padhi <adi.uoh at gmail.com> wrote:

> Dear Chimera Users,
> 
> I have a cryo-em map file and I would like to convert it into a PDB file. How can I do that? I tried saving the .pdb file but it throws an error saying ?No model chosen to save?.
> 
> Another question, If I open a .map file of a protein complex in Chimera, how can I select a subregion (a particular chain) and colour the surface of that part differently? I am not able to select the chain when I upload the .map file.
> 
> Thank you,
> Aditya




From miguel.ortiz-lombardia at igs.cnrs-mrs.fr  Mon Oct 26 09:51:21 2015
From: miguel.ortiz-lombardia at igs.cnrs-mrs.fr (=?UTF-8?B?TWlndWVsIE9ydGl6IExvbWJhcmTDrWE=?=)
Date: Mon, 26 Oct 2015 17:51:21 +0100
Subject: [Chimera-users] Access to "Match Align" programmatically
Message-ID: <562E5A09.7010406@igs.cnrs-mrs.fr>


Hi,

Is it possible to call "Match Align" from a script or a 'com' file
without using the GUI? I would use that possibility, if it does exist,
to check pair-wise rmsd's of previously superimposed structures.

I guess people may have asked this question before, but I couldn't find
an answer in the usual places...

Cheers,

   Miguel


From meng at cgl.ucsf.edu  Mon Oct 26 12:17:50 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 26 Oct 2015 12:17:50 -0700
Subject: [Chimera-users] Access to "Match Align" programmatically
In-Reply-To: <562E5A09.7010406@igs.cnrs-mrs.fr>
References: <562E5A09.7010406@igs.cnrs-mrs.fr>
Message-ID: <9748E0BD-E4E5-4C31-87AA-9F311467E49C@cgl.ucsf.edu>

Hi Miguel,
There is no command for Match->Align, but this previous post has some information on how to call it with Python:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html

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


> On Oct 26, 2015, at 9:51 AM, Miguel Ortiz Lombard?a <miguel.ortiz-lombardia at igs.cnrs-mrs.fr> wrote:
> 
> Hi,
> Is it possible to call "Match Align" from a script or a 'com' file
> without using the GUI? I would use that possibility, if it does exist,
> to check pair-wise rmsd's of previously superimposed structures.
> 
> I guess people may have asked this question before, but I couldn't find
> an answer in the usual places...
> Cheers,
>   Miguel




From meng at cgl.ucsf.edu  Mon Oct 26 13:58:24 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 26 Oct 2015 13:58:24 -0700
Subject: [Chimera-users] Non-alphanumeric character in keyword
In-Reply-To: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
Message-ID: <A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>

Dear Dwey,
Sorry about that ? it was a bug that keywords with underscores in them did not work.

You can get the fix in the next successful daily build (probably tomorrow). Check for daily build dated Oct 22, 2015 or later:
<http://www.rbvi.ucsf.edu/chimera/download.html#daily>

Thanks for reporting the problem!
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
> 
> Dear users,
>   In Chimera, I tried to run a vina docking in command line like
> 
> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
> 
> There is an error:
> 
> Non-alphanumeric character in keyword 'search_center'
> 
> I have tried tweaking  the keyword 'search_center' in  different ways
> but  the error won't go.
> 
> Dose anyone know how to fix it ? or is this format correct ?
> Many thanks,
> Dwey




From miguel.ortiz-lombardia at igs.cnrs-mrs.fr  Mon Oct 26 14:16:56 2015
From: miguel.ortiz-lombardia at igs.cnrs-mrs.fr (=?UTF-8?B?TWlndWVsIE9ydGl6IExvbWJhcmTDrWE=?=)
Date: Mon, 26 Oct 2015 22:16:56 +0100
Subject: [Chimera-users] Access to "Match Align" programmatically
In-Reply-To: <9748E0BD-E4E5-4C31-87AA-9F311467E49C@cgl.ucsf.edu>
References: <562E5A09.7010406@igs.cnrs-mrs.fr>
	<9748E0BD-E4E5-4C31-87AA-9F311467E49C@cgl.ucsf.edu>
Message-ID: <562E9848.90403@igs.cnrs-mrs.fr>


Hi Elaine,

Thank you for the link!
I think it will help :-)

Best regards,

   Miguel

El 26/10/15 a las 20:17, Elaine Meng escribi?:
> Hi Miguel,
> There is no command for Match->Align, but this previous post has some information on how to call it with Python:
> 
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Oct 26, 2015, at 9:51 AM, Miguel Ortiz Lombard?a <miguel.ortiz-lombardia at igs.cnrs-mrs.fr> wrote:
>>
>> Hi,
>> Is it possible to call "Match Align" from a script or a 'com' file
>> without using the GUI? I would use that possibility, if it does exist,
>> to check pair-wise rmsd's of previously superimposed structures.
>>
>> I guess people may have asked this question before, but I couldn't find
>> an answer in the usual places...
>> Cheers,
>>   Miguel
> 


From ramale at arnet.com.ar  Sun Oct 25 06:21:14 2015
From: ramale at arnet.com.ar (=?iso-8859-1?Q?Jos=E9_Luis?=)
Date: Sun, 25 Oct 2015 10:21:14 -0300
Subject: [Chimera-users] AM1-BCC: Question
Message-ID: <003001d10f28$0676ea20$1364be60$@com.ar>

Dears Devepolers:

 

 

My name is Jos? Luis. PhD student and to run docking and MD I was using
Chimera 1.3 for AM1-BCC partial charges calculationwithour problem.

Now, I?m using 1.10 and 1.10.2 but in the firt one the calculation doesn?t
complete it and in the second one the following message appears:

?the system can?t find C:\Program Files\Chimera
1.10.2\share\chimeraInit.py", line 259, in CreateProcess

    current_directory, startup_info).

 

Can you help me?

 

Many thanks in advance.

 

Jos? Luis

 



---
El software de antivirus Avast ha analizado este correo electr?nico en busca de virus.
https://www.avast.com/antivirus
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From pett at cgl.ucsf.edu  Mon Oct 26 15:19:59 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 26 Oct 2015 15:19:59 -0700
Subject: [Chimera-users] AM1-BCC: Question
In-Reply-To: <003001d10f28$0676ea20$1364be60$@com.ar>
References: <003001d10f28$0676ea20$1364be60$@com.ar>
Message-ID: <57065091-A639-44F0-A289-C898BD33A0F3@cgl.ucsf.edu>

Hi Jos? Luis,
	I sense that maybe it was you who sent in an anonymous bug report earlier.  If so, your translation of the Spanish error text to English is slightly misleading.  It isn?t the chimeraInit.py file that can?t be found, it?s the Amber antechamber executable that Chimera is trying to execute that can?t be found (or possibly one of the subprograms that antechamber in turn executes).  Can you submit another bug report, this time including your email address and attach the ?ML 7 AN 2.pdb? input file you were using?  I am curious how a PDB file produced a residue whose name is "+LIG++++++++++++++++++++++? (i.e. way more that 4 characters long).

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 25, 2015, at 6:21 AM, Jos? Luis <ramale at arnet.com.ar> wrote:
> 
> Dears Devepolers:
>  
>  
> My name is Jos? Luis. PhD student and to run docking and MD I was using Chimera 1.3 for AM1-BCC partial charges calculationwithour problem.
> Now, I?m using 1.10 and 1.10.2 but in the firt one the calculation doesn?t complete it and in the second one the following message appears:
> ?the system can?t find C:\Program Files\Chimera 1.10.2\share\chimeraInit.py", line 259, in CreateProcess
>     current_directory, startup_info).
>  
> Can you help me?
>  
> Many thanks in advance.
>  
> Jos? Luis
>  
> 
> 
>  <https://www.avast.com/antivirus>	
> El software de antivirus Avast ha analizado este correo electr?nico en busca de virus. 
> www.avast.com <https://www.avast.com/antivirus>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From mpi566 at gmail.com  Mon Oct 26 18:43:23 2015
From: mpi566 at gmail.com (MPI)
Date: Mon, 26 Oct 2015 21:43:23 -0400
Subject: [Chimera-users] Non-alphanumeric character in keyword
In-Reply-To: <A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
	<A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
Message-ID: <CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>

Dear Elaine,

 Thanks for your kind help !    Would you please let me know which
file is to be modified  in old ver. if a single file is responsible
for that keywords  ?  because I have mulitple manchines.   I'll
download a daily build and update that modifiled file if this would
work.

Regards,
Dwey

On 10/26/15, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Dwey,
> Sorry about that ? it was a bug that keywords with underscores in them did
> not work.
>
> You can get the fix in the next successful daily build (probably tomorrow).
> Check for daily build dated Oct 22, 2015 or later:
> <http://www.rbvi.ucsf.edu/chimera/download.html#daily>
>
> Thanks for reporting the problem!
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>>
>> Dear users,
>>   In Chimera, I tried to run a vina docking in command line like
>>
>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>>
>> There is an error:
>>
>> Non-alphanumeric character in keyword 'search_center'
>>
>> I have tried tweaking  the keyword 'search_center' in  different ways
>> but  the error won't go.
>>
>> Dose anyone know how to fix it ? or is this format correct ?
>> Many thanks,
>> Dwey
>
>



From pett at cgl.ucsf.edu  Mon Oct 26 19:14:16 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 26 Oct 2015 19:14:16 -0700
Subject: [Chimera-users] Non-alphanumeric character in keyword
In-Reply-To: <CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
	<A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
	<CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>
Message-ID: <54A29827-1CEE-433F-A4CC-158626BB550D@cgl.ucsf.edu>

The file to be modified is <your Chimera installation>/share/Midas/midas_text.py.  Here?s the diff:

@@ -3352,9 +3353,9 @@
                except:
                        raise MidasError, "No value provided for keyword '%s'" \
                                                                        % typed
-               if not keyword.isalnum():
-                       raise MidasError, "Non-alphanumeric character in" \
-                               " keyword '%s'" % keyword
+               if not keyword.replace('_', '').isalnum():
+                       raise MidasError, "Non-alphanumeric or underscore " \
+                               " character in keyword '%s'" % keyword
                if keyword[0].isdigit():
                        raise MidasError, "Leading digit in keyword '%s'" % (
                                                                        keyword)

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 26, 2015, at 6:43 PM, MPI <mpi566 at gmail.com> wrote:
> 
> Dear Elaine,
> 
> Thanks for your kind help !    Would you please let me know which
> file is to be modified  in old ver. if a single file is responsible
> for that keywords  ?  because I have mulitple manchines.   I'll
> download a daily build and update that modifiled file if this would
> work.
> 
> Regards,
> Dwey
> 
> On 10/26/15, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Dear Dwey,
>> Sorry about that ? it was a bug that keywords with underscores in them did
>> not work.
>> 
>> You can get the fix in the next successful daily build (probably tomorrow).
>> Check for daily build dated Oct 22, 2015 or later:
>> <http://www.rbvi.ucsf.edu/chimera/download.html#daily>
>> 
>> Thanks for reporting the problem!
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>>> 
>>> Dear users,
>>>  In Chimera, I tried to run a vina docking in command line like
>>> 
>>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>>> 
>>> There is an error:
>>> 
>>> Non-alphanumeric character in keyword 'search_center'
>>> 
>>> I have tried tweaking  the keyword 'search_center' in  different ways
>>> but  the error won't go.
>>> 
>>> Dose anyone know how to fix it ? or is this format correct ?
>>> Many thanks,
>>> Dwey
>> 
>> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From smith_liu123 at 163.com  Mon Oct 26 22:25:45 2015
From: smith_liu123 at 163.com (Smith Liu)
Date: Tue, 27 Oct 2015 13:25:45 +0800 (CST)
Subject: [Chimera-users] movie related commands
Message-ID: <3465507b.9f9d.150a7c26179.Coremail.smith_liu123@163.com>

Dear All,


For the scale command, it will change (enlarge or decrease) the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames?


For the center command,  it will also change the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames?




Best regards.


Smith
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From mpi566 at gmail.com  Tue Oct 27 08:51:32 2015
From: mpi566 at gmail.com (MPI)
Date: Tue, 27 Oct 2015 11:51:32 -0400
Subject: [Chimera-users] Non-alphanumeric character in keyword
In-Reply-To: <54A29827-1CEE-433F-A4CC-158626BB550D@cgl.ucsf.edu>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
	<A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
	<CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>
	<54A29827-1CEE-433F-A4CC-158626BB550D@cgl.ucsf.edu>
Message-ID: <CAN4niDR8w-S=4BFAyw1LuAhtv=oNs0H3UEZX-8+=iMvCDT7=Kg@mail.gmail.com>

Dear  Eric and Elaine,

 Thanks for the solution.

It works but one of result files ( say, mytest.pdbqt  if mytest is
prefix) will NOT come out  if  the command of vina   is provided in a
script instead of GUI.

I guess  that the main output ( mytest.pdbqt) will directly be given
into viewdock  in GUI mode and  it will be saved but not in a script.

I wonder if  there is a way to save the main output (mytest.pdbqt)  in
a script so that I can view the result of mytest.pdbqt later.


Thanks,
Dwey











On 10/26/15, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> The file to be modified is <your Chimera
> installation>/share/Midas/midas_text.py.  Here?s the diff:
>
> @@ -3352,9 +3353,9 @@
>                 except:
>                         raise MidasError, "No value provided for keyword
> '%s'" \
>                                                                         %
> typed
> -               if not keyword.isalnum():
> -                       raise MidasError, "Non-alphanumeric character in" \
> -                               " keyword '%s'" % keyword
> +               if not keyword.replace('_', '').isalnum():
> +                       raise MidasError, "Non-alphanumeric or underscore "
> \
> +                               " character in keyword '%s'" % keyword
>                 if keyword[0].isdigit():
>                         raise MidasError, "Leading digit in keyword '%s'" %
> (
>
> keyword)
>
> ?Eric
>
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>
>
>> On Oct 26, 2015, at 6:43 PM, MPI <mpi566 at gmail.com> wrote:
>>
>> Dear Elaine,
>>
>> Thanks for your kind help !    Would you please let me know which
>> file is to be modified  in old ver. if a single file is responsible
>> for that keywords  ?  because I have mulitple manchines.   I'll
>> download a daily build and update that modifiled file if this would
>> work.
>>
>> Regards,
>> Dwey
>>
>> On 10/26/15, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> Dear Dwey,
>>> Sorry about that ? it was a bug that keywords with underscores in them
>>> did
>>> not work.
>>>
>>> You can get the fix in the next successful daily build (probably
>>> tomorrow).
>>> Check for daily build dated Oct 22, 2015 or later:
>>> <http://www.rbvi.ucsf.edu/chimera/download.html#daily>
>>>
>>> Thanks for reporting the problem!
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>
>>>
>>>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>>>>
>>>> Dear users,
>>>>  In Chimera, I tried to run a vina docking in command line like
>>>>
>>>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>>>>
>>>> There is an error:
>>>>
>>>> Non-alphanumeric character in keyword 'search_center'
>>>>
>>>> I have tried tweaking  the keyword 'search_center' in  different ways
>>>> but  the error won't go.
>>>>
>>>> Dose anyone know how to fix it ? or is this format correct ?
>>>> Many thanks,
>>>> Dwey
>>>
>>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>



From meng at cgl.ucsf.edu  Tue Oct 27 09:35:11 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 27 Oct 2015 09:35:11 -0700
Subject: [Chimera-users] movie related commands
In-Reply-To: <3465507b.9f9d.150a7c26179.Coremail.smith_liu123@163.com>
References: <3465507b.9f9d.150a7c26179.Coremail.smith_liu123@163.com>
Message-ID: <5859D5DE-C684-4171-ABAE-CCEC75625666@cgl.ucsf.edu>

Hi Smith,
If you look at the ?scale? description, you will see it can take a frames number.   Use command ?help scale? or see here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scale.html>

Just be aware that the scale factor is applied at EACH frame.  So if you use ?scale 1.01 100? the resulting total scale factor will be 1.01 to the 100th power, approximately 2.7X.

Alternatively, you can save all the positions ahead of time with ?savepos? and then use ?reset? with a frame number to restore them gradually.  For example if you had saved the position before using ?scale" as p1 and the position after using ?scale" as p2, you could first go back to p1 and then gradually change to p2 with:

reset p1
reset p2 100

Use ?help savepos? and ?help reset? to see the details.  Several movie-related commands are listed here, with links to their manual pages:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>

The ?center? command does not have a frames argument, so you would have to use the savepos/reset approach similar to that above.  In other words, save the positions before and after using center, then use reset to return to those positions either immediately or gradually.

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



> On Oct 26, 2015, at 10:25 PM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
> Dear All,
> 
> For the scale command, it will change (enlarge or decrease) the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames?
> 
> For the center command,  it will also change the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames?
> 
> Best regards.
> 
> Smith




From meng at cgl.ucsf.edu  Tue Oct 27 09:59:45 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 27 Oct 2015 09:59:45 -0700
Subject: [Chimera-users] Non-alphanumeric character in keyword
In-Reply-To: <CAN4niDR8w-S=4BFAyw1LuAhtv=oNs0H3UEZX-8+=iMvCDT7=Kg@mail.gmail.com>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
	<A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
	<CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>
	<54A29827-1CEE-433F-A4CC-158626BB550D@cgl.ucsf.edu>
	<CAN4niDR8w-S=4BFAyw1LuAhtv=oNs0H3UEZX-8+=iMvCDT7=Kg@mail.gmail.com>
Message-ID: <0820E583-F87B-46D1-9F3A-7AC588C9F5FA@cgl.ucsf.edu>

Dear Dwey,
My guess is that you must be careful specify an output location where you have permission to write files, e.g. ?output  ~/Desktop/mytest?

Maybe when you used the GUI, you had browsed to such a location.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 27, 2015, at 8:51 AM, MPI <mpi566 at gmail.com> wrote:
> 
> Dear  Eric and Elaine,
> 
> Thanks for the solution.
> 
> It works but one of result files ( say, mytest.pdbqt  if mytest is
> prefix) will NOT come out  if  the command of vina   is provided in a
> script instead of GUI.
> 
> I guess  that the main output ( mytest.pdbqt) will directly be given
> into viewdock  in GUI mode and  it will be saved but not in a script.
> 
> I wonder if  there is a way to save the main output (mytest.pdbqt)  in
> a script so that I can view the result of mytest.pdbqt later.
> 
> 
> Thanks,
> Dwey
> 
> 
>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>> 
>> Dear users,
>> In Chimera, I tried to run a vina docking in command line like
>> 
>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>> 
>> There is an error:
>> 
>> Non-alphanumeric character in keyword 'search_center'
>> 
>> I have tried tweaking  the keyword 'search_center' in  different ways
>> but  the error won't go.
>> 
>> Dose anyone know how to fix it ? or is this format correct ?
>> Many thanks,
>> Dwey




From mpi566 at gmail.com  Tue Oct 27 10:42:57 2015
From: mpi566 at gmail.com (MPI)
Date: Tue, 27 Oct 2015 13:42:57 -0400
Subject: [Chimera-users] Non-alphanumeric character in keyword
In-Reply-To: <0820E583-F87B-46D1-9F3A-7AC588C9F5FA@cgl.ucsf.edu>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
	<A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
	<CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>
	<54A29827-1CEE-433F-A4CC-158626BB550D@cgl.ucsf.edu>
	<CAN4niDR8w-S=4BFAyw1LuAhtv=oNs0H3UEZX-8+=iMvCDT7=Kg@mail.gmail.com>
	<0820E583-F87B-46D1-9F3A-7AC588C9F5FA@cgl.ucsf.edu>
Message-ID: <CAN4niDSp6=QefPu05p9Ct0N41P5QSJ6YAYGZ-Rg8JWsm92LODQ@mail.gmail.com>

Dear Elaine,

Thanks for the suggestion but no main output.

In GUI mode at Chimera ver 1.10.1,  I can collect all 6 files but
runing a script, I   have 5 files and do NOT see mytest.pdbqt.


Thanks,
Dwey






On 10/27/15, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Dwey,
> My guess is that you must be careful specify an output location where you
> have permission to write files, e.g. ?output  ~/Desktop/mytest?
>
> Maybe when you used the GUI, you had browsed to such a location.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Oct 27, 2015, at 8:51 AM, MPI <mpi566 at gmail.com> wrote:
>>
>> Dear  Eric and Elaine,
>>
>> Thanks for the solution.
>>
>> It works but one of result files ( say, mytest.pdbqt  if mytest is
>> prefix) will NOT come out  if  the command of vina   is provided in a
>> script instead of GUI.
>>
>> I guess  that the main output ( mytest.pdbqt) will directly be given
>> into viewdock  in GUI mode and  it will be saved but not in a script.
>>
>> I wonder if  there is a way to save the main output (mytest.pdbqt)  in
>> a script so that I can view the result of mytest.pdbqt later.
>>
>>
>> Thanks,
>> Dwey
>>
>>
>>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>>>
>>> Dear users,
>>> In Chimera, I tried to run a vina docking in command line like
>>>
>>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>>>
>>> There is an error:
>>>
>>> Non-alphanumeric character in keyword 'search_center'
>>>
>>> I have tried tweaking  the keyword 'search_center' in  different ways
>>> but  the error won't go.
>>>
>>> Dose anyone know how to fix it ? or is this format correct ?
>>> Many thanks,
>>> Dwey
>
>



From olibclarke at gmail.com  Wed Oct 28 06:53:21 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 28 Oct 2015 09:53:21 -0400
Subject: [Chimera-users] Move molecule to center of rotation?
Message-ID: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>

Hi all,

Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.

Cheers,
Oliver.


From goddard at sonic.net  Wed Oct 28 11:01:01 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 28 Oct 2015 11:01:01 -0700
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
Message-ID: <ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>

Hi Oliver,

  I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.

  At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.

	Tom



> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
> 
> Hi all,
> 
> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
> 
> Cheers,
> Oliver.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From olibclarke at gmail.com  Wed Oct 28 11:08:50 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 28 Oct 2015 14:08:50 -0400
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
	<ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
Message-ID: <ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>

Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n?, where n is the model id absent the hash, although your shortcuts look much more convenient.

It?s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5? if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.

Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It?s not a necessity of course, but it would certainly make things faster.

Cheers,
Oli.
> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>  I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.
> 
>  At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.
> 
> 	Tom
> 
> 
> 
>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>> 
>> Hi all,
>> 
>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>> 
>> Cheers,
>> Oliver.
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




From goddard at sonic.net  Wed Oct 28 12:23:54 2015
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 28 Oct 2015 12:23:54 -0700
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
	<ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
	<ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>
Message-ID: <93E70CE4-ED2E-4B1F-AA6D-B0B8E4DDC666@sonic.net>

Hi Oliver,

  Ok, you do a rotational search so all you need is to get the molecule close to where you want to fit it.  What you are asking for is more like the ?match? command which aligns one molecule with another, than the ?move? command which displaces a molecule by an offset from its current position.  But the match command won?t work because the center of rotation is not a molecule so you can?t align to it.  I?m more convinced of the need now, but I don?t see a good way to fit this in as an option to a current Chimera command.  Do you have a proposal for exactly the command syntax you want?

	Tom



> On Oct 28, 2015, at 11:08 AM, Oliver Clarke  wrote:
> 
> Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n?, where n is the model id absent the hash, although your shortcuts look much more convenient.
> 
> It?s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5? if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.
> 
> Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It?s not a necessity of course, but it would certainly make things faster.
> 
> Cheers,
> Oli.
>> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Oliver,
>> 
>> I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.
>> 
>> At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.
>> 
>> 	Tom
>> 
>> 
>> 
>>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>>> 
>>> Hi all,
>>> 
>>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>>> 
>>> Cheers,
>>> Oliver.
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 
> 




From olibclarke at gmail.com  Wed Oct 28 12:33:42 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Wed, 28 Oct 2015 15:33:42 -0400
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <93E70CE4-ED2E-4B1F-AA6D-B0B8E4DDC666@sonic.net>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
	<ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
	<ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>
	<93E70CE4-ED2E-4B1F-AA6D-B0B8E4DDC666@sonic.net>
Message-ID: <09518A30-9DDC-4542-892F-B3F9F3279D43@gmail.com>

Match could work - matching a pseudo-atom at the center of rotation of the selected molecule to a pseudo atom at the current cofr would do the trick.

Move also works - if i measure the centers of rotation of two independent models I can match their positions by using move with the x,y,z offsets (after selecting/unselecting models for motion).

Syntax would be something like move_mol_here #model_id, no need for any extra flags that I can think of.

Thanks!

Oli.
> On Oct 28, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>  Ok, you do a rotational search so all you need is to get the molecule close to where you want to fit it.  What you are asking for is more like the ?match? command which aligns one molecule with another, than the ?move? command which displaces a molecule by an offset from its current position.  But the match command won?t work because the center of rotation is not a molecule so you can?t align to it.  I?m more convinced of the need now, but I don?t see a good way to fit this in as an option to a current Chimera command.  Do you have a proposal for exactly the command syntax you want?
> 
> 	Tom
> 
> 
> 
>> On Oct 28, 2015, at 11:08 AM, Oliver Clarke  wrote:
>> 
>> Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n?, where n is the model id absent the hash, although your shortcuts look much more convenient.
>> 
>> It?s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5? if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.
>> 
>> Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It?s not a necessity of course, but it would certainly make things faster.
>> 
>> Cheers,
>> Oli.
>>> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
>>> 
>>> Hi Oliver,
>>> 
>>> I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.
>>> 
>>> At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.
>>> 
>>> 	Tom
>>> 
>>> 
>>> 
>>>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>>>> 
>>>> Cheers,
>>>> Oliver.
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>> 
>>> 
>> 
>> 
> 




From olibclarke at gmail.com  Thu Oct 29 08:58:42 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 29 Oct 2015 11:58:42 -0400
Subject: [Chimera-users] Molmap incorporation of B-factors
Message-ID: <9151A10D-5AFE-4CC7-982D-234411D81880@gmail.com>

Hi all,

For the purposes of model validation, I?d like to analyze local correlation of my model with the experimental map (and color it on either/both the model or map). I figured the easiest way to do this is to use molmap to generate a synthetic map, then use vop local correlation to generate a correlation map which I can use to color either the model or map (using scolor or ?Values at Atom Positions?). 

This works fine, and generates informative looking pictures, I just wanted to clarify exactly what molmap is doing, to make sure I understand it. 

Am I correct in thinking molmap does not use a per-atom temperature factor (or alter the width of the gaussian depending on the atomic B-factor)? 

Because if this is the case I guess the way I am doing things will exaggerate how bad the model is in regions where the B-factor is high and the density weak (which is not the worst thing in the world - better than having an unrealistically rosy view of one?s model!). 

Would it be possible to incorporate atomic B-factors into molmap calculations for Chimera 2? Or does anyone know of an external program that will perform a similar calculation (I know I can generate RSCC plots in Phenix which must be doing this internally, but I rather like displaying it on the model and map for ease of interpretation).

Cheers,
Oliver.


From goddard at sonic.net  Thu Oct 29 10:20:48 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 29 Oct 2015 10:20:48 -0700
Subject: [Chimera-users] Keep electrostatic surface color without using map
In-Reply-To: <D5E3128D5233DE48A39ED4BF376E1C7D0105C7A4@SGWAEXM005.mc.cumc.columbia.edu>
References: <D5E3128D5233DE48A39ED4BF376E1C7D0105C7A4@SGWAEXM005.mc.cumc.columbia.edu>
Message-ID: <685B6D08-3CDC-4EEA-B0D8-47A4CF34B2DB@sonic.net>

Hi Joshua,

  If you color a molecular surface with the Electrostatic Coloring tool in Chimera (menu Tools / Surface & Binding Analysis) using a Delphi or APBS electrostatics map, then close the map file using Model Panel (menu Favorites), then save the session (menu File / Save Session As?), then restart Chimera and load the session and the surface coloring is still there but the map is not used.  Tested in current Chimera version 1.10.2.

	Tom



> On Oct 28, 2015, at 8:22 PM, Broyde, Joshua E.  wrote:
> 
> Dear Tom,
> Hope all is going well. I had a quick question about coloring surfaces by electrostatics and other properties. Currently, when you color surfaces with electrostatic potentials (e.g. with delphi .phi files) the molecular surfaces are colored by the delphi files, which are loaded into the chimera session everytime the chimera session is loaded. If the delphi files are deleted, the surfaces cannot be colored. Also, the delphi file has to be loaded every time the session is started, which can take a very long time (some of these delphi files are > 1 G). Is there a way to "permanently" color the molecular surfaces with the electrostatic potential, so that the delphi files have to be loaded only once?
> 
> Sincerely,
> Joshua Broyde

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From goddard at sonic.net  Thu Oct 29 10:37:20 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 29 Oct 2015 10:37:20 -0700
Subject: [Chimera-users] Molmap incorporation of B-factors
In-Reply-To: <9151A10D-5AFE-4CC7-982D-234411D81880@gmail.com>
References: <9151A10D-5AFE-4CC7-982D-234411D81880@gmail.com>
Message-ID: <C2BA8ABE-5601-489E-BCF0-954545175749@sonic.net>

Would be nice to include B-factors in the molmap calculation of a density map from an atomic model.  Currently adds a Gaussian for each atom and all Gaussians have the same width (standard deviation) computed from the specified resolution and sigmaFactor as described in the documentation.

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

I?ve made a Chimera feature request for this ? more likely to go into Chimera 2 than Chimera 1.

	https://plato.cgl.ucsf.edu/trac/chimera/ticket/14258

  Tom




> On Oct 29, 2015, at 8:58 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi all,
> 
> For the purposes of model validation, I?d like to analyze local correlation of my model with the experimental map (and color it on either/both the model or map). I figured the easiest way to do this is to use molmap to generate a synthetic map, then use vop local correlation to generate a correlation map which I can use to color either the model or map (using scolor or ?Values at Atom Positions?). 
> 
> This works fine, and generates informative looking pictures, I just wanted to clarify exactly what molmap is doing, to make sure I understand it. 
> 
> Am I correct in thinking molmap does not use a per-atom temperature factor (or alter the width of the gaussian depending on the atomic B-factor)? 
> 
> Because if this is the case I guess the way I am doing things will exaggerate how bad the model is in regions where the B-factor is high and the density weak (which is not the worst thing in the world - better than having an unrealistically rosy view of one?s model!). 
> 
> Would it be possible to incorporate atomic B-factors into molmap calculations for Chimera 2? Or does anyone know of an external program that will perform a similar calculation (I know I can generate RSCC plots in Phenix which must be doing this internally, but I rather like displaying it on the model and map for ease of interpretation).
> 
> Cheers,
> Oliver.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From goddard at sonic.net  Thu Oct 29 15:52:23 2015
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 29 Oct 2015 15:52:23 -0700
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <09518A30-9DDC-4542-892F-B3F9F3279D43@gmail.com>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
	<ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
	<ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>
	<93E70CE4-ED2E-4B1F-AA6D-B0B8E4DDC666@sonic.net>
	<09518A30-9DDC-4542-892F-B3F9F3279D43@gmail.com>
Message-ID: <B202B415-554B-4835-9978-1281865B387A@sonic.net>

Hi Oliver,

  Ok, in tonight?s daily build you can save

	move cofr model #3

to move model #3 so that its center is at the current center of rotation.

  Tom


> On Oct 28, 2015, at 12:33 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Match could work - matching a pseudo-atom at the center of rotation of the selected molecule to a pseudo atom at the current cofr would do the trick.
> 
> Move also works - if i measure the centers of rotation of two independent models I can match their positions by using move with the x,y,z offsets (after selecting/unselecting models for motion).
> 
> Syntax would be something like move_mol_here #model_id, no need for any extra flags that I can think of.
> 
> Thanks!
> 
> Oli.
>> On Oct 28, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Oliver,
>> 
>> Ok, you do a rotational search so all you need is to get the molecule close to where you want to fit it.  What you are asking for is more like the ?match? command which aligns one molecule with another, than the ?move? command which displaces a molecule by an offset from its current position.  But the match command won?t work because the center of rotation is not a molecule so you can?t align to it.  I?m more convinced of the need now, but I don?t see a good way to fit this in as an option to a current Chimera command.  Do you have a proposal for exactly the command syntax you want?
>> 
>> 	Tom
>> 
>> 
>> 
>>> On Oct 28, 2015, at 11:08 AM, Oliver Clarke  wrote:
>>> 
>>> Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n?, where n is the model id absent the hash, although your shortcuts look much more convenient.
>>> 
>>> It?s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5? if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.
>>> 
>>> Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It?s not a necessity of course, but it would certainly make things faster.
>>> 
>>> Cheers,
>>> Oli.
>>>> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
>>>> 
>>>> Hi Oliver,
>>>> 
>>>> I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.
>>>> 
>>>> At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.
>>>> 
>>>> 	Tom
>>>> 
>>>> 
>>>> 
>>>>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>>>>> 
>>>>> Cheers,
>>>>> Oliver.
>>>>> _______________________________________________
>>>>> Chimera-users mailing list
>>>>> Chimera-users at cgl.ucsf.edu
>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>> 
>>>> 
>>> 
>>> 
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From olibclarke at gmail.com  Thu Oct 29 18:44:37 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 29 Oct 2015 21:44:37 -0400
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <B202B415-554B-4835-9978-1281865B387A@sonic.net>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
	<ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
	<ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>
	<93E70CE4-ED2E-4B1F-AA6D-B0B8E4DDC666@sonic.net>
	<09518A30-9DDC-4542-892F-B3F9F3279D43@gmail.com>
	<B202B415-554B-4835-9978-1281865B387A@sonic.net>
Message-ID: <F3F1C977-68EF-4B33-9212-65A6FB4DDB3F@gmail.com>

Fantastic, thanks Tom! Very useful!

Cheers,
Oliver.
> On Oct 29, 2015, at 6:52 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>  Ok, in tonight?s daily build you can save
> 
> 	move cofr model #3
> 
> to move model #3 so that its center is at the current center of rotation.
> 
>  Tom
> 
> 
>> On Oct 28, 2015, at 12:33 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Match could work - matching a pseudo-atom at the center of rotation of the selected molecule to a pseudo atom at the current cofr would do the trick.
>> 
>> Move also works - if i measure the centers of rotation of two independent models I can match their positions by using move with the x,y,z offsets (after selecting/unselecting models for motion).
>> 
>> Syntax would be something like move_mol_here #model_id, no need for any extra flags that I can think of.
>> 
>> Thanks!
>> 
>> Oli.
>>> On Oct 28, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
>>> 
>>> Hi Oliver,
>>> 
>>> Ok, you do a rotational search so all you need is to get the molecule close to where you want to fit it.  What you are asking for is more like the ?match? command which aligns one molecule with another, than the ?move? command which displaces a molecule by an offset from its current position.  But the match command won?t work because the center of rotation is not a molecule so you can?t align to it.  I?m more convinced of the need now, but I don?t see a good way to fit this in as an option to a current Chimera command.  Do you have a proposal for exactly the command syntax you want?
>>> 
>>> 	Tom
>>> 
>>> 
>>> 
>>>> On Oct 28, 2015, at 11:08 AM, Oliver Clarke  wrote:
>>>> 
>>>> Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n?, where n is the model id absent the hash, although your shortcuts look much more convenient.
>>>> 
>>>> It?s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5? if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.
>>>> 
>>>> Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It?s not a necessity of course, but it would certainly make things faster.
>>>> 
>>>> Cheers,
>>>> Oli.
>>>>> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
>>>>> 
>>>>> Hi Oliver,
>>>>> 
>>>>> I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.
>>>>> 
>>>>> At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.
>>>>> 
>>>>> 	Tom
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>>>>>> 
>>>>>> Cheers,
>>>>>> Oliver.
>>>>>> _______________________________________________
>>>>>> Chimera-users mailing list
>>>>>> Chimera-users at cgl.ucsf.edu
>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




From R.I.Koning at lumc.nl  Fri Oct 30 08:24:26 2015
From: R.I.Koning at lumc.nl (R.I.Koning at lumc.nl)
Date: Fri, 30 Oct 2015 15:24:26 +0000
Subject: [Chimera-users] resmap
Message-ID: <D2594A39.74E9%r.i.koning@lumc.nl>

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and ?? color the surface of your input map with the results of ResMap??. This last thing does not happen.  Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now.

Best regards,

Roman
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From olibclarke at gmail.com  Fri Oct 30 09:04:39 2015
From: olibclarke at gmail.com (Oliver Clarke)
Date: Fri, 30 Oct 2015 12:04:39 -0400
Subject: [Chimera-users] Move molecule to center of rotation?
In-Reply-To: <F3F1C977-68EF-4B33-9212-65A6FB4DDB3F@gmail.com>
References: <4792BA3A-2E0E-4119-BEE7-2AB4F1D2D839@gmail.com>
	<ADF33EF7-CC4E-4F7F-B0EC-88760CC2C160@sonic.net>
	<ACAA98CF-1D1E-4524-9B2B-068B5EC45D26@gmail.com>
	<93E70CE4-ED2E-4B1F-AA6D-B0B8E4DDC666@sonic.net>
	<09518A30-9DDC-4542-892F-B3F9F3279D43@gmail.com>
	<B202B415-554B-4835-9978-1281865B387A@sonic.net>
	<F3F1C977-68EF-4B33-9212-65A6FB4DDB3F@gmail.com>
Message-ID: <041A7E40-6B61-4E4E-863F-738417941D4D@gmail.com>

Just tried this in the latest daily build - works great. In addition to helping with model/map fitting, this also makes it much faster to align symmetric ion channel maps (assuming they are centered with C4 axis along z), as I can now align both maps on the symmetry axis and then refine rotation. Thanks!

Oliver.


> On Oct 29, 2015, at 9:44 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Fantastic, thanks Tom! Very useful!
> 
> Cheers,
> Oliver.
>> On Oct 29, 2015, at 6:52 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Oliver,
>> 
>> Ok, in tonight?s daily build you can save
>> 
>> 	move cofr model #3
>> 
>> to move model #3 so that its center is at the current center of rotation.
>> 
>> Tom
>> 
>> 
>>> On Oct 28, 2015, at 12:33 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>>> 
>>> Match could work - matching a pseudo-atom at the center of rotation of the selected molecule to a pseudo atom at the current cofr would do the trick.
>>> 
>>> Move also works - if i measure the centers of rotation of two independent models I can match their positions by using move with the x,y,z offsets (after selecting/unselecting models for motion).
>>> 
>>> Syntax would be something like move_mol_here #model_id, no need for any extra flags that I can think of.
>>> 
>>> Thanks!
>>> 
>>> Oli.
>>>> On Oct 28, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
>>>> 
>>>> Hi Oliver,
>>>> 
>>>> Ok, you do a rotational search so all you need is to get the molecule close to where you want to fit it.  What you are asking for is more like the ?match? command which aligns one molecule with another, than the ?move? command which displaces a molecule by an offset from its current position.  But the match command won?t work because the center of rotation is not a molecule so you can?t align to it.  I?m more convinced of the need now, but I don?t see a good way to fit this in as an option to a current Chimera command.  Do you have a proposal for exactly the command syntax you want?
>>>> 
>>>> 	Tom
>>>> 
>>>> 
>>>> 
>>>>> On Oct 28, 2015, at 11:08 AM, Oliver Clarke  wrote:
>>>>> 
>>>>> Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n?, where n is the model id absent the hash, although your shortcuts look much more convenient.
>>>>> 
>>>>> It?s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5? if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.
>>>>> 
>>>>> Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It?s not a necessity of course, but it would certainly make things faster.
>>>>> 
>>>>> Cheers,
>>>>> Oli.
>>>>>> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
>>>>>> 
>>>>>> Hi Oliver,
>>>>>> 
>>>>>> I?m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut ?ao? (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut ?at? (activate toggle) or ?aa? (activate all) which returns to all models moving.  Using ?at? is particularly good because then hitting ?at? again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the ?Movement Mouse Mode? tool (menu Tools / Movement) in ?Move molecule? mode, then when you click and drag on any molecule it moves just that molecule.
>>>>>> 
>>>>>> At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera ? I found it so rarely useful.
>>>>>> 
>>>>>> 	Tom
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>>>>>>> 
>>>>>>> Hi all,
>>>>>>> 
>>>>>>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the ?move? command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>>>>>>> 
>>>>>>> Cheers,
>>>>>>> Oliver.
>>>>>>> _______________________________________________
>>>>>>> Chimera-users mailing list
>>>>>>> Chimera-users at cgl.ucsf.edu
>>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 




From j.eiros-zamora14 at imperial.ac.uk  Fri Oct 30 09:47:25 2015
From: j.eiros-zamora14 at imperial.ac.uk (Eiros Zamora, Juan)
Date: Fri, 30 Oct 2015 16:47:25 +0000
Subject: [Chimera-users] Keep path when opening chimera from command line
Message-ID: <120B3B6D-A1D3-4884-980F-F764863C6518@imperial.ac.uk>

Dear Chimera experts, 

I am working with Mac OS X version 10.11.1 and Chimera 1.10.2

I use Chimera to visualize MD trajectories. Usually I launch the program through the command line. I?ve got a pretty deep hierarchy of directories to keep my data organized, so I?ve been trying to look for a way to make Chimera keep the path of the directory where I launched it from, with no success. 

What I mean is, if I launch it from a given directory and then try to load MD NetCDF files with the ?MD Movie? option, is there a way for it to show me the files in the directory where I opened it from?. Because now what it does is show me the ones from the last time I used this. 

Also, is there a way to load the topology and trajectories directly from the command line? I have looked for this option but haven?t found anything. 

Thanks for your help

Juan



From meng at cgl.ucsf.edu  Fri Oct 30 10:00:51 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 30 Oct 2015 10:00:51 -0700
Subject: [Chimera-users] resmap
In-Reply-To: <D2594A39.74E9%r.i.koning@lumc.nl>
References: <D2594A39.74E9%r.i.koning@lumc.nl>
Message-ID: <4B9F0E3A-DC30-4104-994F-CF8F9EBFECD8@cgl.ucsf.edu>

Hi Roman,
This may be a question for the authors of Resmap.  I don?t know if they read this chimera-users mailing list.  

I see some information at their Sourceforge site, where I assume you got the program and documentation: <http://resmap.sourceforge.net/>

Sorry I couldn?t help more directly,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 30, 2015, at 8:24 AM, <R.I.Koning at lumc.nl> <R.I.Koning at lumc.nl> wrote:

> I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and ?? color the surface of your input map with the results of ResMap??. This last thing does not happen.  Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. 
>  
> Best regards,
> 
> Roman




From meng at cgl.ucsf.edu  Fri Oct 30 10:09:24 2015
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 30 Oct 2015 10:09:24 -0700
Subject: [Chimera-users] Keep path when opening chimera from command line
In-Reply-To: <120B3B6D-A1D3-4884-980F-F764863C6518@imperial.ac.uk>
References: <120B3B6D-A1D3-4884-980F-F764863C6518@imperial.ac.uk>
Message-ID: <7C25C7AC-884C-46F6-A581-855B834D1982@cgl.ucsf.edu>

Hi Juan,
Regarding your last question:  yes, you can open an ?MD metafile? at the command line.  It?s basically a text file with the information you would otherwise input into the MD Movie dialog.  You can indicate that file type with prefix md: or movie: , for details see:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile>
also mentioned here
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct>

That might partly avoid your other issues since you would just specify pathname to the metafile, and within the metafile, you would give pathnames of the actual input files relative to the metafile location.

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

On Oct 30, 2015, at 9:47 AM, Eiros Zamora, Juan <j.eiros-zamora14 at imperial.ac.uk> wrote:

> Dear Chimera experts, 
> I am working with Mac OS X version 10.11.1 and Chimera 1.10.2
> 
> I use Chimera to visualize MD trajectories. Usually I launch the program through the command line. I?ve got a pretty deep hierarchy of directories to keep my data organized, so I?ve been trying to look for a way to make Chimera keep the path of the directory where I launched it from, with no success. 
> 
> What I mean is, if I launch it from a given directory and then try to load MD NetCDF files with the ?MD Movie? option, is there a way for it to show me the files in the directory where I opened it from?. Because now what it does is show me the ones from the last time I used this. 
> 
> Also, is there a way to load the topology and trajectories directly from the command line? I have looked for this option but haven?t found anything. 
> Thanks for your help
> Juan




From goddard at sonic.net  Fri Oct 30 10:23:19 2015
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 30 Oct 2015 10:23:19 -0700
Subject: [Chimera-users] resmap
In-Reply-To: <D2594A39.74E9%r.i.koning@lumc.nl>
References: <D2594A39.74E9%r.i.koning@lumc.nl>
Message-ID: <4ADD00B7-71F8-40AB-A7B1-A327C607AD95@sonic.net>

Hi Roman,

  I tried ResMap and it produced a Chimera command script for my map emd_1007.map with file name

	emd_1007_resmap_chimera.cmd

That script tries to do both the surface coloring and the plane slicing animation.  First it does the surface coloring, then it immediately shows only a single plane of the map so you can?t see the surface.  So the script is messed up.  If you make a copy of the script, delete all the lines below the one that says OPTIONAL: ResMap Slice Animation, then start Chimera (with no data open) and open the new edited script it will show the colored surface.  You would have to talk to the author of ResMap, Alp Kucukelbir to get this fixed.

	Tom

Here is what the Chimera script produced by ResMap looks like for reference:

# Color a map by local resolution computed by ResMap
#   Initial version of script courtesy of Tom Goddard, UCSF.

# Open both volumes and hide the ResMap volume.
set bg_color white
open #0 emd_1007.map
open #1 emd_1007_resmap.map
volume #1 hide

# Color the original map with the values from the ResMap output.
scolor #0 volume #1 cmap 12.40,blue:14.42,cyan:16.44,green:18.46,yellow:20.48,orange:22.50,red:22.51,gray



# OPTIONAL: ResMap Slice Animation.

# Show midway slice of the original map with contour level below the minimum map value.
volume #0 planes z,65 step 1 level -1 style surface

# Show a smooth transparent contour surface indicating the structure boundaries.
vop gaussian #0 sDev 5 model #2
volume #2 level 0.02 step 1 color .9,.7,.7,.5

# Zoom out a bit and tilt to a nice viewing angle.
turn x -45
turn y -30
turn z -30
scale 0.5

# Cycle through planes from N/2 to 4N/5 up to N/5 and back to N/2.
volume #0 planes z,65,104,0.25
wait 156
volume #0 planes z,104,26,0.25
wait 312
volume #0 planes z,26,65,0.25



> On Oct 30, 2015, at 8:24 AM,  wrote:
> 
> I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and ?? color the surface of your input map with the results of ResMap??. This last thing does not happen.  Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. 
>  
> Best regards,
> 
> Roman
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From pett at cgl.ucsf.edu  Fri Oct 30 10:41:47 2015
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 30 Oct 2015 10:41:47 -0700
Subject: [Chimera-users] Keep path when opening chimera from command line
In-Reply-To: <120B3B6D-A1D3-4884-980F-F764863C6518@imperial.ac.uk>
References: <120B3B6D-A1D3-4884-980F-F764863C6518@imperial.ac.uk>
Message-ID: <0599FAA9-A3B9-4744-A058-CFB9907F19BC@cgl.ucsf.edu>


> On Oct 30, 2015, at 9:47 AM, Eiros Zamora, Juan <j.eiros-zamora14 at imperial.ac.uk> wrote:
> 
> I use Chimera to visualize MD trajectories. Usually I launch the program through the command line. I?ve got a pretty deep hierarchy of directories to keep my data organized, so I?ve been trying to look for a way to make Chimera keep the path of the directory where I launched it from, with no success. 
> 
> What I mean is, if I launch it from a given directory and then try to load MD NetCDF files with the ?MD Movie? option, is there a way for it to show me the files in the directory where I opened it from?. Because now what it does is show me the ones from the last time I used this. 

There?s a preference for this.  In the General category of Preferences (Favorites->Preferences) change ?Open dialog starts in directory from last session? from true to false.  Assuming you want it to apply to future uses of Chimera, click Save.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab
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From conrad at cgl.ucsf.edu  Sat Oct 31 16:23:44 2015
From: conrad at cgl.ucsf.edu (Conrad Huang)
Date: Sat, 31 Oct 2015 16:23:44 -0700
Subject: [Chimera-users] vina output file misnamed
In-Reply-To: <CAN4niDR8w-S=4BFAyw1LuAhtv=oNs0H3UEZX-8+=iMvCDT7=Kg@mail.gmail.com>
References: <CAN4niDRwLfUZGm46z3-p8eQC=DG==3KQisGGwbL+UUZFkWvPKQ@mail.gmail.com>
	<A4A3859F-F231-4BB4-99CA-C9007FCDD89D@cgl.ucsf.edu>
	<CAN4niDTHpEzmNuKXe8h6Bd05=dsGmJ29Hg7MqNmj4zWvcpLaNA@mail.gmail.com>
	<54A29827-1CEE-433F-A4CC-158626BB550D@cgl.ucsf.edu>
	<CAN4niDR8w-S=4BFAyw1LuAhtv=oNs0H3UEZX-8+=iMvCDT7=Kg@mail.gmail.com>
Message-ID: <56354D80.1090200@cgl.ucsf.edu>

The problem is that the GUI does a little extra work that the command 
line does not when you use the "Browse" button to select the output 
file, there is a checked check button (in small text) "add .pdbqt suffix 
if none given", so the file name that you supply actually has the .pdbqt 
appended automatically even if you do not type it.  The command line, on 
the other hand, uses the value of the "output" option without 
modification and does NOT add the .pdbqt suffix.  (I think the rationale 
is that you should be able to name your file exactly.  Even the "add 
suffix" check button allows you to turn off that behavior.  I'm not 
saying that's the RIGHT behavior, just that's the reasoning for the 
current behavior.)  In any case, your command:

> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30

creates the output in file "mytest" rather than "mytest.pdbqt".  I'm 
pretty sure if you say:

> vina docking receptor #0 ligand #1 output mytest.pdbqt search_center 10,20,30

you should get the results in a properly named file.

Conrad

On 10/27/2015 8:51 AM, MPI wrote:
> Dear  Eric and Elaine,
>
>   Thanks for the solution.
>
> It works but one of result files ( say, mytest.pdbqt  if mytest is
> prefix) will NOT come out  if  the command of vina   is provided in a
> script instead of GUI.
>
> I guess  that the main output ( mytest.pdbqt) will directly be given
> into viewdock  in GUI mode and  it will be saved but not in a script.
>
> I wonder if  there is a way to save the main output (mytest.pdbqt)  in
> a script so that I can view the result of mytest.pdbqt later.
>
>
> Thanks,
> Dwey
>
>
>
>
>
>
>
>
>
>
>
> On 10/26/15, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> The file to be modified is <your Chimera
>> installation>/share/Midas/midas_text.py.  Here?s the diff:
>>
>> @@ -3352,9 +3353,9 @@
>>                  except:
>>                          raise MidasError, "No value provided for keyword
>> '%s'" \
>>                                                                          %
>> typed
>> -               if not keyword.isalnum():
>> -                       raise MidasError, "Non-alphanumeric character in" \
>> -                               " keyword '%s'" % keyword
>> +               if not keyword.replace('_', '').isalnum():
>> +                       raise MidasError, "Non-alphanumeric or underscore "
>> \
>> +                               " character in keyword '%s'" % keyword
>>                  if keyword[0].isdigit():
>>                          raise MidasError, "Leading digit in keyword '%s'" %
>> (
>>
>> keyword)
>>
>> ?Eric
>>
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>>
>>
>>> On Oct 26, 2015, at 6:43 PM, MPI <mpi566 at gmail.com> wrote:
>>>
>>> Dear Elaine,
>>>
>>> Thanks for your kind help !    Would you please let me know which
>>> file is to be modified  in old ver. if a single file is responsible
>>> for that keywords  ?  because I have mulitple manchines.   I'll
>>> download a daily build and update that modifiled file if this would
>>> work.
>>>
>>> Regards,
>>> Dwey
>>>
>>> On 10/26/15, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> Dear Dwey,
>>>> Sorry about that ? it was a bug that keywords with underscores in them
>>>> did
>>>> not work.
>>>>
>>>> You can get the fix in the next successful daily build (probably
>>>> tomorrow).
>>>> Check for daily build dated Oct 22, 2015 or later:
>>>> <http://www.rbvi.ucsf.edu/chimera/download.html#daily>
>>>>
>>>> Thanks for reporting the problem!
>>>> Elaine
>>>> ----------
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>>
>>>>
>>>>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at gmail.com> wrote:
>>>>>
>>>>> Dear users,
>>>>>   In Chimera, I tried to run a vina docking in command line like
>>>>>
>>>>> vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
>>>>>
>>>>> There is an error:
>>>>>
>>>>> Non-alphanumeric character in keyword 'search_center'
>>>>>
>>>>> I have tried tweaking  the keyword 'search_center' in  different ways
>>>>> but  the error won't go.
>>>>>
>>>>> Dose anyone know how to fix it ? or is this format correct ?
>>>>> Many thanks,
>>>>> Dwey
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>