From kjh950429 at gmail.com  Mon Oct  1 07:57:02 2018
From: kjh950429 at gmail.com (=?UTF-8?B?6rmA66+87J6s?=)
Date: Mon, 1 Oct 2018 23:57:02 +0900
Subject: [Chimera-users] Calculating surface area of a single atom
Message-ID: <CAAFwr=zvbwhd6H-iN3-BiZXN6wZF6PWmjwdP4+xQRJXPp8GsrA@mail.gmail.com>

Hey everyone!
I've been trying to calculate the solvent excluded surface area of a single
hydrogen atom, but Chimera keeps returning an error "miscalc code 5"
message whenever I run the "surface probeRadius" command.
I would really appreciate anyone's help.
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From Joanne.Williams at ucsf.edu  Mon Oct  1 07:52:35 2018
From: Joanne.Williams at ucsf.edu (Williams, Joanne)
Date: Mon, 1 Oct 2018 14:52:35 +0000
Subject: [Chimera-users] FW: Contributing to ChimeraX ?
In-Reply-To: <CADYXiJJZ7i7WpeVVDhcjEjeHwftF+NOPSumYgfJXzJdCrw1ZDw@mail.gmail.com>
References: <CADYXiJJZ7i7WpeVVDhcjEjeHwftF+NOPSumYgfJXzJdCrw1ZDw@mail.gmail.com>
Message-ID: <8DE6A1DC-C9FD-46F1-9B2C-A6F1B89B1C87@ucsf.edu>



From: Nicholas Yue <yue.nicholas at gmail.com>
Date: Sunday, September 30, 2018 at 3:40 AM
To: "chimerax at cgl.ucsf.edu" <chimerax at cgl.ucsf.edu>
Subject: Contributing to ChimeraX ?

Hi,

  I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly.

  I was hoping I can take a look at the source code to attempt to fix it myself.

  I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to?

  If I need to sign any documents before contributing, let me know :-)

  I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc.

Cheers
--
Nicholas Yue
Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5
Custom Dev - C++ porting, OSX, Linux, Windows
http://au.linkedin.com/in/nicholasyue
https://vimeo.com/channels/naiadtools
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From meng at cgl.ucsf.edu  Mon Oct  1 09:42:31 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 1 Oct 2018 09:42:31 -0700
Subject: [Chimera-users] Calculating surface area of a single atom
In-Reply-To: <CAAFwr=zvbwhd6H-iN3-BiZXN6wZF6PWmjwdP4+xQRJXPp8GsrA@mail.gmail.com>
References: <CAAFwr=zvbwhd6H-iN3-BiZXN6wZF6PWmjwdP4+xQRJXPp8GsrA@mail.gmail.com>
Message-ID: <F2465894-11CB-4277-BC9D-2ECBA475E92B@cgl.ucsf.edu>

The surface calculation is not meant for single atoms.  Even if it did work on single atoms, the radius would not be appropriate because the H radius in Chimera program is only meant for H bonded to other atoms in the context of a molecule.

You have to research for yourself the radius you think is correct for what you want to do, and then just use simple geometry to calculate the area of a sphere with that radius, or for that radius + 1.4 if you are trying to get some (very approximate) solvent-accessible surface.

Google ?area of sphere? to see the formula.

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

> On Oct 1, 2018, at 7:57 AM, ??? <kjh950429 at gmail.com> wrote:
> 
> Hey everyone!
> I've been trying to calculate the solvent excluded surface area of a single hydrogen atom, but Chimera keeps returning an error "miscalc code 5" message whenever I run the "surface probeRadius" command. 
> I would really appreciate anyone's help.





From meng at cgl.ucsf.edu  Mon Oct  1 10:12:27 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 1 Oct 2018 10:12:27 -0700
Subject: [Chimera-users] rmsd graph
In-Reply-To: <CACzUTu+Z_Zmc109imfzhr4DhJhiYpv3A4o-JEyAM-D315AJuVA@mail.gmail.com>
References: <CACzUTu+Z_Zmc109imfzhr4DhJhiYpv3A4o-JEyAM-D315AJuVA@mail.gmail.com>
Message-ID: <3AFC04A8-781A-4DFA-BA53-19964CB8D8CF@cgl.ucsf.edu>

Dear Dr. Sefa Celik,
The ?frames? are already ?time? ? each time step saved is one frame in MD Movie. I do not know if you are viewing the equilibration trajectory output or the production trajectory output, but both of those dialogs say ?Time step (fs) = 1? and  5000 steps.  However, you have 1001 and not 5000.  You did not show the other ?Other runtime options? section which includes ?Save once every [N] steps? where N is some integer. 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#other>

 How to convert between time and frames is 1 frame = N (1 fs), but you would have to look in the "Other runtime options" to see what you used for N. Maybe it?s 5. The extra 1 frame is probably just the starting structure.

If you mean you want the graph to say ?time? instead of ?frames,? sorry there is no option to do that.  You?d have to use the ?Dump Values? button at the bottom of the graph dialog to save the values to a text file and then use some other program to make a graph with the labels etc. that you want.  

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

> On Sep 30, 2018, at 11:28 PM, SEFA ?EL?K <scelik at istanbul.edu.tr> wrote:
> 
> Dear Dr.
> 
> I am using Chimera software(windows platform). I tried to get rmsd graph(using the plotting in the MD Movie trajectory viewer). And I got the result. But, graph's x-axis "frame" and y-axis "rmsd" value. I want the x axis to be the "time".  Briefly, I want to see how the value of rmsd changes with time.
> I added files to the e-mail. Can you explain what "1001 frames" mean? And how do I convert "1001 frames" to time. I want to see the RMSD change by time.
> Can you help with this? Could you explain in detail?
> 
> Best regard
> 
> Assoc Prof. Dr. Sefa Celik
> <chimera-5.jpg><chimera-4.jpg><chimera-1.jpg><chimera-3.jpg><chimera-2.jpg>




From meng at cgl.ucsf.edu  Mon Oct  1 10:31:03 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 1 Oct 2018 10:31:03 -0700
Subject: [Chimera-users] Hiding models one by one?
In-Reply-To: <CAL1o8vOyqKzQLgd+Hgtxr51GNjTDoBMYbb_0yNbepptciUuMfA@mail.gmail.com>
References: <CAL1o8vOyqKzQLgd+Hgtxr51GNjTDoBMYbb_0yNbepptciUuMfA@mail.gmail.com>
Message-ID: <4A45206C-A5C6-47C2-B011-001CA309BEEB@cgl.ucsf.edu>

Hi Ahmad,
This kind of looping can be done with the ?perframe? command, at least for individual models. For example, maybe something like:

perframe "~modeldisp #$1" range 16,60 interval 20

You may need to experiment, just try a few different things (your interval was 5, was but that?s pretty fast).  See ?perframe? description, including other options and examples.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>

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

> On Sep 30, 2018, at 9:17 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 
> I'm trying to hide a range of models using ~modeldisplay #16-60.
> 
> For display purposes, I want to to make them disappear one by one or in groups. I can of course write down a bunch of ~modeldisplay #16; wait 5; ~modeldisplay #17; wait 5;...etc.
> 
> Is there a way to for loop that process in the command line or do it in a better way? 
> 
> Regards. 




From pett at cgl.ucsf.edu  Mon Oct  1 13:49:04 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 1 Oct 2018 13:49:04 -0700
Subject: [Chimera-users] [Chimera-announce] MacOS Mojave
In-Reply-To: <0B8F0A65-70E4-40B9-8C09-5C7B876FDBAF@cgl.ucsf.edu>
References: <0B8F0A65-70E4-40B9-8C09-5C7B876FDBAF@cgl.ucsf.edu>
Message-ID: <8B956A1C-D861-4AA8-B0D7-56F4AD34D55A@cgl.ucsf.edu>

Hi again all,
	The daily build now has a fix for the non-showing buttons problem on MacOS Mojave (10.14).  If you have some spare time, we?d appreciate it if you could try it out if you?re a  Mac user ? whether or not you?re running Mojave ? and let us know if there are any other major problems you run into (before we put it into the release candidate build!) because it uses a new version of TclTk.  Thanks in advance.  Here?s a link to the download page: Download UCSF Chimera <https://www.cgl.ucsf.edu/chimera/download.html> (the Daily Builds table has the fixed version).  Note that the fixed version only runs on Mac OS 10.10 or later, whereas the old version also ran on 10.8 and 10.9.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




> On Sep 20, 2018, at 3:20 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi all,
> 	MacOS Mojave will be released this Monday, Sept. 24.  On Mojave, Chimera buttons and popup menus are not shown until the window containing them is resized.  Therefore we advise against upgrading to Mojave until we come up with a fix for this issue ? which we will announce on this list as soon as it is available.
> 
> ?Eric
> 
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
> 
> 
> _______________________________________________
> Chimera-announce mailing list
> Chimera-announce at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-announce

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From kjh950429 at gmail.com  Wed Oct  3 03:51:38 2018
From: kjh950429 at gmail.com (=?UTF-8?B?6rmA66+87J6s?=)
Date: Wed, 3 Oct 2018 19:51:38 +0900
Subject: [Chimera-users] Chimera pdb error
Message-ID: <CAAFwr=xG8tPCM4r=xZNwyiVCcCJF920_xEKWvzwQavXnwADiCg@mail.gmail.com>

Hi! Thanks for all of your help, but I got another problem...
I uploaded a picture of the Chimera error. The HG hydrogen atoms are not
being shown in Chimera. When I extract just the CG and HG pdb lines and
input them, Chimera works fine and can even calculate the surface. But,
when I run it with the pdb file that I have right now, it keeps returning
that error. I thought that maybe Chimera could only calculate the surface
for atoms which are connected, and that the program was looking for
mandatory bond between the atoms. I was wondering if there was a settings
change I could make to fix this, or if there was any other way to go about
straightening things out to calculate the solvent excluded area of this pdb
file.
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From meng at cgl.ucsf.edu  Wed Oct  3 08:51:40 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 3 Oct 2018 08:51:40 -0700
Subject: [Chimera-users] Chimera pdb error
In-Reply-To: <CAAFwr=xG8tPCM4r=xZNwyiVCcCJF920_xEKWvzwQavXnwADiCg@mail.gmail.com>
References: <CAAFwr=xG8tPCM4r=xZNwyiVCcCJF920_xEKWvzwQavXnwADiCg@mail.gmail.com>
Message-ID: <E993938D-9F83-4DDD-B3AB-40B846C2BCA1@cgl.ucsf.edu>

Hello,
This surface area calculation is meant for ?real? (or at least possible) molecules, not for weird sets of atoms that might be disconnected.

If you have disconnected atoms, just calculate the surface area of a sphere with the atom radius (your choice of what radius value to use, because what are you trying to model with this disconnected atom??) to get something like solvent-excluded area, or the area of a sphere with radius = (atom radius + 1.4) to get something like solvent-accessible area.

Google ?surface area of sphere? for the formula.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 3, 2018, at 3:51 AM, ??? <kjh950429 at gmail.com> wrote:
> 
> Hi! Thanks for all of your help, but I got another problem...
> I uploaded a picture of the Chimera error. The HG hydrogen atoms are not being shown in Chimera. When I extract just the CG and HG pdb lines and input them, Chimera works fine and can even calculate the surface. But, when I run it with the pdb file that I have right now, it keeps returning that error. I thought that maybe Chimera could only calculate the surface for atoms which are connected, and that the program was looking for mandatory bond between the atoms. I was wondering if there was a settings change I could make to fix this, or if there was any other way to go about straightening things out to calculate the solvent excluded area of this pdb file.



From olibclarke at gmail.com  Thu Oct  4 11:27:37 2018
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 4 Oct 2018 14:27:37 -0400
Subject: [Chimera-users] Maps/models display/activate checkboxes? [Feature
	suggestion]
Message-ID: <DC9D9399-1BBC-44E7-A4A5-5212D2B4DA63@gmail.com>

Hi,

It would be very helpful to have a way to undisplay all maps, or all models, at once. This would be particularly handy when inspecting the fit of a model in a map, as the residue tooltips don?t work when there is a surface in front of the atoms. 

Would it be possible to add two checkboxes in addition to the model specific checkboxes and the ?all? checkbox that controls whether models, maps, or both are displayed? I would envision both the model and map checkboxes working as toggles, checked by default, but one could uncheck either to temporarily undisplay all maps/models, and then check the box again to return to the previous state.

I know most effort is going into ChimeraX, so please disregard if this is difficult to implement.

Cheers
OIi


From meng at cgl.ucsf.edu  Thu Oct  4 12:15:52 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 4 Oct 2018 12:15:52 -0700
Subject: [Chimera-users] Maps/models display/activate checkboxes?
 [Feature suggestion]
In-Reply-To: <DC9D9399-1BBC-44E7-A4A5-5212D2B4DA63@gmail.com>
References: <DC9D9399-1BBC-44E7-A4A5-5212D2B4DA63@gmail.com>
Message-ID: <F7711FF7-BB00-4236-A77B-BEAEF7BA9B05@cgl.ucsf.edu>

Hi Oliver,
In the meanwhile, you could use something like the following, directly or as aliases:

~modeldisp ~@*
~modeldisp @*

...for nonatomic (e.g. map) or atomic models only, respectively.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 4, 2018, at 11:27 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi,
> 
> It would be very helpful to have a way to undisplay all maps, or all models, at once. This would be particularly handy when inspecting the fit of a model in a map, as the residue tooltips don?t work when there is a surface in front of the atoms. 
> 
> Would it be possible to add two checkboxes in addition to the model specific checkboxes and the ?all? checkbox that controls whether models, maps, or both are displayed? I would envision both the model and map checkboxes working as toggles, checked by default, but one could uncheck either to temporarily undisplay all maps/models, and then check the box again to return to the previous state.
> 
> I know most effort is going into ChimeraX, so please disregard if this is difficult to implement.
> 
> Cheers
> OIi





From underoath006 at gmail.com  Thu Oct  4 23:01:50 2018
From: underoath006 at gmail.com (Ahmad Khalifa)
Date: Fri, 5 Oct 2018 02:01:50 -0400
Subject: [Chimera-users] Recording movie at 720p
Message-ID: <CAL1o8vNFp_3RfqC1V73KS+C+p+g-AaN=VGJK+1PhHictcV6jxA@mail.gmail.com>

I'm recording a movie in the command line using:

movie record
movie stop
movie encode output ~/

I tried to include the option preset dvd for movie encode, I recieved the
following error:

"Error reading paper_movie.txt:
AttributeError: 'module' object has no attribute 'standard_formats'

  File "/opt/UCSF/Chimera64-1.12/share/MovieRecorder/moviecmd.py", line
124, in encode_op
    settings = RG.standard_formats.get(preset)

See reply log for Python traceback."

What am I doing wrong and how can I record my movie at 720p?

Regards.
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From meng at cgl.ucsf.edu  Fri Oct  5 09:12:27 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 5 Oct 2018 09:12:27 -0700
Subject: [Chimera-users] Recording movie at 720p
In-Reply-To: <CAL1o8vNFp_3RfqC1V73KS+C+p+g-AaN=VGJK+1PhHictcV6jxA@mail.gmail.com>
References: <CAL1o8vNFp_3RfqC1V73KS+C+p+g-AaN=VGJK+1PhHictcV6jxA@mail.gmail.com>
Message-ID: <8ABF9A48-8886-4784-AFFC-8F50E49911F1@cgl.ucsf.edu>

Hi Ahmad,
Looks like that option is broken? as far as I know it is very rarely (never?) used.  It may be that those standards are old anyway, and not really standard for modern times.  However, I submitted a bug report.

In the meanwhile just change the Chimera graphics window size to what you want before recording, e.g. command ?windowsize 720 480?   There are also  movie encode options to control bit rate if you wanted to do that (quality, bitrate).

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/windowsize.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>

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

> On Oct 4, 2018, at 11:01 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 
> I'm recording a movie in the command line using:
> 
> movie record
> movie stop
> movie encode output ~/ 
> 
> I tried to include the option preset dvd for movie encode, I recieved the following error:
> 
> "Error reading paper_movie.txt:
> AttributeError: 'module' object has no attribute 'standard_formats'
> 
>   File "/opt/UCSF/Chimera64-1.12/share/MovieRecorder/moviecmd.py", line 124, in encode_op
>     settings = RG.standard_formats.get(preset)
> 
> See reply log for Python traceback."
> 
> What am I doing wrong and how can I record my movie at 720p?
> 
> Regards. 




From chiendarret at gmail.com  Sat Oct  6 08:39:04 2018
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sat, 6 Oct 2018 17:39:04 +0200
Subject: [Chimera-users] error opening .cif file
Message-ID: <CAEv0nmvvcGBw7qHPgD6RxDtaujLdAZuJQirE6N2CSV+i0H1B3A@mail.gmail.com>

Hi
With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in
opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are
mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44
are missing. I have not checked anything else.
cheers
francesco pietra
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From meng at cgl.ucsf.edu  Sat Oct  6 10:10:13 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 6 Oct 2018 10:10:13 -0700
Subject: [Chimera-users] error opening .cif file
In-Reply-To: <CAEv0nmvvcGBw7qHPgD6RxDtaujLdAZuJQirE6N2CSV+i0H1B3A@mail.gmail.com>
References: <CAEv0nmvvcGBw7qHPgD6RxDtaujLdAZuJQirE6N2CSV+i0H1B3A@mail.gmail.com>
Message-ID: <8C99B19E-112B-4F34-81B1-914743F288E3@cgl.ucsf.edu>

Hi Francesco,
The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this,  I believe Chimera is reading the file correctly. 

Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> Hi
> With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else.
> cheers
> francesco pietra
> 




From chiendarret at gmail.com  Sat Oct  6 12:43:52 2018
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sat, 6 Oct 2018 21:43:52 +0200
Subject: [Chimera-users] error opening .cif file
In-Reply-To: <8C99B19E-112B-4F34-81B1-914743F288E3@cgl.ucsf.edu>
References: <CAEv0nmvvcGBw7qHPgD6RxDtaujLdAZuJQirE6N2CSV+i0H1B3A@mail.gmail.com>
 <8C99B19E-112B-4F34-81B1-914743F288E3@cgl.ucsf.edu>
Message-ID: <CAEv0nmuWMVyQiKJ22msdiOEZc_36eCoiHFXHbiSEAi7KwmeawA@mail.gmail.com>

Hi Elaine
I had better waited, examining the sequence, before claiming an error.
I'll also update chimera.
francesco

On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45,
> and no residues 43 or 44. Although I have no idea why the data is like
> this,  I believe Chimera is reading the file correctly.
>
> Your version of Chimera is a couple of years old (1.11 is from 2016 and
> 1.13 was released this year), but that would not have any effect on this
> issue.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >
> > Hi
> > With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in
> opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are
> mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44
> are missing. I have not checked anything else.
> > cheers
> > francesco pietra
> >
>
>
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From chiendarret at gmail.com  Sun Oct  7 01:55:47 2018
From: chiendarret at gmail.com (Francesco Pietra)
Date: Sun, 7 Oct 2018 10:55:47 +0200
Subject: [Chimera-users] Fwd:  error opening .cif file
In-Reply-To: <CAEv0nmuWMVyQiKJ22msdiOEZc_36eCoiHFXHbiSEAi7KwmeawA@mail.gmail.com>
References: <CAEv0nmvvcGBw7qHPgD6RxDtaujLdAZuJQirE6N2CSV+i0H1B3A@mail.gmail.com>
 <8C99B19E-112B-4F34-81B1-914743F288E3@cgl.ucsf.edu>
 <CAEv0nmuWMVyQiKJ22msdiOEZc_36eCoiHFXHbiSEAi7KwmeawA@mail.gmail.com>
Message-ID: <CAEv0nmvYyMe_YxrGYGcXkv_HM8DZ8QVtB1opviKCSnzK-C0WHw@mail.gmail.com>

Hi Elaine:
If the deposited sequence for 4i4t is correct, the deposited pdb is wrong
(void between 42-45 and 360-369 in chain D).
The deposited cif file is correct, however, for reasons that I do not know,
chimera follows the error that I said above in extracting pdb. VMD extracts
correctly the pdb, at least as far as chain D is concerned (no voids, so
that 431 residues, as indicated on RCSB, i.e., missing 442-455).
Best regards
francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Sat, Oct 6, 2018 at 9:43 PM
Subject: Re: [Chimera-users] error opening .cif file
To: chimera <chimera-users at cgl.ucsf.edu>


Hi Elaine
I had better waited, examining the sequence, before claiming an error.
I'll also update chimera.
francesco

On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45,
> and no residues 43 or 44. Although I have no idea why the data is like
> this,  I believe Chimera is reading the file correctly.
>
> Your version of Chimera is a couple of years old (1.11 is from 2016 and
> 1.13 was released this year), but that would not have any effect on this
> issue.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >
> > Hi
> > With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in
> opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are
> mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44
> are missing. I have not checked anything else.
> > cheers
> > francesco pietra
> >
>
>
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From meng at cgl.ucsf.edu  Sun Oct  7 10:50:16 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 7 Oct 2018 10:50:16 -0700
Subject: [Chimera-users] Fwd:  error opening .cif file
In-Reply-To: <CAEv0nmvYyMe_YxrGYGcXkv_HM8DZ8QVtB1opviKCSnzK-C0WHw@mail.gmail.com>
References: <CAEv0nmvvcGBw7qHPgD6RxDtaujLdAZuJQirE6N2CSV+i0H1B3A@mail.gmail.com>
 <8C99B19E-112B-4F34-81B1-914743F288E3@cgl.ucsf.edu>
 <CAEv0nmuWMVyQiKJ22msdiOEZc_36eCoiHFXHbiSEAi7KwmeawA@mail.gmail.com>
 <CAEv0nmvYyMe_YxrGYGcXkv_HM8DZ8QVtB1opviKCSnzK-C0WHw@mail.gmail.com>
Message-ID: <19A7A4D9-5A22-420E-BEE9-8CC385248866@cgl.ucsf.edu>

Hi Francesco,
I believe Chimera is using the auth_seq_id  (author residue numbering).  In mmCIF, there is also another residue numbering value, label_seq_id, and sometimes they are different.  Usually there is some reason why the authors numbered differently, but I don?t know in this case.  

If it bothers you, you can just renumber the chain sequentially (Tools.. Structure Editing? Renumber Residues, or command ?resrenumber?).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html>

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

> On Oct 7, 2018, at 1:55 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> Hi Elaine:
> If the deposited sequence for 4i4t is correct, the deposited pdb is wrong (void between 42-45 and 360-369 in chain D).
> The deposited cif file is correct, however, for reasons that I do not know, chimera follows the error that I said above in extracting pdb. VMD extracts correctly the pdb, at least as far as chain D is concerned (no voids, so that 431 residues, as indicated on RCSB, i.e., missing 442-455).
> Best regards
> francesco
> 
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Sat, Oct 6, 2018 at 9:43 PM
> Subject: Re: [Chimera-users] error opening .cif file
> To: chimera <chimera-users at cgl.ucsf.edu>
> 
> 
> Hi Elaine
> I had better waited, examining the sequence, before claiming an error. 
> I'll also update chimera.
> francesco
> 
> On Sat, Oct 6, 2018, 19:10 Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> The PDB and mmCIF files for 4i4t have chain D 42 directly bonded to 45, and no residues 43 or 44. Although I have no idea why the data is like this,  I believe Chimera is reading the file correctly. 
> 
> Your version of Chimera is a couple of years old (1.11 is from 2016 and 1.13 was released this year), but that would not have any effect on this issue.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Oct 6, 2018, at 8:39 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> > 
> > Hi
> > With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else.
> > cheers
> > francesco pietra
> > 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From emilyxu202 at gmail.com  Mon Oct  8 09:15:40 2018
From: emilyxu202 at gmail.com (Emily Xu)
Date: Mon, 8 Oct 2018 12:15:40 -0400
Subject: [Chimera-users] C-N peptide bond within one peptide
Message-ID: <CAB5zsgS62fE394j52ayPOkPS-Rc5jbXD27gN6L6+06KNpVcdag@mail.gmail.com>

Hello,

Is there a way to join two ends of a peptide in Chimera? I am trying the
create a peptide bond linking the C and N termini in a singular peptide to
form a cyclotide. Is this possible in Chimera?
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From meng at cgl.ucsf.edu  Mon Oct  8 15:04:37 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 8 Oct 2018 15:04:37 -0700
Subject: [Chimera-users] C-N peptide bond within one peptide
In-Reply-To: <CAB5zsgS62fE394j52ayPOkPS-Rc5jbXD27gN6L6+06KNpVcdag@mail.gmail.com>
References: <CAB5zsgS62fE394j52ayPOkPS-Rc5jbXD27gN6L6+06KNpVcdag@mail.gmail.com>
Message-ID: <CB1FE836-4FD4-4DBD-958B-879B7D868D7E@cgl.ucsf.edu>

Hi Emily,
Sure!  One way is to just use the ?bond? command.  E.g., select the two atoms to be bonded (carbonyl C on last residue and N on first residue) and then enter command:

bond sel

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

Alternatively if you are in the Build Structure tool, the Adjust Bonds section has an option to add bond between selected atoms.  You might have to change from ?reasonable? to ?all possible? if the bond would be longer than normal.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

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

> On Oct 8, 2018, at 9:15 AM, Emily Xu <emilyxu202 at gmail.com> wrote:
> 
> Hello,
> Is there a way to join two ends of a peptide in Chimera? I am trying the create a peptide bond linking the C and N termini in a singular peptide to form a cyclotide. Is this possible in Chimera?




From vani.pande at students.iiserpune.ac.in  Wed Oct 10 09:29:56 2018
From: vani.pande at students.iiserpune.ac.in (Vani Pande)
Date: Wed, 10 Oct 2018 21:59:56 +0530
Subject: [Chimera-users] Generating symmetry mates
Message-ID: <CAA=Om-8hBWko=5GupWuqEXSrctrQUkQFTPGeaZgcdMy4XXy0aw@mail.gmail.com>

Hello,

I wanted to generate symmetry mates for the protein, I am not finding a way
to do so in chimera.The protein is a monomer in an asymmetric unit.

Thanks
Vani Pande
Int PhD Biological sciences
IISER Pune
20162013
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From meng at cgl.ucsf.edu  Wed Oct 10 09:54:06 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 10 Oct 2018 09:54:06 -0700
Subject: [Chimera-users] Generating symmetry mates
In-Reply-To: <CAA=Om-8hBWko=5GupWuqEXSrctrQUkQFTPGeaZgcdMy4XXy0aw@mail.gmail.com>
References: <CAA=Om-8hBWko=5GupWuqEXSrctrQUkQFTPGeaZgcdMy4XXy0aw@mail.gmail.com>
Message-ID: <2D83FF55-9B57-41FC-88AE-830FCFE0768C@cgl.ucsf.edu>

Hello Vani,
Several possibilities if the file is from the PDB and contains symmetry information:

Unit Cell tool (in menu under Tools? Higher-order structure)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html>

Multiscale Models tool (in menu under Tools? Higher-order structure)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

?sym? command
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

These 3 have overlapping capabilities and it might be that any/all of them would work in your case.  See the links for details on what kinds of informatino they use.

You could also go directly to the RCSB PDB website and download the biological assembly instead of just the  asymmetric unit.

If the file does not contain symmetry information, that is a different matter.  You might have to find another similar structure that does have symmetry information, then in the ?sym? command tell the program to use the other protein?s symmetry to make the multimer of your protein.

In case you didn?t know: you can use menu: Help? Search Documentation and look for topics like ?symmetry?  and it would give the same links as I gave above, plus a few others (Crystal Contacts tool may also be relevant)

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

> On Oct 10, 2018, at 9:29 AM, Vani Pande <vani.pande at students.iiserpune.ac.in> wrote:
> 
> Hello,
> I wanted to generate symmetry mates for the protein, I am not finding a way to do so in chimera.The protein is a monomer in an asymmetric unit.




From vani.pande at students.iiserpune.ac.in  Wed Oct 10 10:12:13 2018
From: vani.pande at students.iiserpune.ac.in (Vani Pande)
Date: Wed, 10 Oct 2018 22:42:13 +0530
Subject: [Chimera-users] Generating symmetry mates
In-Reply-To: <2D83FF55-9B57-41FC-88AE-830FCFE0768C@cgl.ucsf.edu>
References: <CAA=Om-8hBWko=5GupWuqEXSrctrQUkQFTPGeaZgcdMy4XXy0aw@mail.gmail.com>
 <2D83FF55-9B57-41FC-88AE-830FCFE0768C@cgl.ucsf.edu>
Message-ID: <CAA=Om-_ckbpK5Bbq=CwWEfraPuWwNC_jJm=gdFhM83LGfqA9aw@mail.gmail.com>

Thank you for your help!
Vani Pande
Int PhD Biological sciences
IISER Pune
20162013


On Wed, Oct 10, 2018 at 10:24 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Vani,
> Several possibilities if the file is from the PDB and contains symmetry
> information:
>
> Unit Cell tool (in menu under Tools? Higher-order structure)
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html
> >
>
> Multiscale Models tool (in menu under Tools? Higher-order structure)
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html
> >
>
> ?sym? command
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
>
> These 3 have overlapping capabilities and it might be that any/all of them
> would work in your case.  See the links for details on what kinds of
> informatino they use.
>
> You could also go directly to the RCSB PDB website and download the
> biological assembly instead of just the  asymmetric unit.
>
> If the file does not contain symmetry information, that is a different
> matter.  You might have to find another similar structure that does have
> symmetry information, then in the ?sym? command tell the program to use the
> other protein?s symmetry to make the multimer of your protein.
>
> In case you didn?t know: you can use menu: Help? Search Documentation and
> look for topics like ?symmetry?  and it would give the same links as I gave
> above, plus a few others (Crystal Contacts tool may also be relevant)
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 10, 2018, at 9:29 AM, Vani Pande <
> vani.pande at students.iiserpune.ac.in> wrote:
> >
> > Hello,
> > I wanted to generate symmetry mates for the protein, I am not finding a
> way to do so in chimera.The protein is a monomer in an asymmetric unit.
>
>
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From mhl2468 at rit.edu  Thu Oct 11 17:16:12 2018
From: mhl2468 at rit.edu (Minh Le)
Date: Thu, 11 Oct 2018 20:16:12 -0400
Subject: [Chimera-users] Morphing code
Message-ID: <CAHGwYwu1WGtTOu0UJx92=E--1GQi7DHzegPPj8twDi7o4nj4Gw@mail.gmail.com>

Hello there,

I'm currently having trouble with the morphing code in chimera and I
don't know how to use Python to make the morph.py. Is there any way
you can help me with this?

Thank you,
Minh


From matthias.fellner at otago.ac.nz  Thu Oct 11 19:58:12 2018
From: matthias.fellner at otago.ac.nz (Matthias Fellner)
Date: Fri, 12 Oct 2018 02:58:12 +0000
Subject: [Chimera-users] MD movie metafile
Message-ID: <1539313089273.31893@otago.ac.nz>

Good day


I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere.

I tried some versions of this command:

md: D:\script.txt or movie: D:\script.txt


The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs.

I am also not sure if the script command would even work like this:


namd(psf/dcd)
D:\structure.psf
structure_MD001.dcd - D:\


Any advice is appreciated

Thank you

Matthias Fellner


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From meng at cgl.ucsf.edu  Fri Oct 12 09:18:35 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 12 Oct 2018 09:18:35 -0700
Subject: [Chimera-users] Morphing code
In-Reply-To: <CAHGwYwu1WGtTOu0UJx92=E--1GQi7DHzegPPj8twDi7o4nj4Gw@mail.gmail.com>
References: <CAHGwYwu1WGtTOu0UJx92=E--1GQi7DHzegPPj8twDi7o4nj4Gw@mail.gmail.com>
Message-ID: <86E6430E-7C2D-44CC-8792-1F3BA25C4B13@cgl.ucsf.edu>

Hello MInh,
It?s not really intended for use with Python.  Is there a reason you can?t use the Chimera Morph Conformations tool or the ?morph? command? 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html>

You might also consider trying ChimeraX instead, since the ?morph? command is easier to use and has more options than in Chimera.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>

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

> On Oct 11, 2018, at 5:16 PM, Minh Le <mhl2468 at rit.edu> wrote:
> 
> Hello there,
> I'm currently having trouble with the morphing code in chimera and I
> don't know how to use Python to make the morph.py. Is there any way
> you can help me with this?
> Thank you,
> Minh




From meng at cgl.ucsf.edu  Fri Oct 12 11:03:06 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 12 Oct 2018 11:03:06 -0700
Subject: [Chimera-users] MD movie metafile
In-Reply-To: <1539313089273.31893@otago.ac.nz>
References: <1539313089273.31893@otago.ac.nz>
Message-ID: <086E3278-B528-4BDF-B993-87AD34E4980A@cgl.ucsf.edu>

HI Matthias,
Sounds like you almost had it right.  However, you have to use the ?open? command to open the metafile.  The ?md? part is just a format specifier for the open command, not a command in itself.

(command list: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>)

Summary:
To bypass the MD Movie input-files dialog you would create a ?metafile? which is just a short plain text file of the same things you would enter into that dialog.  The "startup and input" section of the MD Movie help has a couple examples of metafile contents:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

Your metafile would just contain something like this:
namd(prmtop/dcd)
D:\structure.psf
D:\structure_MD001.dcd

?and you?d open it with command:
open md:metafile-name

?where metafile-name is a pathname if it is not in the current working directory.  However, I suspect that pathname with a colon might cause problejms. Chimera command ?cd? changes the current working directory, so if giving the pathname directly in the open command causes a problem, instead use ?cd? to go that folder and then just use the metafile name in the open command.   I?m a little uncertain of what you?ll need to do, since I?m not a Windows user.  On Mac, all my pathnames don?t have colons in them so it?s not an issue.

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


> On Oct 11, 2018, at 7:58 PM, Matthias Fellner <matthias.fellner at otago.ac.nz> wrote:
> 
> Good day
> 
> I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere.
> I tried some versions of this command:
> md: D:\script.txt or movie: D:\script.txt
> 
> The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs.
> I am also not sure if the script command would even work like this:
> 
> namd(psf/dcd)
> D:\structure.psf
> structure_MD001.dcd - D:\
> 
> Any advice is appreciated
> Thank you
> Matthias Fellner
> 



From meng at cgl.ucsf.edu  Fri Oct 12 11:28:27 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 12 Oct 2018 11:28:27 -0700
Subject: [Chimera-users] MD movie metafile
In-Reply-To: <086E3278-B528-4BDF-B993-87AD34E4980A@cgl.ucsf.edu>
References: <1539313089273.31893@otago.ac.nz>
 <086E3278-B528-4BDF-B993-87AD34E4980A@cgl.ucsf.edu>
Message-ID: <7FA842F8-0A49-4AE2-8EA7-28EA54BD76E8@cgl.ucsf.edu>

Hi Matthias,
Now I see that the documentation says the metafile should contain paths relative to the metafile location, so I?m not absolutely sure that it will work to include the absolute paths as in my previous reply.

Instead (and how I usually do it) is to omit paths within the metafile and just put the metafile in the same place as the data.  E.g. metafile contents

namd(prmtop/dcd)
structure.psf
structure_MD001.dcd

and then use command something like 

open md:D:\metafile-name

I?m told the open command should be able to interpret the second colon correctly as indicating the drive.  If not, could try ?cd? first as mentioned below.
Best,
Elaine


> On Oct 12, 2018, at 11:03 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> HI Matthias,
> Sounds like you almost had it right.  However, you have to use the ?open? command to open the metafile.  The ?md? part is just a format specifier for the open command, not a command in itself.
> 
> (command list: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>)
> 
> Summary:
> To bypass the MD Movie input-files dialog you would create a ?metafile? which is just a short plain text file of the same things you would enter into that dialog.  The "startup and input" section of the MD Movie help has a couple examples of metafile contents:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> 
> Your metafile would just contain something like this:
> namd(prmtop/dcd)
> D:\structure.psf
> D:\structure_MD001.dcd
> 
> ?and you?d open it with command:
> open md:metafile-name
> 
> ?where metafile-name is a pathname if it is not in the current working directory.  However, I suspect that pathname with a colon might cause problejms. Chimera command ?cd? changes the current working directory, so if giving the pathname directly in the open command causes a problem, instead use ?cd? to go that folder and then just use the metafile name in the open command.   I?m a little uncertain of what you?ll need to do, since I?m not a Windows user.  On Mac, all my pathnames don?t have colons in them so it?s not an issue.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Oct 11, 2018, at 7:58 PM, Matthias Fellner <matthias.fellner at otago.ac.nz> wrote:
>> 
>> Good day
>> 
>> I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere.
>> I tried some versions of this command:
>> md: D:\script.txt or movie: D:\script.txt
>> 
>> The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs.
>> I am also not sure if the script command would even work like this:
>> 
>> namd(psf/dcd)
>> D:\structure.psf
>> structure_MD001.dcd - D:\
>> 
>> Any advice is appreciated
>> Thank you
>> Matthias Fellner
>> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Fri Oct 12 11:39:34 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 12 Oct 2018 11:39:34 -0700
Subject: [Chimera-users] MD movie metafile
In-Reply-To: <7FA842F8-0A49-4AE2-8EA7-28EA54BD76E8@cgl.ucsf.edu>
References: <1539313089273.31893@otago.ac.nz>
 <086E3278-B528-4BDF-B993-87AD34E4980A@cgl.ucsf.edu>
 <7FA842F8-0A49-4AE2-8EA7-28EA54BD76E8@cgl.ucsf.edu>
Message-ID: <046E6031-9E5C-4145-BDE5-E1C712B1E4EA@cgl.ucsf.edu>

Absolute paths will also work, though relative paths are typically shorter/easier.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




> On Oct 12, 2018, at 11:28 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Matthias,
> Now I see that the documentation says the metafile should contain paths relative to the metafile location, so I?m not absolutely sure that it will work to include the absolute paths as in my previous reply.
> 
> Instead (and how I usually do it) is to omit paths within the metafile and just put the metafile in the same place as the data.  E.g. metafile contents
> 
> namd(prmtop/dcd)
> structure.psf
> structure_MD001.dcd
> 
> and then use command something like 
> 
> open md:D:\metafile-name
> 
> I?m told the open command should be able to interpret the second colon correctly as indicating the drive.  If not, could try ?cd? first as mentioned below.
> Best,
> Elaine
> 
> 
>> On Oct 12, 2018, at 11:03 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> HI Matthias,
>> Sounds like you almost had it right.  However, you have to use the ?open? command to open the metafile.  The ?md? part is just a format specifier for the open command, not a command in itself.
>> 
>> (command list: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>)
>> 
>> Summary:
>> To bypass the MD Movie input-files dialog you would create a ?metafile? which is just a short plain text file of the same things you would enter into that dialog.  The "startup and input" section of the MD Movie help has a couple examples of metafile contents:
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
>> 
>> Your metafile would just contain something like this:
>> namd(prmtop/dcd)
>> D:\structure.psf
>> D:\structure_MD001.dcd
>> 
>> ?and you?d open it with command:
>> open md:metafile-name
>> 
>> ?where metafile-name is a pathname if it is not in the current working directory.  However, I suspect that pathname with a colon might cause problejms. Chimera command ?cd? changes the current working directory, so if giving the pathname directly in the open command causes a problem, instead use ?cd? to go that folder and then just use the metafile name in the open command.   I?m a little uncertain of what you?ll need to do, since I?m not a Windows user.  On Mac, all my pathnames don?t have colons in them so it?s not an issue.
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Oct 11, 2018, at 7:58 PM, Matthias Fellner <matthias.fellner at otago.ac.nz> wrote:
>>> 
>>> Good day
>>> 
>>> I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere.
>>> I tried some versions of this command:
>>> md: D:\script.txt or movie: D:\script.txt
>>> 
>>> The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs.
>>> I am also not sure if the script command would even work like this:
>>> 
>>> namd(psf/dcd)
>>> D:\structure.psf
>>> structure_MD001.dcd - D:\
>>> 
>>> Any advice is appreciated
>>> Thank you
>>> Matthias Fellner
>>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From mhl2468 at rit.edu  Fri Oct 12 10:22:15 2018
From: mhl2468 at rit.edu (Minh Le)
Date: Fri, 12 Oct 2018 13:22:15 -0400
Subject: [Chimera-users] Morphing code
In-Reply-To: <86E6430E-7C2D-44CC-8792-1F3BA25C4B13@cgl.ucsf.edu>
References: <CAHGwYwu1WGtTOu0UJx92=E--1GQi7DHzegPPj8twDi7o4nj4Gw@mail.gmail.com>
 <86E6430E-7C2D-44CC-8792-1F3BA25C4B13@cgl.ucsf.edu>
Message-ID: <CAHGwYwu=QmSgvKp-6Ux4CHXo-g2PtRr9_x8NXAdZfsNt11=G3g@mail.gmail.com>

Hi,

I have tried using the "morph" command line as follow:

morph start #0 frames 60
morph interpolate #1 frames 60
morph movie nogui true

coordset #2 41,1
wait 30
coordset #2 1,
wait 30
coordset #2 41,1
wait 30
coordset #2 1,
wait 30
coordset #2 41,1
wait 30
coordset #2 1,
wait 30

but the error box said that I have already define the default?

Regards,
Minh
On Fri, Oct 12, 2018 at 12:21 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hello MInh,
> It?s not really intended for use with Python.  Is there a reason you can?t use the Chimera Morph Conformations tool or the ?morph? command?
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html>
>
> You might also consider trying ChimeraX instead, since the ?morph? command is easier to use and has more options than in Chimera.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 11, 2018, at 5:16 PM, Minh Le <mhl2468 at rit.edu> wrote:
> >
> > Hello there,
> > I'm currently having trouble with the morphing code in chimera and I
> > don't know how to use Python to make the morph.py. Is there any way
> > you can help me with this?
> > Thank you,
> > Minh
>



From meng at cgl.ucsf.edu  Fri Oct 12 13:20:07 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 12 Oct 2018 13:20:07 -0700
Subject: [Chimera-users] Morphing code
In-Reply-To: <CAHGwYwu=QmSgvKp-6Ux4CHXo-g2PtRr9_x8NXAdZfsNt11=G3g@mail.gmail.com>
References: <CAHGwYwu1WGtTOu0UJx92=E--1GQi7DHzegPPj8twDi7o4nj4Gw@mail.gmail.com>
 <86E6430E-7C2D-44CC-8792-1F3BA25C4B13@cgl.ucsf.edu>
 <CAHGwYwu=QmSgvKp-6Ux4CHXo-g2PtRr9_x8NXAdZfsNt11=G3g@mail.gmail.com>
Message-ID: <64A8521E-2D18-417A-8389-6FDAB09197AD@cgl.ucsf.edu>

Hi MInh,
Your commands are fine the first time you use them after starting Chimera to create the morph.  The ?default already defined? warning is just when you use the morph commands again before quitting from Chimera.  It is saying you already set up and created the morph and there is no need to do it again.

You could just use the first 3 commands one time (morph start, morph interpolate, morph movie) after starting Chimera and opening your input structures #0 and #1. Then save session.  Then restore session and just use the coordset commands to play the morph.  There is no need to try to create the morph trajectory #2 multiple times once it has already been created.

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


> On Oct 12, 2018, at 10:22 AM, Minh Le <mhl2468 at rit.edu> wrote:
> 
> Hi,
> 
> I have tried using the "morph" command line as follow:
> 
> morph start #0 frames 60
> morph interpolate #1 frames 60
> morph movie nogui true
> 
> coordset #2 41,1
> wait 30
> coordset #2 1,
> wait 30
> coordset #2 41,1
> wait 30
> coordset #2 1,
> wait 30
> coordset #2 41,1
> wait 30
> coordset #2 1,
> wait 30
> 
> but the error box said that I have already define the default?
> 
> Regards,
> Minh
> On Fri, Oct 12, 2018 at 12:21 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hello MInh,
>> It?s not really intended for use with Python.  Is there a reason you can?t use the Chimera Morph Conformations tool or the ?morph? command?
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html>
>> 
>> You might also consider trying ChimeraX instead, since the ?morph? command is easier to use and has more options than in Chimera.
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Oct 11, 2018, at 5:16 PM, Minh Le <mhl2468 at rit.edu> wrote:
>>> 
>>> Hello there,
>>> I'm currently having trouble with the morphing code in chimera and I
>>> don't know how to use Python to make the morph.py. Is there any way
>>> you can help me with this?
>>> Thank you,
>>> Minh




From ammadaslamkhan at gmail.com  Sat Oct 13 00:38:36 2018
From: ammadaslamkhan at gmail.com (ammad aslam)
Date: Sat, 13 Oct 2018 12:38:36 +0500
Subject: [Chimera-users] problem with autodock vina page
Message-ID: <CAH7PxSTE5JKUxm=wRLCarUcCFktCX8AZBLHFXW7wMRVN8uk8Fw@mail.gmail.com>

I wonder, is there any problem with autodock vina website
vina.scripps.edu/download.html ?
I and my friends here cannot open it. Can anyone update me about the real
problem.
Regards,

Ammad
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From meng at cgl.ucsf.edu  Sat Oct 13 10:02:52 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 13 Oct 2018 10:02:52 -0700
Subject: [Chimera-users] problem with autodock vina page
In-Reply-To: <CAH7PxSTE5JKUxm=wRLCarUcCFktCX8AZBLHFXW7wMRVN8uk8Fw@mail.gmail.com>
References: <CAH7PxSTE5JKUxm=wRLCarUcCFktCX8AZBLHFXW7wMRVN8uk8Fw@mail.gmail.com>
Message-ID: <3E5D48A4-1664-4BD7-B010-0A3A79968525@cgl.ucsf.edu>

Hi Ammad,
Sorry, our group (Chimera developers at UCSF) does not control that website (Autodock Vina at Scripps), so we don?t know anything more about it than you do!   Right now, I can?t reach it either.
Regards,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 13, 2018, at 12:38 AM, ammad aslam <ammadaslamkhan at gmail.com> wrote:
> 
> I wonder, is there any problem with autodock vina website vina.scripps.edu/download.html ?
> I and my friends here cannot open it. Can anyone update me about the real problem.
> Regards,
> Ammad 
> 




From yangqi.gu at yale.edu  Mon Oct 15 11:47:25 2018
From: yangqi.gu at yale.edu (BuddySphinx)
Date: Mon, 15 Oct 2018 14:47:25 -0400
Subject: [Chimera-users] Visualize 3-10 helix
Message-ID: <5bc4e0bc.1c69fb81.7178d.0520@mx.google.com>

Dear Chimera users,
I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds?
Best,
Yangqi

Sent from Mail for Windows 10

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From meng at cgl.ucsf.edu  Mon Oct 15 14:02:42 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 15 Oct 2018 14:02:42 -0700
Subject: [Chimera-users] Visualize 3-10 helix
In-Reply-To: <5bc4e0bc.1c69fb81.7178d.0520@mx.google.com>
References: <5bc4e0bc.1c69fb81.7178d.0520@mx.google.com>
Message-ID: <997C0C4E-70EF-4497-86F1-B0712D2B9908@cgl.ucsf.edu>

Hi Yangqi
Even though it is often included in the PDB file HELIX lines, Chimera does not automatically tag different kinds of helix.  They are all lumped together in ?helix?

Although it is not very convenient, to find out which residues are in 3-10 helices in many deposited structures, you can look in the PDB file text for the HELIX lines, and then see the number in column 40 as described here (?1? is right-handed alpha, ?5? is right-handed 3-10, etc.):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary>>

For example, I see that 3KK4 has several 3-10 helices by looking in the text of its PDB file.  Looking at chain A only, the HELIX lines are:

HELIX    1   1 ASN A   -1  ARG A    7  1                                   9
HELIX    2   2 ASN A    9  TYR A   13  5                                   5
HELIX    3   3 GLN A   33  ASP A   46  1                                  14
HELIX    4   4 ARG A   49  GLY A   66  1                                  18
HELIX    5   5 ASN A   70  GLU A   88  1                                  19
HELIX    6   6 PRO A   98  LEU A  102  5                                   5
HELIX    7   7 ASP A  103  ARG A  109  1                                   7
HELIX    8   8 PRO A  112  TYR A  116  5                                   5

That means chain A residues 9-13, 98-102, and 112-116 were  identified as 3-10 helix.  

If you wanted to use that information, you could (for example) make an alias for that set of residues for convenience in later commands, or just specify them directly, say

open 3kk4
delete ~ :.a
alias tthel :9-13,98-102,112-116
color red tthel
sel tthel

(B) If you wanted to identify 3-10 helices directly from the structure (say it was just a model you built or some other undeposited structure), you could use the FindHBond tool or command and then identify where the mainchain H-bonds are i,i+3, and whether the conformation appears helical.  I don?t think it is obvious from the backbone angles whether it is alpha or 3-10 helix.   For example with 3kk4

select helix & @n,o
hbonds selRestrict both log true

?and then look in the Reply Log for i,i+3 backbone H-bonds.  For chain A I get:

H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLU 3.A N    ASN -1.A O    no hydrogen  2.948  N/A
ILE 4.A N    ALA 0.A O     no hydrogen  2.993  N/A
PHE 5.A N    MSE 1.A O     no hydrogen  3.085  N/A
ILE 6.A N    CME 2.A O     no hydrogen  2.832  N/A
SER 12.A N   ASN 9.A O     no hydrogen  2.979  N/A
TYR 13.A N   GLN 10.A O    no hydrogen  3.327  N/A
LEU 34.A N   SER 12.A O    no hydrogen  2.914  N/A
ASP 37.A N   GLN 33.A O    no hydrogen  2.912  N/A
VAL 38.A N   LEU 34.A O    no hydrogen  2.904  N/A
[?]
GLU 88.A N   VAL 84.A O    no hydrogen  2.885  N/A
SER 101.A N  PRO 98.A O    no hydrogen  3.050  N/A
LEU 102.A N  ILE 99.A O    no hydrogen  2.968  N/A
VAL 107.A N  ASP 103.A O   no hydrogen  2.991  N/A
LEU 108.A N  ALA 104.A O   no hydrogen  3.010  N/A
ARG 109.A N  GLN 105.A O   no hydrogen  3.055  N/A
LEU 115.A N  PRO 112.A O   no hydrogen  3.035  N/A
53 hydrogen bonds found

? whereas if I just select the residues that the PDB file says are 3-10 

select tthel & @n,o
hbonds selRes both log t

I get:
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
SER 12.A N   ASN 9.A O    no hydrogen  2.979  N/A
SER 12.A N   ASN 9.A OD1  no hydrogen  3.067  N/A
SER 12.A OG  ASN 9.A O    no hydrogen  2.589  N/A
TYR 13.A N   GLN 10.A O   no hydrogen  3.327  N/A
SER 101.A N  PRO 98.A O   no hydrogen  3.050  N/A
LEU 102.A N  ILE 99.A O   no hydrogen  2.968  N/A
LEU 115.A N  PRO 112.A O  no hydrogen  3.035  N/A
7 hydrogen bonds found

(C) I don?t think you can tell 3-10 from other helix using just phi-psi angles, but to examine those angles you can show the protein Ramachandran Plot (Favorites? Model Panel, choose model on the left and then the Ramachandran plot button on the right).  Then when you select any residue(s) they will show up on the plot as red dots.    
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html>>
Or, you can select any single residue and click the green magnifying glass on the lower right corner of the Chimera window to show the Selection Inspector, then in that dialog choose to Inspect: ?Residue?  and it shows you the phi angle and psi angle values.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>>

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

> On Oct 15, 2018, at 11:47 AM, BuddySphinx <yangqi.gu at yale.edu> wrote:
> 
> Dear Chimera users,
> I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds?
> Best,
> Yangqi

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From yangqi.gu at yale.edu  Mon Oct 15 14:15:42 2018
From: yangqi.gu at yale.edu (Yangqi Gu)
Date: Mon, 15 Oct 2018 17:15:42 -0400
Subject: [Chimera-users] Visualize 3-10 helix
In-Reply-To: <997C0C4E-70EF-4497-86F1-B0712D2B9908@cgl.ucsf.edu>
References: <5bc4e0bc.1c69fb81.7178d.0520@mx.google.com>
 <997C0C4E-70EF-4497-86F1-B0712D2B9908@cgl.ucsf.edu>
Message-ID: <CAO9VScvh4vmnfscg_0CJn_PkiMq5kU+9t9rk8U3Tpkz3tiR3Ag@mail.gmail.com>

Hi Elaine,
Thank you for such a detailed answer! I am actually just checking the model
we built (undeposited). Some helices we built look like a 3-10 helices,
that's why I am interested. I will definitely try your suggestions!
Best,
Yangqi

On Monday, October 15, 2018, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Yangqi
> Even though it is often included in the PDB file HELIX lines, Chimera does
> not automatically tag different kinds of helix.  They are all lumped
> together in ?helix?
>
> Although it is not very convenient, to find out which residues are in 3-10
> helices in many deposited structures, you can look in the PDB file text for
> the HELIX lines, and then see the number in column 40 as described here
> (?1? is right-handed alpha, ?5? is right-handed 3-10, etc.):
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#
> secondary>
>
> For example, I see that 3KK4 has several 3-10 helices by looking in the
> text of its PDB file.  Looking at chain A only, the HELIX lines are:
>
> HELIX    1   1 ASN A   -1  ARG A    7  1
> 9
> HELIX    2   2 ASN A    9  TYR A   13  5
> 5
> HELIX    3   3 GLN A   33  ASP A   46  1
>  14
> HELIX    4   4 ARG A   49  GLY A   66  1
>  18
> HELIX    5   5 ASN A   70  GLU A   88  1
>  19
> HELIX    6   6 PRO A   98  LEU A  102  5
> 5
> HELIX    7   7 ASP A  103  ARG A  109  1
> 7
> HELIX    8   8 PRO A  112  TYR A  116  5
> 5
>
> That means chain A residues 9-13, 98-102, and 112-116 were  identified as
> 3-10 helix.
>
> If you wanted to use that information, you could (for example) make an
> alias for that set of residues for convenience in later commands, or just
> specify them directly, say
>
> open 3kk4
> delete ~ :.a
> alias tthel :9-13,98-102,112-116
> color red tthel
> sel tthel
>
> (B) If you wanted to identify 3-10 helices directly from the structure
> (say it was just a model you built or some other undeposited structure),
> you could use the FindHBond tool or command and then identify where the
> mainchain H-bonds are i,i+3, and whether the conformation appears helical.
> I don?t think it is obvious from the backbone angles whether it is alpha or
> 3-10 helix.   For example with 3kk4
>
> select helix & @n,o
> hbonds selRestrict both log true
>
> ?and then look in the Reply Log for i,i+3 backbone H-bonds.  For chain A I
> get:
>
> H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
> GLU 3.A N    ASN -1.A O    no hydrogen  2.948  N/A
> ILE 4.A N    ALA 0.A O     no hydrogen  2.993  N/A
> PHE 5.A N    MSE 1.A O     no hydrogen  3.085  N/A
> ILE 6.A N    CME 2.A O     no hydrogen  2.832  N/A
> SER 12.A N   ASN 9.A O     no hydrogen  2.979  N/A
> TYR 13.A N   GLN 10.A O    no hydrogen  3.327  N/A
> LEU 34.A N   SER 12.A O    no hydrogen  2.914  N/A
> ASP 37.A N   GLN 33.A O    no hydrogen  2.912  N/A
> VAL 38.A N   LEU 34.A O    no hydrogen  2.904  N/A
> [?]
> GLU 88.A N   VAL 84.A O    no hydrogen  2.885  N/A
> SER 101.A N  PRO 98.A O    no hydrogen  3.050  N/A
> LEU 102.A N  ILE 99.A O    no hydrogen  2.968  N/A
> VAL 107.A N  ASP 103.A O   no hydrogen  2.991  N/A
> LEU 108.A N  ALA 104.A O   no hydrogen  3.010  N/A
> ARG 109.A N  GLN 105.A O   no hydrogen  3.055  N/A
> LEU 115.A N  PRO 112.A O   no hydrogen  3.035  N/A
> 53 hydrogen bonds found
>
> ? whereas if I just select the residues that the PDB file says are 3-10
>
> select tthel & @n,o
> hbonds selRes both log t
>
> I get:
> H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
> SER 12.A N   ASN 9.A O    no hydrogen  2.979  N/A
> SER 12.A N   ASN 9.A OD1  no hydrogen  3.067  N/A
> SER 12.A OG  ASN 9.A O    no hydrogen  2.589  N/A
> TYR 13.A N   GLN 10.A O   no hydrogen  3.327  N/A
> SER 101.A N  PRO 98.A O   no hydrogen  3.050  N/A
> LEU 102.A N  ILE 99.A O   no hydrogen  2.968  N/A
> LEU 115.A N  PRO 112.A O  no hydrogen  3.035  N/A
> 7 hydrogen bonds found
>
> (C) I don?t think you can tell 3-10 from other helix using just phi-psi
> angles, but to examine those angles you can show the protein Ramachandran
> Plot (Favorites? Model Panel, choose model on the left and then the
> Ramachandran plot button on the right).  Then when you select any
> residue(s) they will show up on the plot as red dots.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> ramachandran/ramachandran.html>
> Or, you can select any single residue and click the green magnifying glass
> on the lower right corner of the Chimera window to show the Selection
> Inspector, then in that dialog choose to Inspect: ?Residue?  and it shows
> you the phi angle and psi angle values.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Oct 15, 2018, at 11:47 AM, BuddySphinx <yangqi.gu at yale.edu> wrote:
>
> Dear Chimera users,
> I am wondering if there is a quick way in Chimera to visualize 3-10 helix?
> Or showing the dihedral angle of the peptide bonds?
> Best,
> Yangqi
>
>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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From meng at cgl.ucsf.edu  Tue Oct 16 10:38:23 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 16 Oct 2018 10:38:23 -0700
Subject: [Chimera-users] [chimera-dev] Chimera orbitals alias question
In-Reply-To: <CAAgCWJt2KaC99SM3Ff5NwBuAU1HU8x6NuN2MP+7fmy68oNWNnA@mail.gmail.com>
References: <CAAgCWJt2KaC99SM3Ff5NwBuAU1HU8x6NuN2MP+7fmy68oNWNnA@mail.gmail.com>
Message-ID: <95D26A22-5D9E-4E32-A505-8AF61549FFC4@cgl.ucsf.edu>

> On Oct 13, 2018, at 2:34 PM, Benjamin Looker <bgl44 at cornell.edu> wrote:
> 
> Hello!
> My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. 
> 
> When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. 
> 
> My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function?
> 
> An alias such as:
> alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface
> 
> Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. 
> 
> Any help would be greatly appreciated!
> Best, 
> -- 
> Benjamin G. Looker
> Graduate Student 
> Lancaster Group

Hi Benjamin,
I don't have an example cube file to test with, but from your description I'm guessing it has signed data and that is why Chimera automatically shows two isosurfaces when you open a single file.  The levels are the same magnitude, just the opposite signs.  How the initial display values are set is described in the ?surface and mesh display? section of the Volume Viewer documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

"For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero."

In that case, there is no way to specify in the command line changing only one isosurface and not the other.  You can see in the Model Panel (open from Favorites) that the entire dataset is listed as one model.

Although you could open the data twice and use your volume command on only one copy (specified by the model number as shown in the Model Panel) that would still leave both the isosurfaces on the other copy as initially shown.

However, there is nothing magical about the initial display setting other than it is meant to be easily viewable.  There is no knowledge used about the type of data (i.e. it doesn?t care or know that orbitals are what you?re showing) so you may want to go ahead and set all the isosurfaces using your values rather than relying on initial display.  You can specify level and color multiple times in the volume command for multiple isosurfaces, e.g.

volume #0 style mesh level 0.8 color red level 1.2 color 0,.5,.8

This is one of the examples in the ?volume? command manpage
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>

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

P.S. for future reference, the chimera-dev list is mainly for programming questions.  General usage questions are better sent to chimera-users at cgl.ucsf.edu CC?d here





From goddard at sonic.net  Tue Oct 16 15:26:55 2018
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 16 Oct 2018 15:26:55 -0700
Subject: [Chimera-users] [chimera-dev] Chimera orbitals alias question
In-Reply-To: <95D26A22-5D9E-4E32-A505-8AF61549FFC4@cgl.ucsf.edu>
References: <CAAgCWJt2KaC99SM3Ff5NwBuAU1HU8x6NuN2MP+7fmy68oNWNnA@mail.gmail.com>
 <95D26A22-5D9E-4E32-A505-8AF61549FFC4@cgl.ucsf.edu>
Message-ID: <7A59C90C-FB28-42EB-8312-D392F4C1E0CE@sonic.net>

Hi Benjamin,

  When you open a Gaussian cube file with multiple orbitals in Chimera it assigns them to be model numbers #0.1, #0.2, #0.3, ?.  You can see these numbers in the Volume Viewer menu Data.  You can also see them in Model Panel (menu Favorites / Model Panel) ? they will be grouped because they were read from one file so press the Group / Ungroup button on Model Panel to see them all.  Also all orbitals are shown at once initially ? not too useful.  To hide them all (#0 refers to all #0.x models):

	volume #0 hide

To show the first orbital

	volume #0.1 show

To set the displayed surface level of the first orbital but not the others

	volume #0.1 level 0.001

To set the levels for the first 5 oribitals

	volume #0.1-5 level 0.002

  Tom



> On Oct 16, 2018, at 10:38 AM, Elaine Meng wrote:
> 
>> On Oct 13, 2018, at 2:34 PM, Benjamin Looker  wrote:
>> 
>> Hello!
>> My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. 
>> 
>> When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. 
>> 
>> My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function?
>> 
>> An alias such as:
>> alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface
>> 
>> Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. 
>> 
>> Any help would be greatly appreciated!
>> Best, 
>> -- 
>> Benjamin G. Looker
>> Graduate Student 
>> Lancaster Group
> 
> Hi Benjamin,
> I don't have an example cube file to test with, but from your description I'm guessing it has signed data and that is why Chimera automatically shows two isosurfaces when you open a single file.  The levels are the same magnitude, just the opposite signs.  How the initial display values are set is described in the ?surface and mesh display? section of the Volume Viewer documentation:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> 
> "For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero."
> 
> In that case, there is no way to specify in the command line changing only one isosurface and not the other.  You can see in the Model Panel (open from Favorites) that the entire dataset is listed as one model.
> 
> Although you could open the data twice and use your volume command on only one copy (specified by the model number as shown in the Model Panel) that would still leave both the isosurfaces on the other copy as initially shown.
> 
> However, there is nothing magical about the initial display setting other than it is meant to be easily viewable.  There is no knowledge used about the type of data (i.e. it doesn?t care or know that orbitals are what you?re showing) so you may want to go ahead and set all the isosurfaces using your values rather than relying on initial display.  You can specify level and color multiple times in the volume command for multiple isosurfaces, e.g.
> 
> volume #0 style mesh level 0.8 color red level 1.2 color 0,.5,.8
> 
> This is one of the examples in the ?volume? command manpage
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> P.S. for future reference, the chimera-dev list is mainly for programming questions.  General usage questions are better sent to chimera-users at cgl.ucsf.edu CC?d here
> 
> 
> 
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> 




From bgl44 at cornell.edu  Wed Oct 17 07:31:49 2018
From: bgl44 at cornell.edu (Benjamin Looker)
Date: Wed, 17 Oct 2018 10:31:49 -0400
Subject: [Chimera-users] Alias commands for volume pieces
Message-ID: <CAAgCWJtwTNLMggm5JztUC=w9hk9ZWEkq3cjMgi9ZCiXpF5hiwg@mail.gmail.com>

Hello!

I have recently received emails from Tom Goddard and Elaine Meng on this
subject, but I believe it can be further clarified.

The research group I am a part of routinely generates Gaussian cube files
for molecular orbitals using the DFT program ORCA, we then manually use
Chimera to change the level and color of the two phases of the resulting
wave function, *which appear in Chimera as two **surface pieces* belonging
to the same surface.

In the volume viewer menu Data, *and* in the Model Panel, there is no way
to see a #0.1 #0.2 model subnumber, and Group/Ungroup returns the error
"Cannot group a single molecule."

Is there a way to refer to volume pieces in the command line? Such that an
alias can be written to do this formatting in a more efficient manner?

Best,
-- 
Benjamin G. Looker
Graduate Student
Lancaster Group
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From meng at cgl.ucsf.edu  Wed Oct 17 10:54:50 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 17 Oct 2018 10:54:50 -0700
Subject: [Chimera-users] Alias commands for volume pieces
In-Reply-To: <CAAgCWJtwTNLMggm5JztUC=w9hk9ZWEkq3cjMgi9ZCiXpF5hiwg@mail.gmail.com>
References: <CAAgCWJtwTNLMggm5JztUC=w9hk9ZWEkq3cjMgi9ZCiXpF5hiwg@mail.gmail.com>
Message-ID: <84F2E561-4D86-489F-9199-7A93403C31E4@cgl.ucsf.edu>

Hi Benjamin,
Can you please provide an example file as an attachment so we don?t have to guess what it contains?

If it is indeed 2 surface pieces of a single model, then I believe my previous reply applies, and there isn?t a way to specify the pieces separately in the ?volume? command, sorry. Although you can select one of the pieces with the mouse and not the other, and then use ?sel? as the command-line specification, the ?volume? command still acts on the whole model, or at least it did when I tried it just now on my example electrostatic potential (ESP) file with positive and negative isosurfaces.

However, we?d need one of your files as an example to fully understand your situation.  We have tried other cube files but their contents are not representative of all cases.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 17, 2018, at 7:31 AM, Benjamin Looker <bgl44 at cornell.edu> wrote:
> 
> Hello!
> I have recently received emails from Tom Goddard and Elaine Meng on this subject, but I believe it can be further clarified. 
> 
> The research group I am a part of routinely generates Gaussian cube files  for molecular orbitals using the DFT program ORCA, we then manually use Chimera to change the level and color of the two phases of the resulting wave function, which appear in Chimera as two surface pieces belonging to the same surface. 
> 
> In the volume viewer menu Data, and in the Model Panel, there is no way to see a #0.1 #0.2 model subnumber, and Group/Ungroup returns the error "Cannot group a single molecule."
> 
> Is there a way to refer to volume pieces in the command line? Such that an alias can be written to do this formatting in a more efficient manner? 
> Best, 




From jielliott at wustl.edu  Wed Oct 17 14:11:14 2018
From: jielliott at wustl.edu (Elliott, Jabari)
Date: Wed, 17 Oct 2018 21:11:14 +0000
Subject: [Chimera-users] Saving PDBs
Message-ID: <67C657A0-8FA0-4C3F-8ED2-D51B5C254D09@wustl.edu>

When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.
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From meng at cgl.ucsf.edu  Wed Oct 17 14:44:14 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 17 Oct 2018 14:44:14 -0700
Subject: [Chimera-users] Saving PDBs
In-Reply-To: <67C657A0-8FA0-4C3F-8ED2-D51B5C254D09@wustl.edu>
References: <67C657A0-8FA0-4C3F-8ED2-D51B5C254D09@wustl.edu>
Message-ID: <CC644159-AD33-4E7D-892D-FDE3B6078F7B@cgl.ucsf.edu>

Hello,
I do not have this problem when saving multiple models to a single PDB file.  When I reopen the saved file in Chimera, the atoms/models are all present.  All I can say is that in the PDB-saving dialog, make sure you haven?t turned on (checked) the options ?Save displayed atoms only? or ?Save selected atoms only? because if you don?t have displayed atoms or selected atoms, respectively, then your file will contain zero atoms.

In Chimera ?selection? means specifically highlighted in the structure with green outlines, like when you Ctrl-click on some atom.  It does not mean the models you chose (highlighted) in the PDB-saving dialog.

Saving PDB files:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

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


> On Oct 17, 2018, at 2:11 PM, Elliott, Jabari <jielliott at wustl.edu> wrote:
> 
> When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.




From jielliott at wustl.edu  Wed Oct 17 14:47:09 2018
From: jielliott at wustl.edu (Elliott, Jabari)
Date: Wed, 17 Oct 2018 21:47:09 +0000
Subject: [Chimera-users] Saving PDBs
In-Reply-To: <CC644159-AD33-4E7D-892D-FDE3B6078F7B@cgl.ucsf.edu>
References: <67C657A0-8FA0-4C3F-8ED2-D51B5C254D09@wustl.edu>,
 <CC644159-AD33-4E7D-892D-FDE3B6078F7B@cgl.ucsf.edu>
Message-ID: <E2089BB5-2E07-437C-A7A0-E1E4AF5A8B88@wustl.edu>

Elaine,

I believe that the ?selection? option is the issue. 

Thank you 

> On Oct 17, 2018, at 16:44, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hello,
> I do not have this problem when saving multiple models to a single PDB file.  When I reopen the saved file in Chimera, the atoms/models are all present.  All I can say is that in the PDB-saving dialog, make sure you haven?t turned on (checked) the options ?Save displayed atoms only? or ?Save selected atoms only? because if you don?t have displayed atoms or selected atoms, respectively, then your file will contain zero atoms.
> 
> In Chimera ?selection? means specifically highlighted in the structure with green outlines, like when you Ctrl-click on some atom.  It does not mean the models you chose (highlighted) in the PDB-saving dialog.
> 
> Saving PDB files:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Oct 17, 2018, at 2:11 PM, Elliott, Jabari <jielliott at wustl.edu> wrote:
>> 
>> When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.
> 



From davidsaez at udec.cl  Thu Oct 18 21:33:26 2018
From: davidsaez at udec.cl (=?UTF-8?Q?David_S=C3=A1ez?=)
Date: Fri, 19 Oct 2018 01:33:26 -0300
Subject: [Chimera-users] Finding files my session is showing
Message-ID: <CAHC+6jgch+QB+eMHkLfreEjnQR5mTaaNrLVOfGfsZyw-4GX96g@mail.gmail.com>

Hello everyone.

I saved some sessions time ago. Now I found the .py files, and they work
fine, but I do not remember what files I am opening when I restore the
session.
In the .py file I could not find any information about loaded topologies
or  pdb files. Can these data be recovered from a session?

Thanks in advance
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From meng at cgl.ucsf.edu  Fri Oct 19 07:50:35 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 19 Oct 2018 07:50:35 -0700
Subject: [Chimera-users] Finding files my session is showing
In-Reply-To: <CAHC+6jgch+QB+eMHkLfreEjnQR5mTaaNrLVOfGfsZyw-4GX96g@mail.gmail.com>
References: <CAHC+6jgch+QB+eMHkLfreEjnQR5mTaaNrLVOfGfsZyw-4GX96g@mail.gmail.com>
Message-ID: <0A2F794D-9B3B-491B-B469-0D1142D56AE9@cgl.ucsf.edu>

Hi David,
You may be able to tell by looking in the Model Panel (open from Favorites menu) after restoring your session.  It should be showing whatever it was showing originally, which often includes things like PDB IDs and/or filenames.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 18, 2018, at 9:33 PM, David S?ez <davidsaez at udec.cl> wrote:
> 
> Hello everyone. 
> 
> I saved some sessions time ago. Now I found the .py files, and they work fine, but I do not remember what files I am opening when I restore the session. 
> In the .py file I could not find any information about loaded topologies or  pdb files. Can these data be recovered from a session? 
> 
> Thanks in advance




From pett at cgl.ucsf.edu  Fri Oct 19 15:57:33 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 19 Oct 2018 15:57:33 -0700
Subject: [Chimera-users] Finding files my session is showing
In-Reply-To: <0A2F794D-9B3B-491B-B469-0D1142D56AE9@cgl.ucsf.edu>
References: <CAHC+6jgch+QB+eMHkLfreEjnQR5mTaaNrLVOfGfsZyw-4GX96g@mail.gmail.com>
 <0A2F794D-9B3B-491B-B469-0D1142D56AE9@cgl.ucsf.edu>
Message-ID: <F7C79045-4A0E-4C87-A167-447EE1744FA3@cgl.ucsf.edu>

Additionally, if you use the ?Configure?" button at the bottom of the Model Panel and configure the ?Input file? column to show, it will show the full path to the original input file.

?Eric

> On Oct 19, 2018, at 7:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi David,
> You may be able to tell by looking in the Model Panel (open from Favorites menu) after restoring your session.  It should be showing whatever it was showing originally, which often includes things like PDB IDs and/or filenames.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Oct 18, 2018, at 9:33 PM, David S?ez <davidsaez at udec.cl> wrote:
>> 
>> Hello everyone. 
>> 
>> I saved some sessions time ago. Now I found the .py files, and they work fine, but I do not remember what files I am opening when I restore the session. 
>> In the .py file I could not find any information about loaded topologies or  pdb files. Can these data be recovered from a session? 
>> 
>> Thanks in advance
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From davidsaez at udec.cl  Fri Oct 19 16:41:52 2018
From: davidsaez at udec.cl (=?UTF-8?Q?David_S=C3=A1ez?=)
Date: Fri, 19 Oct 2018 20:41:52 -0300
Subject: [Chimera-users] Finding files my session is showing
In-Reply-To: <0A2F794D-9B3B-491B-B469-0D1142D56AE9@cgl.ucsf.edu>
References: <CAHC+6jgch+QB+eMHkLfreEjnQR5mTaaNrLVOfGfsZyw-4GX96g@mail.gmail.com>
 <0A2F794D-9B3B-491B-B469-0D1142D56AE9@cgl.ucsf.edu>
Message-ID: <CAHC+6jhZeWHamgPwmuFHTch6-ibcdE0QB1b0sctBBpgPZ0cWsw@mail.gmail.com>

Thanks Elaine.

El vie., 19 de oct. de 2018 11:50, Elaine Meng <meng at cgl.ucsf.edu> escribi?:

> Hi David,
> You may be able to tell by looking in the Model Panel (open from Favorites
> menu) after restoring your session.  It should be showing whatever it was
> showing originally, which often includes things like PDB IDs and/or
> filenames.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 18, 2018, at 9:33 PM, David S?ez <davidsaez at udec.cl> wrote:
> >
> > Hello everyone.
> >
> > I saved some sessions time ago. Now I found the .py files, and they work
> fine, but I do not remember what files I am opening when I restore the
> session.
> > In the .py file I could not find any information about loaded topologies
> or  pdb files. Can these data be recovered from a session?
> >
> > Thanks in advance
>
>
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From davidsaez at udec.cl  Fri Oct 19 16:42:17 2018
From: davidsaez at udec.cl (=?UTF-8?Q?David_S=C3=A1ez?=)
Date: Fri, 19 Oct 2018 20:42:17 -0300
Subject: [Chimera-users] Finding files my session is showing
In-Reply-To: <F7C79045-4A0E-4C87-A167-447EE1744FA3@cgl.ucsf.edu>
References: <CAHC+6jgch+QB+eMHkLfreEjnQR5mTaaNrLVOfGfsZyw-4GX96g@mail.gmail.com>
 <0A2F794D-9B3B-491B-B469-0D1142D56AE9@cgl.ucsf.edu>
 <F7C79045-4A0E-4C87-A167-447EE1744FA3@cgl.ucsf.edu>
Message-ID: <CAHC+6jhQo68qXVPkDVKVG+t5Y-RebkjihiW96uCswXd_2_G=1Q@mail.gmail.com>

Thanks Eric.

El vie., 19 de oct. de 2018 19:57, Eric Pettersen <pett at cgl.ucsf.edu>
escribi?:

> Additionally, if you use the ?Configure?" button at the bottom of the
> Model Panel and configure the ?Input file? column to show, it will show the
> full path to the original input file.
>
> ?Eric
>
> > On Oct 19, 2018, at 7:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi David,
> > You may be able to tell by looking in the Model Panel (open from
> Favorites menu) after restoring your session.  It should be showing
> whatever it was showing originally, which often includes things like PDB
> IDs and/or filenames.
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Oct 18, 2018, at 9:33 PM, David S?ez <davidsaez at udec.cl> wrote:
> >>
> >> Hello everyone.
> >>
> >> I saved some sessions time ago. Now I found the .py files, and they
> work fine, but I do not remember what files I am opening when I restore the
> session.
> >> In the .py file I could not find any information about loaded
> topologies or  pdb files. Can these data be recovered from a session?
> >>
> >> Thanks in advance
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
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From meng at cgl.ucsf.edu  Sat Oct 20 12:00:10 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 20 Oct 2018 12:00:10 -0700
Subject: [Chimera-users] Chimera problems
In-Reply-To: <DM6PR01MB4187AD59B94273D3B6195F8AA5FA0@DM6PR01MB4187.prod.exchangelabs.com>
References: <DM6PR01MB4187AD59B94273D3B6195F8AA5FA0@DM6PR01MB4187.prod.exchangelabs.com>
Message-ID: <22454B86-28F8-492C-B538-179EB552BE92@cgl.ucsf.edu>


> On Oct 19, 2018, at 8:41 PM, Shriwas, Pratik <ps774614 at ohio.edu> wrote:
> 
> Hi,
> I am trying to use USCF chimera for studying docking between my compound and the receptor called GLUT1 (PDB - 4pyp or 1SUK). My concerns are:
> 
> 	? I find different scores everytime I use the same compound and receptor

Hi Pratik,
Sounds like you are using the Autodock Vina interface of Chimera.  Chimera does not calculate the docking, it just sends/receives data from an outside web service that is running the Autodock Vina program.  It may be that the docking process uses some random numbers, and because the web service does not allow a high amount of sampling, it cannot always find the same top score(s).  However, I do not know the details of Autodock Vina and you would have to look at its website <http://vina.scripps.edu/> and/or paper to learn about that.  I?m guessing you are using Chimera?s Autodock Vina GUI to enter inputs, not the ?vina? command.  However, if you are using the command make sure you get a recent version of Chimera, because some problems with the command were fixed.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

> 	? I am not able to show my hydorgen bonds between compound snd receptor in GUI. Although I can see them in the list box.

Maybe the atoms are not shown (for example, if the sidechain is not shown, the H-bond to the sidechain won?t be shown). To make sure the H-bonding atoms are shown, in the H-bond parameters dialog turn on the option ?If endpoint atom hidden, show endpoint residue.?  However, if that is not the problem, then maybe the graphics on your computer has trouble showing lines.  You could try updating your graphics driver, or try showing the H-bonds as sticks instead of lines with command: setattr p drawMode 1.  Or maybe it can draw lines but they are too thin for you to see.  In that case, in the H-bond parameters dialog increase the ?Line width? value.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

> 	? I am not able to find exact binding energy.

This is the central problem of docking!  Firstly docking scores are not binding energies, only approximations, and secondly, one has to do a lot of conformational and positional sampling to find the most accurate position.  The Autodock Vina website does not allow a high amount of sampling, as it is a shared resource provided for free. If you want to do more intensive docking you can download Autodock Vina (or some other docking progam like DOCK, Gold, ...) and run it directly.

> 	? My ligand is not on pubchem/NIH servers. What is best way to find its smiles string. Different websites have different smiles string and I get different interactions.

Usually there are multiple ways of writing the SMILES string for the same compound.  As long as the compound looks right to you (has the correct covalent structure, the right elements connected in the right way) then the results should be equally valid even though the coordinates might be slightly different (e.g. rotated or translated or different conformation).  Any slight change in inputs will change docking outputs, since sampling is not exhaustive, but the change does not mean one answer is ?wrong? and the other is ?right".
> 
> Regards,
> Pratik Shriwas
> Phd Candidate,
> Molecular and Cellular Biology program,
> Edison Biotechnology Institute,
> Ohio University.

For future reference, Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC?d here).  For Autodock Vina questions, see <http://vina.scripps.edu/questions.html>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco





From pett at cgl.ucsf.edu  Mon Oct 22 15:32:41 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 22 Oct 2018 15:32:41 -0700
Subject: [Chimera-users] MacOS Mojave
Message-ID: <8F033F57-A6AA-448F-872C-58A691427837@cgl.ucsf.edu>

Hi all,
	A fix for the non-showing buttons problem on MacOS Mojave (10.14) is now in the Chimera daily build and the 1.13.1 release candidate.  If you encounter any problems with the new version please use Chimera?s Help?Report A Bug to let us know about them.  Note that the fixed version only runs on Mac OS 10.10 or later, whereas the previous version also ran on 10.8 and 10.9.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab





From anas.khawaja at ki.se  Tue Oct 23 06:55:09 2018
From: anas.khawaja at ki.se (Anas)
Date: Tue, 23 Oct 2018 06:55:09 -0700
Subject: [Chimera-users] Chimera bug report submission
Message-ID: <201810231355.w9NDt9bf060610@plato.cgl.ucsf.edu>

The following bug report has been submitted:
Platform:        osx_x11
Chimera Version: (None given)
Description
Hello,

I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn?t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.



From meng at cgl.ucsf.edu  Tue Oct 23 08:51:58 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 23 Oct 2018 08:51:58 -0700
Subject: [Chimera-users] saving PDB and saving maps
In-Reply-To: <201810231355.w9NDt9bf060610@plato.cgl.ucsf.edu>
References: <201810231355.w9NDt9bf060610@plato.cgl.ucsf.edu>
Message-ID: <46C0A416-7B2C-4F13-BAFF-5C01E40FDE91@cgl.ucsf.edu>

Hi Anas,
This is not a bug:  You cannot save a density map as PDB format, only the atoms.

However, you do not need to save the map if you just save the atomic structure in the fitted position.  Then you can just open the original map and your new PDB structure with the fitted atoms in the right position.

To save the fitted position, in the ?Save PDB? dialog, choose ?Save models?: [your atomic model] and also the option ?Save relative to model?: [your map model].

See ?Saving Data?
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
Saving PDB
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
Saving after fitting
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

If you want to save the map you can do it with Volume Viewer tool?s File menu, but the map formats do not include PDB.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization>

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

> On Oct 23, 2018, at 6:55 AM, Anas <anas.khawaja at ki.se> wrote:
> 
> The following bug report has been submitted:
> Platform:        osx_x11
> Chimera Version: (None given)
> Description
> Hello,
> 
> I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn?t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.




From anastasia at campus.technion.ac.il  Wed Oct 24 06:33:10 2018
From: anastasia at campus.technion.ac.il (anastasia at campus.technion.ac.il)
Date: Wed, 24 Oct 2018 13:33:10 +0000
Subject: [Chimera-users] Accessible surface area and ASA per residue
Message-ID: <DB6PR0101MB22130B9D7C214845350E21EDA5F60@DB6PR0101MB2213.eurprd01.prod.exchangelabs.com>

Dear User,


I'll appreciate your help.

I've worked with Chimera previously, but have not used it recently.

Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version).

I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue.

[cid:7c648fa9-c7cf-4dab-bf40-f0b4a95b8f47]


What I tried to do this time is :

  1.  Show a molecular surface..
  2.  Depiction --> render by attr , when attr is set to areaSAS on residues



[cid:f46b071c-36ab-4792-bfc2-31eb50fc2be3]


The result I got was:


[cid:6b44e796-b2c2-42f8-aac8-1ab725121d38]


Am I doing it right? how can export the calculated areaSAS per atom and residue from chimera?

How the SAS values calculated in Chimera? Does the higher value means that this residue is more exposed?



Thank you for your help,

Anastasia
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From meng at cgl.ucsf.edu  Wed Oct 24 08:25:00 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 24 Oct 2018 08:25:00 -0700
Subject: [Chimera-users] Accessible surface area and ASA per residue
In-Reply-To: <DB6PR0101MB22130B9D7C214845350E21EDA5F60@DB6PR0101MB2213.eurprd01.prod.exchangelabs.com>
References: <DB6PR0101MB22130B9D7C214845350E21EDA5F60@DB6PR0101MB2213.eurprd01.prod.exchangelabs.com>
Message-ID: <97BF9264-A18D-4941-9A25-5D44E42C4992@cgl.ucsf.edu>

HI Anastasia,
It sounds like you figured this out already:

Surface area (both SAS and SES) per atom and per residue is automatically calculated when you display a molecular surface.  For any structure, if you can show the surface, you can see a histogram of the surface area values, color by those values, save them to a file, etc. using "Render by Attribute" (in menu under Tools? Structure Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

SES is what Chimera shows, although it gives values for both SAS and SES.  An image here shows the difference:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

Yes, the values are areas in square angstroms, so larger is more surface area of that atom or residue.  The values are not normalized to % exposed, so bigger residues can have bigger values.  The areas are calculated by MSMS, as mentioned in the link above.

Yes, you are using the right process for coloring.  The brownish colors are for the values between where you put red and green, so they are a mix of red and green.  I usually avoid using red next to green, but of course you can use whatever colors you like.

Use the File menu on the Render by Attribute dialog to save the values to a file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

To calculate normalized values (% exposure) it would be more complicated, but there are instructions here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>

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

> On Oct 24, 2018, at 6:33 AM, anastasia at campus.technion.ac.il wrote:
> 
> Dear User,
> 
> I'll appreciate your help.
> I've worked with Chimera previously, but have not used it recently.
> Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version).
> I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue. 
> <pastedImage.png>
> 
> What I tried to do this time is :
> 	? Show a molecular surface
> ..
> 
> 	?
> Depiction --> render by attr , when attr is set to areaSAS on
> 
> residues
> 
> 
> <pastedImage.png>
> 
> 
> The result I got was:
> 
> <pastedImage.png>
> 
> Am I doing it right? how can export the calculated 
> areaSAS
>  per atom and residue from chimera?
> 
> How
>  the SAS values calculated in Chimera? Does t
> he higher value means that this residue is more exposed?
> 
> 
> Thank you for your help,
> Anastasia  




From aycardonab at unal.edu.co  Wed Oct 24 12:49:10 2018
From: aycardonab at unal.edu.co (Andrea Yimena Cardona Barreto)
Date: Wed, 24 Oct 2018 14:49:10 -0500
Subject: [Chimera-users] Help SASA
Message-ID: <CACi2LR+T2kZaUG738urfpv7iogRjB2ky+QHpoZ0y0L5MJJWnag@mail.gmail.com>

Good afternoon,

my name is Andrea Cardona and I?m a student of a magister in Human Genetics
at Universidad Nacional de Colombia. In my thesis I?m interested in obtain
the  surface accessible solvent area of a homotetrameric protein (fumarate
hydratase) but I have some troubles with Chimera. Can you give some help?

-- 
Andrea Yimena Cardona Barreto
Maestr?a en Gen?tica Humana
Universidad Nacional de Colombia
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From meng at cgl.ucsf.edu  Wed Oct 24 13:00:52 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 24 Oct 2018 13:00:52 -0700
Subject: [Chimera-users] Help SASA
In-Reply-To: <CACi2LR+T2kZaUG738urfpv7iogRjB2ky+QHpoZ0y0L5MJJWnag@mail.gmail.com>
References: <CACi2LR+T2kZaUG738urfpv7iogRjB2ky+QHpoZ0y0L5MJJWnag@mail.gmail.com>
Message-ID: <B33D9159-EF3C-4D5F-AEC2-883038ECC73D@cgl.ucsf.edu>

Hi Andrea,
What is the question?  You need to be a little more specific about what you tried and/or what problems you had, because it is too difficult to guess which part you don?t understand. 

If you show a molecular surface, then the surface area will automatically be reported in the Reply Log, which can be shown from the Favorites menu.
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 24, 2018, at 12:49 PM, Andrea Yimena Cardona Barreto <aycardonab at unal.edu.co> wrote:
> 
> Good afternoon,
> 
> my name is Andrea Cardona and I?m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I?m interested in obtain the  surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help?
> 
> -- 
> Andrea Yimena Cardona Barreto
> Maestr?a en Gen?tica Humana
> Universidad Nacional de Colombia




From aycardonab at unal.edu.co  Thu Oct 25 01:55:09 2018
From: aycardonab at unal.edu.co (Andrea Yimena Cardona Barreto)
Date: Thu, 25 Oct 2018 03:55:09 -0500
Subject: [Chimera-users] Help SASA
In-Reply-To: <B33D9159-EF3C-4D5F-AEC2-883038ECC73D@cgl.ucsf.edu>
References: <CACi2LR+T2kZaUG738urfpv7iogRjB2ky+QHpoZ0y0L5MJJWnag@mail.gmail.com>
 <B33D9159-EF3C-4D5F-AEC2-883038ECC73D@cgl.ucsf.edu>
Message-ID: <CACi2LRJOCakOqMrv30b-ERtTOWZoWo1w_fBPfut0rs3eMoTx6g@mail.gmail.com>

The point is that I want to obtein the SASA, it returns code 5 and
recomends to use the comand split, but I want to obtein the surface of the
complete protein, not the surface of each subunit and don't know how to do
that.

Thank you again

El mi?., 24 oct. 2018 3:00 p. m., Elaine Meng <meng at cgl.ucsf.edu> escribi?:

> Hi Andrea,
> What is the question?  You need to be a little more specific about what
> you tried and/or what problems you had, because it is too difficult to
> guess which part you don?t understand.
>
> If you show a molecular surface, then the surface area will automatically
> be reported in the Reply Log, which can be shown from the Favorites menu.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 24, 2018, at 12:49 PM, Andrea Yimena Cardona Barreto <
> aycardonab at unal.edu.co> wrote:
> >
> > Good afternoon,
> >
> > my name is Andrea Cardona and I?m a student of a magister in Human
> Genetics at Universidad Nacional de Colombia. In my thesis I?m interested
> in obtain the  surface accessible solvent area of a homotetrameric protein
> (fumarate hydratase) but I have some troubles with Chimera. Can you give
> some help?
> >
> > --
> > Andrea Yimena Cardona Barreto
> > Maestr?a en Gen?tica Humana
> > Universidad Nacional de Colombia
>
>
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From marta.perez at cnb.csic.es  Thu Oct 25 02:37:07 2018
From: marta.perez at cnb.csic.es (Marta Perez Illana)
Date: Thu, 25 Oct 2018 11:37:07 +0200
Subject: [Chimera-users] Saving a moved PDB only moved in a new session
Message-ID: <bc58d5e0-3fc1-2097-ab64-e232fe3d37c4@cnb.csic.es>

Hi all

I am working with chimera, and I have a map and a pdb.

1) I have split the pdb into several fragments in order to fit them into 
the map

2) I have successfully moved the PDBs and fitted them into the map

3) I have "write each PDB" "relative to the map, which seems to make 
sense :)


4) In the current session I keep the map and the moved PDB open ...plus 
I open the just saved "wrote PDB" (intended to be on the same position I 
moved it).

To me both, the opened PDB (which I have moved) and the just saved PDB, 
might be in the same position, fitting into the map... But... the just 
save-written PDB is clearly somewhere else... :(


5) But... If I make a NEW session, opening the map and the "wrote PDB", 
everything make sense, and the PDB is where I in fact moved to keep it 
fitted...

Why is that that in the current session the written-PDB is not where it 
was "moved"; but when a new session is opened it is displayed where it 
was moved?

It seems that everything works fine, it is just a bit confusing to me. 
Thanks in advanced!


Marta



From anastasia at campus.technion.ac.il  Thu Oct 25 00:02:56 2018
From: anastasia at campus.technion.ac.il (anastasia at campus.technion.ac.il)
Date: Thu, 25 Oct 2018 07:02:56 +0000
Subject: [Chimera-users] Accessible surface area and ASA per residue
In-Reply-To: <97BF9264-A18D-4941-9A25-5D44E42C4992@cgl.ucsf.edu>
References: <DB6PR0101MB22130B9D7C214845350E21EDA5F60@DB6PR0101MB2213.eurprd01.prod.exchangelabs.com>,
 <97BF9264-A18D-4941-9A25-5D44E42C4992@cgl.ucsf.edu>
Message-ID: <DB6PR0101MB2213EE58091B0704440EB756A5F70@DB6PR0101MB2213.eurprd01.prod.exchangelabs.com>

Great ! Thank you for your valuable input.


Best,

Anastasia

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, October 24, 2018 6:25:00 PM
To: Anastasia Shapiro
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Accessible surface area and ASA per residue

HI Anastasia,
It sounds like you figured this out already:

Surface area (both SAS and SES) per atom and per residue is automatically calculated when you display a molecular surface.  For any structure, if you can show the surface, you can see a histogram of the surface area values, color by those values, save them to a file, etc. using "Render by Attribute" (in menu under Tools? Structure Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

SES is what Chimera shows, although it gives values for both SAS and SES.  An image here shows the difference:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

Yes, the values are areas in square angstroms, so larger is more surface area of that atom or residue.  The values are not normalized to % exposed, so bigger residues can have bigger values.  The areas are calculated by MSMS, as mentioned in the link above.

Yes, you are using the right process for coloring.  The brownish colors are for the values between where you put red and green, so they are a mix of red and green.  I usually avoid using red next to green, but of course you can use whatever colors you like.

Use the File menu on the Render by Attribute dialog to save the values to a file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

To calculate normalized values (% exposure) it would be more complicated, but there are instructions here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>

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

> On Oct 24, 2018, at 6:33 AM, anastasia at campus.technion.ac.il wrote:
>
> Dear User,
>
> I'll appreciate your help.
> I've worked with Chimera previously, but have not used it recently.
> Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version).
> I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue.
> <pastedImage.png>
>
> What I tried to do this time is :
>        ? Show a molecular surface
> ..
>
>        ?
> Depiction --> render by attr , when attr is set to areaSAS on
>
> residues
>
>
> <pastedImage.png>
>
>
> The result I got was:
>
> <pastedImage.png>
>
> Am I doing it right? how can export the calculated
> areaSAS
>  per atom and residue from chimera?
>
> How
>  the SAS values calculated in Chimera? Does t
> he higher value means that this residue is more exposed?
>
>
> Thank you for your help,
> Anastasia

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From meng at cgl.ucsf.edu  Thu Oct 25 09:47:07 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 25 Oct 2018 09:47:07 -0700
Subject: [Chimera-users] Help SASA
In-Reply-To: <CACi2LRJOCakOqMrv30b-ERtTOWZoWo1w_fBPfut0rs3eMoTx6g@mail.gmail.com>
References: <CACi2LR+T2kZaUG738urfpv7iogRjB2ky+QHpoZ0y0L5MJJWnag@mail.gmail.com>
 <B33D9159-EF3C-4D5F-AEC2-883038ECC73D@cgl.ucsf.edu>
 <CACi2LRJOCakOqMrv30b-ERtTOWZoWo1w_fBPfut0rs3eMoTx6g@mail.gmail.com>
Message-ID: <74B571D7-86AD-4B76-B142-29C39D14811F@cgl.ucsf.edu>

Hi Andrea,
Oh, in that case we have a page describing different possible workarounds (not just ?split?):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

However, these workarounds are mostly for display purposes rather than calculating SASA.  Solution #2 might work but is unpredictable, since there lots of different parameters you could try changing, and none of them are guaranteed to make the calculation work.  If it works, the area would be reported in the Reply Log, but it would be slightly different than the area that would be obtained with default parameters.

Given these issues, I recommend just using ChimeraX to get the SASA instead of Chimera.  It uses a different surface calculation that doesn?t have these numerical failures.   It?s pretty easy in ChimeraX; commands would be something like:

open 4hhb
measure sasa protein

(or, you can open a local file instead of giving a PDB ID).

UCSF ChimeraX (see Download link on left)
<http://www.rbvi.ucsf.edu/chimerax/index.html>

? ChimeraX measure command:
<http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html>

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

> On Oct 25, 2018, at 1:55 AM, Andrea Yimena Cardona Barreto <aycardonab at unal.edu.co> wrote:
> 
> The point is that I want to obtein the SASA, it returns code 5 and recomends to use the comand split, but I want to obtein the surface of the complete protein, not the surface of each subunit and don't know how to do that.
> 
> Thank you again
> 
> El mi?., 24 oct. 2018 3:00 p. m., Elaine Meng <meng at cgl.ucsf.edu> escribi?:
> Hi Andrea,
> What is the question?  You need to be a little more specific about what you tried and/or what problems you had, because it is too difficult to guess which part you don?t understand. 
> 
> If you show a molecular surface, then the surface area will automatically be reported in the Reply Log, which can be shown from the Favorites menu.
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Oct 24, 2018, at 12:49 PM, Andrea Yimena Cardona Barreto <aycardonab at unal.edu.co> wrote:
> > 
> > Good afternoon,
> > 
> > my name is Andrea Cardona and I?m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I?m interested in obtain the  surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help?
> > 
> > -- 
> > Andrea Yimena Cardona Barreto
> > Maestr?a en Gen?tica Humana
> > Universidad Nacional de Colombia




From meng at cgl.ucsf.edu  Thu Oct 25 09:57:38 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 25 Oct 2018 09:57:38 -0700
Subject: [Chimera-users] Saving a moved PDB only moved in a new session
In-Reply-To: <bc58d5e0-3fc1-2097-ab64-e232fe3d37c4@cnb.csic.es>
References: <bc58d5e0-3fc1-2097-ab64-e232fe3d37c4@cnb.csic.es>
Message-ID: <3CA8E4AD-7D2C-42E9-BC9C-EDE1B1300D93@cgl.ucsf.edu>

Hi Maria,
It makes sense to me.  When you save ?relative to map? it means if you open the map and then all those PDBs they will be in the right position relative to the map.

However, in the current session, you have rotated/zoomed the view interactively (moving the map from its original position), and when you open the PDBs it does automatically apply all those other changes unless the map is the lowest-ID model.  When you start a new session you haven?t moved the map around yet.

Here?s a more advanced suggestion that you could ignore (and I?m not even 100% sure it would work):
Maybe in the current session you can bring the saved PDBs to the right positions relative to the map by additionallly applying whatever transformations you had done manually to the map with the matrixcopy command.  E.g. if map is #5 and one of the saved PDBs was opened as #6, it may work to use command

matrixcopy #5 #6

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

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

> On Oct 25, 2018, at 2:37 AM, Marta Perez Illana <marta.perez at cnb.csic.es> wrote:
> 
> Hi all
> 
> I am working with chimera, and I have a map and a pdb.
> 
> 1) I have split the pdb into several fragments in order to fit them into the map
> 
> 2) I have successfully moved the PDBs and fitted them into the map
> 
> 3) I have "write each PDB" "relative to the map, which seems to make sense :)
> 
> 
> 4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it).
> 
> To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :(
> 
> 
> 5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted...
> 
> Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved?
> 
> It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced!
> 
> 
> Marta




From hernando.sosa at einstein.yu.edu  Thu Oct 25 09:50:27 2018
From: hernando.sosa at einstein.yu.edu (Hernando J Sosa)
Date: Thu, 25 Oct 2018 16:50:27 +0000
Subject: [Chimera-users] python script
In-Reply-To: <F0E461AAE34D0448B6EE7D31E433B70801237EBABD@AEWEXCPM21.yuad.uds.yu.edu>
References: <CAGWgEQ4yck_CEW9SNUDrPGzjoupH=zEv4H-F=CuLrDZmXMcvUg@mail.gmail.com>
 <4B12D462-3BA6-4ABE-AAAB-95CB1C5C57EC@cgl.ucsf.edu>
 <CAGWgEQ4hnFWj1Xbv5dAPdB9-MwWq=-25Fu8z=g8rAUw5f6SPug@mail.gmail.com>
 <3877B857-6604-42E6-9A71-0AE1A06EAD44@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B70801237E97D1@AEWEXCPM21.yuad.uds.yu.edu>
 <F4FE9294-1415-4DBB-A328-79F9D5B56402@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B70801237EBABD@AEWEXCPM21.yuad.uds.yu.edu>
Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080154AE8DA4@AEWEXCPM21.yuad.uds.yu.edu>

Dear Chimera,

I am writing a  Chimera python  script  and need to  get a list of the chains and residue numbers  of specific opened models . What would be the command/syntax to do that?  or can you point me to a code  example where something like this is done.

Thanks

Hernando


From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Hernando J Sosa
Sent: Monday, June 11, 2018 2:46 PM
To: Eric Pettersen
Cc: chimera-users BB
Subject: Re: [Chimera-users] python script

Thanks Eric,

These alternatives is what I was looking for.

Best

Hernando

From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: Friday, June 08, 2018 7:27 PM
To: Hernando J Sosa
Cc: chimera-users BB
Subject: Re: [Chimera-users] python script

Hi Hernando,
            Perhaps runCommand should return a value but it doesn?t.  The reasoning there was that the argument to runCommand could be anything, including several commands separated by semi-colons, so in some cases it?s confusing what the return value should be.  In any case that ship has sailed and you have to do something else to get the value.  In most cases it calling the underlying function that performs the command and using it?s return value, but looking at the code that implements the ?measure center? command I can see that it doesn?t return anything either.
            So in the particular case of the example you provided, I can see two options for getting the value:

Option 1)
            atoms = chimera.selection.OSLSelection(?#0:.A at CA?).vertices()
            center = chimera.Point([a.coord() for a in atoms])
            x, y, z = center.data()

Option 2)
            rc(?sel #0:.A at CA?)
            center = chimera.Point([a.coord() for a in chimera.selection.currentAtoms()])
            x, y, z = center.data()

I hope this helps.

?Eric

            Eric Pettersen
            UCSF Computer Graphics Lab


On Jun 8, 2018, at 11:10 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu<mailto:hernando.sosa at einstein.yu.edu>> wrote:

Dear Chimera,

Is it possible to assign the result of running a chimera command in python to a string or something else?  E.g doing something like:

from chimera import runCommand as rc
myresult  = rc('measure center  #0:.A at CA')

And then using the  myresults somewhere else in the script after parsing for the relevant values?

Maybe there is a n easier way to accomplish this?

Thanks

Hernando



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

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From nazlidisalex at gmail.com  Thu Oct 25 10:27:51 2018
From: nazlidisalex at gmail.com (Alex Nazlidis)
Date: Thu, 25 Oct 2018 20:27:51 +0300
Subject: [Chimera-users] Dynamic Protein
Message-ID: <CA+-9WDh1tRBZQ+u6jUCNfEHxOwDM-4g+U0j6T-NogXNR43ewUw@mail.gmail.com>

Dear Elaine,

is there any way in chimera to produce a clip similiar to this (
https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating
the dynamic nature of a protein and its folding process.

Thank you very much in advance,
Alex
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From meng at cgl.ucsf.edu  Thu Oct 25 10:49:15 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 25 Oct 2018 10:49:15 -0700
Subject: [Chimera-users] Dynamic Protein
In-Reply-To: <CA+-9WDh1tRBZQ+u6jUCNfEHxOwDM-4g+U0j6T-NogXNR43ewUw@mail.gmail.com>
References: <CA+-9WDh1tRBZQ+u6jUCNfEHxOwDM-4g+U0j6T-NogXNR43ewUw@mail.gmail.com>
Message-ID: <7D0C7334-B7EC-4EB5-990D-650A2460FDCB@cgl.ucsf.edu>

Dear Alex,
Oooh,  Ken Dill, one of my favorite professors! 

Short answer is you can certainly create movies of trajectories (conformational changes through time), but generally those trajectories are calculated some other program, and you can?t simulate protein folding.

For folding or any other major conformational changes, the hard part would be calculating the trajectory, which Chimera will NOT do for you.  Chimera can create ?morph? trajectories which are fairly simple interpolations between endpoint structures.  However, they are not biophysically accurate calculations of the paths the atoms would really take; instead they are meant to help people understand conformational differences between two states, which are generally not as extremely different as unfolded and folded.  You can give it several intermediate states and then morph piecewise between them (A->B, B->C, C->D etc.), but you?d still to generate all of the input conformations somehow.

Chimera Morph Conformations tool
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
? examples of use in these tutorials
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>

Chimera does have a Molecular Dynamics Simulation (trajectory calculation) tool but it is somewhat limited and slow compared to dedicated MM/MD software packages.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

If you had calculated the trajectory using some separate software (remaining agnostic as to how you?d actually do that), if it were in one of the several standard formats that Chimera understands, you could read it into Chimera and ?play? it back with the MD Movie tool.  In Chimera you can control the colors, display styles, etc., add 2D labels/titles, and record the trajectory as a movie.

MD Movie tool  or  ?coordset? command for trajectory playback
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>

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

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

> On Oct 25, 2018, at 10:27 AM, Alex Nazlidis <nazlidisalex at gmail.com> wrote:
> 
> Dear Elaine, 
> 
> is there any way in chimera to produce a clip similiar to this (https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating the dynamic nature of a protein and its folding process. 
> 
> Thank you very much in advance,
> Alex




From hernando.sosa at einstein.yu.edu  Thu Oct 25 13:35:45 2018
From: hernando.sosa at einstein.yu.edu (Hernando J Sosa)
Date: Thu, 25 Oct 2018 20:35:45 +0000
Subject: [Chimera-users] python script
In-Reply-To: <F0E461AAE34D0448B6EE7D31E433B7080154AE8DA4@AEWEXCPM21.yuad.uds.yu.edu>
References: <CAGWgEQ4yck_CEW9SNUDrPGzjoupH=zEv4H-F=CuLrDZmXMcvUg@mail.gmail.com>
 <4B12D462-3BA6-4ABE-AAAB-95CB1C5C57EC@cgl.ucsf.edu>
 <CAGWgEQ4hnFWj1Xbv5dAPdB9-MwWq=-25Fu8z=g8rAUw5f6SPug@mail.gmail.com>
 <3877B857-6604-42E6-9A71-0AE1A06EAD44@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B70801237E97D1@AEWEXCPM21.yuad.uds.yu.edu>
 <F4FE9294-1415-4DBB-A328-79F9D5B56402@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B70801237EBABD@AEWEXCPM21.yuad.uds.yu.edu>
 <F0E461AAE34D0448B6EE7D31E433B7080154AE8DA4@AEWEXCPM21.yuad.uds.yu.edu>
Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080154AE8E73@AEWEXCPM21.yuad.uds.yu.edu>

An additional question:
Is it possible to retrieve the  atomic coordinates after a transformation (e.g. after an align/superposition  operation) rather than the original coordinate values?

e.g. I am currently using the following commands  to retrieve the coordinates (x,y,z) of  the CA atom in model,residue,chain
atom    = chimera.selection.OSLSelection("#%d:%d.%c at CA" % (model,residue,chain)).vertices()
(x,y,z)  = atom[0].coord()

However, this retrieves  the original coordinates not the coordinates after a transformation.

Thanks

Hernando

Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone (718) 430-3456
FAX (718) 430-8819
email hernando.sosa at einstein.yu.edu<mailto:hernando.sosa at einstein.yu.edu>

From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Hernando J Sosa
Sent: Thursday, October 25, 2018 12:50 PM
To: chimera-users BB
Subject: [Chimera-users] python script

Dear Chimera,

I am writing a  Chimera python  script  and need to  get a list of the chains and residue numbers  of specific opened models . What would be the command/syntax to do that?  or can you point me to a code  example where something like this is done.

Thanks

Hernando


From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Hernando J Sosa
Sent: Monday, June 11, 2018 2:46 PM
To: Eric Pettersen
Cc: chimera-users BB
Subject: Re: [Chimera-users] python script

Thanks Eric,

These alternatives is what I was looking for.

Best

Hernando

From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: Friday, June 08, 2018 7:27 PM
To: Hernando J Sosa
Cc: chimera-users BB
Subject: Re: [Chimera-users] python script

Hi Hernando,
            Perhaps runCommand should return a value but it doesn?t.  The reasoning there was that the argument to runCommand could be anything, including several commands separated by semi-colons, so in some cases it?s confusing what the return value should be.  In any case that ship has sailed and you have to do something else to get the value.  In most cases it calling the underlying function that performs the command and using it?s return value, but looking at the code that implements the ?measure center? command I can see that it doesn?t return anything either.
            So in the particular case of the example you provided, I can see two options for getting the value:

Option 1)
            atoms = chimera.selection.OSLSelection(?#0:.A at CA?).vertices()
            center = chimera.Point([a.coord() for a in atoms])
            x, y, z = center.data()

Option 2)
            rc(?sel #0:.A at CA?)
            center = chimera.Point([a.coord() for a in chimera.selection.currentAtoms()])
            x, y, z = center.data()

I hope this helps.

?Eric

            Eric Pettersen
            UCSF Computer Graphics Lab


On Jun 8, 2018, at 11:10 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu<mailto:hernando.sosa at einstein.yu.edu>> wrote:

Dear Chimera,

Is it possible to assign the result of running a chimera command in python to a string or something else?  E.g doing something like:

from chimera import runCommand as rc
myresult  = rc('measure center  #0:.A at CA')

And then using the  myresults somewhere else in the script after parsing for the relevant values?

Maybe there is a n easier way to accomplish this?

Thanks

Hernando



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

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From goddard at sonic.net  Thu Oct 25 16:27:35 2018
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 25 Oct 2018 16:27:35 -0700
Subject: [Chimera-users] python script
In-Reply-To: <F0E461AAE34D0448B6EE7D31E433B7080154AE8E73@AEWEXCPM21.yuad.uds.yu.edu>
References: <CAGWgEQ4yck_CEW9SNUDrPGzjoupH=zEv4H-F=CuLrDZmXMcvUg@mail.gmail.com>
 <4B12D462-3BA6-4ABE-AAAB-95CB1C5C57EC@cgl.ucsf.edu>
 <CAGWgEQ4hnFWj1Xbv5dAPdB9-MwWq=-25Fu8z=g8rAUw5f6SPug@mail.gmail.com>
 <3877B857-6604-42E6-9A71-0AE1A06EAD44@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B70801237E97D1@AEWEXCPM21.yuad.uds.yu.edu>
 <F4FE9294-1415-4DBB-A328-79F9D5B56402@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B70801237EBABD@AEWEXCPM21.yuad.uds.yu.edu>
 <F0E461AAE34D0448B6EE7D31E433B7080154AE8DA4@AEWEXCPM21.yuad.uds.yu.edu>
 <F0E461AAE34D0448B6EE7D31E433B7080154AE8E73@AEWEXCPM21.yuad.uds.yu.edu>
Message-ID: <1A0068CA-DE7D-44F8-BF6B-BF4709CF0B93@sonic.net>

Hi Hernando,

  Here?s some Python that gets the residues of a molecule.  There is no Python chain object but the code shows how to get the chain ids.  Also it shows atom.xformCoord() that gets the transformed coordinate.  The transformed coordinate includes any rotation and translation you did with the mouse.

    Tom


import chimera
sel = chimera.selection.OSLSelection('#0')
sel.models()
-> [<_molecule.Molecule object at 0x11696ac10>]
m = sel.models[0]
r = m.residues
len(r)
-> 76
type(r)
-> <type 'list'>
r0 = r[0]
r0.id.chainId
-> u'A'
set(r0.id.chainId for r0 in r)
  -> set([u'A', u'B'])
a = r0.atoms[0]
a.xformCoord()
-> chimera.Point(15.491, 7.05, 17.165)





> On Oct 25, 2018, at 1:35 PM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> An additional question:
> Is it possible to retrieve the  atomic coordinates after a transformation (e.g. after an align/superposition  operation) rather than the original coordinate values?
>  
> e.g. I am currently using the following commands  to retrieve the coordinates (x,y,z) of  the CA atom in model,residue,chain
> atom    = chimera.selection.OSLSelection("#%d:%d.%c at CA" % (model,residue,chain)).vertices()
> (x,y,z)  = atom[0].coord()
>  
> However, this retrieves  the original coordinates not the coordinates after a transformation.
>  
> Thanks
>  
> Hernando
>  
> Hernando Sosa
> Dept. of Physiology and Biophysics 
> Albert Einstein College of Medicine 
> 1300 Morris Park Av. 
> Bronx NY 10461 
> phone (718) 430-3456 
> FAX (718) 430-8819 
> email hernando.sosa at einstein.yu.edu <mailto:hernando.sosa at einstein.yu.edu>
>  
> From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Hernando J Sosa
> Sent: Thursday, October 25, 2018 12:50 PM
> To: chimera-users BB
> Subject: [Chimera-users] python script
>  
> Dear Chimera,
>  
> I am writing a  Chimera python  script  and need to  get a list of the chains and residue numbers  of specific opened models . What would be the command/syntax to do that?  or can you point me to a code  example where something like this is done.
>  
> Thanks
>  
> Hernando  
>  
>  
> From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu <mailto:chimera-users-bounces at cgl.ucsf.edu>] On Behalf Of Hernando J Sosa
> Sent: Monday, June 11, 2018 2:46 PM
> To: Eric Pettersen
> Cc: chimera-users BB
> Subject: Re: [Chimera-users] python script
>  
> Thanks Eric,
>  
> These alternatives is what I was looking for.
>  
> Best
>  
> Hernando
>  
> From: Eric Pettersen [mailto:pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>] 
> Sent: Friday, June 08, 2018 7:27 PM
> To: Hernando J Sosa
> Cc: chimera-users BB
> Subject: Re: [Chimera-users] python script
>  
> Hi Hernando,
>             Perhaps runCommand should return a value but it doesn?t.  The reasoning there was that the argument to runCommand could be anything, including several commands separated by semi-colons, so in some cases it?s confusing what the return value should be.  In any case that ship has sailed and you have to do something else to get the value.  In most cases it calling the underlying function that performs the command and using it?s return value, but looking at the code that implements the ?measure center? command I can see that it doesn?t return anything either.
>             So in the particular case of the example you provided, I can see two options for getting the value:
>  
> Option 1)
>             atoms = chimera.selection.OSLSelection(?#0:.A at CA?).vertices()
>             center = chimera.Point([a.coord() for a in atoms])
>             x, y, z = center.data()
>  
> Option 2)
>             rc(?sel #0:.A at CA?)
>             center = chimera.Point([a.coord() for a in chimera.selection.currentAtoms()])
>             x, y, z = center.data()
>  
> I hope this helps.
>  
> ?Eric
>  
>             Eric Pettersen
>             UCSF Computer Graphics Lab
>  
>  
> 
> On Jun 8, 2018, at 11:10 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu <mailto:hernando.sosa at einstein.yu.edu>> wrote:
>  
> Dear Chimera,
>  
> Is it possible to assign the result of running a chimera command in python to a string or something else?  E.g doing something like:
>  
> from chimera import runCommand as rc
> myresult  = rc('measure center  #0:.A at CA')
>  
> And then using the  myresults somewhere else in the script after parsing for the relevant values?
>  
> Maybe there is a n easier way to accomplish this?
>  
> Thanks
>  
> Hernando
>  
>  
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From nazlidisalex at gmail.com  Thu Oct 25 23:44:21 2018
From: nazlidisalex at gmail.com (Alex Nazlidis)
Date: Fri, 26 Oct 2018 09:44:21 +0300
Subject: [Chimera-users] Dynamic Protein
In-Reply-To: <7D0C7334-B7EC-4EB5-990D-650A2460FDCB@cgl.ucsf.edu>
References: <CA+-9WDh1tRBZQ+u6jUCNfEHxOwDM-4g+U0j6T-NogXNR43ewUw@mail.gmail.com>
 <7D0C7334-B7EC-4EB5-990D-650A2460FDCB@cgl.ucsf.edu>
Message-ID: <CA+-9WDjYP=RZSZbguFo9bE10VSZ+6Hry00T8An-Z4bcAt8GvbQ@mail.gmail.com>

This is great, thank you so much for the info Elaine!

Kind regards,
Alex


???? ???, 25 ??? 2018 ???? 8:49 ?.?., ?/? Elaine Meng <meng at cgl.ucsf.edu>
??????:

> Dear Alex,
> Oooh,  Ken Dill, one of my favorite professors!
>
> Short answer is you can certainly create movies of trajectories
> (conformational changes through time), but generally those trajectories are
> calculated some other program, and you can?t simulate protein folding.
>
> For folding or any other major conformational changes, the hard part would
> be calculating the trajectory, which Chimera will NOT do for you.  Chimera
> can create ?morph? trajectories which are fairly simple interpolations
> between endpoint structures.  However, they are not biophysically accurate
> calculations of the paths the atoms would really take; instead they are
> meant to help people understand conformational differences between two
> states, which are generally not as extremely different as unfolded and
> folded.  You can give it several intermediate states and then morph
> piecewise between them (A->B, B->C, C->D etc.), but you?d still to generate
> all of the input conformations somehow.
>
> Chimera Morph Conformations tool
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
> >
> ? examples of use in these tutorials
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
> >
>
> Chimera does have a Molecular Dynamics Simulation (trajectory calculation)
> tool but it is somewhat limited and slow compared to dedicated MM/MD
> software packages.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
>
> If you had calculated the trajectory using some separate software
> (remaining agnostic as to how you?d actually do that), if it were in one of
> the several standard formats that Chimera understands, you could read it
> into Chimera and ?play? it back with the MD Movie tool.  In Chimera you can
> control the colors, display styles, etc., add 2D labels/titles, and record
> the trajectory as a movie.
>
> MD Movie tool  or  ?coordset? command for trajectory playback
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
> >
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
>
> Making movies
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
>
> I hope this clarifies the situation,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 25, 2018, at 10:27 AM, Alex Nazlidis <nazlidisalex at gmail.com>
> wrote:
> >
> > Dear Elaine,
> >
> > is there any way in chimera to produce a clip similiar to this (
> https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating
> the dynamic nature of a protein and its folding process.
> >
> > Thank you very much in advance,
> > Alex
>
>
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From David.Bhella at glasgow.ac.uk  Fri Oct 26 08:05:18 2018
From: David.Bhella at glasgow.ac.uk (David Bhella)
Date: Fri, 26 Oct 2018 15:05:18 +0000
Subject: [Chimera-users] CUDA on Mac OSX 10.14 Mojave
Message-ID: <07B430E1-19BB-4619-B190-A8788766C551@glasgow.ac.uk>

Dear All

I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. 
I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop.

Chimera throws an error now - complaining about the graphics settings being incorrect:
"Display misconfiguration.  Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card.  Also see chimera installation instructions."
Presumably because the graphics driver is not working correctly.

Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading.

Thanks,
D


Dr David Bhella
Director - Scottish Centre for Macromolecular Imaging

MRC-University of Glasgow Centre for Virus Research
Sir Michael Stoker Building
Garscube Campus
464 Bearsden Road
Glasgow G61 1QH
Scotland (UK)

Telephone:  0141-330-3685
Skype: d.bhella





From gregc at cgl.ucsf.edu  Fri Oct 26 08:45:14 2018
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 26 Oct 2018 08:45:14 -0700
Subject: [Chimera-users] CUDA on Mac OSX 10.14 Mojave
In-Reply-To: <07B430E1-19BB-4619-B190-A8788766C551@glasgow.ac.uk>
References: <07B430E1-19BB-4619-B190-A8788766C551@glasgow.ac.uk>
Message-ID: <8941525a-2cb7-57d2-b659-3029c41610f6@cgl.ucsf.edu>

That error is not directly related to CUDA, it is because Chimera is 
unable to use OpenGL to draw 3D graphics.? So if you can reinstall the 
NVIDIA graphics driver so that OpenGL works, then Chimera would work.? 
I'd downgrade or install Ubuntu.

 ??? HTH,

 ??? Greg


On 10/26/2018 8:05 AM, David Bhella wrote:
> Dear All
>
> I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release.
> I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop.
>
> Chimera throws an error now - complaining about the graphics settings being incorrect:
> "Display misconfiguration.  Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card.  Also see chimera installation instructions."
> Presumably because the graphics driver is not working correctly.
>
> Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading.
>
> Thanks,
> D
>
>
> Dr David Bhella
> Director - Scottish Centre for Macromolecular Imaging
>
> MRC-University of Glasgow Centre for Virus Research
> Sir Michael Stoker Building
> Garscube Campus
> 464 Bearsden Road
> Glasgow G61 1QH
> Scotland (UK)
>
> Telephone:  0141-330-3685
> Skype: d.bhella
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From pett at cgl.ucsf.edu  Fri Oct 26 15:00:08 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 26 Oct 2018 15:00:08 -0700
Subject: [Chimera-users] CUDA on Mac OSX 10.14 Mojave
In-Reply-To: <07B430E1-19BB-4619-B190-A8788766C551@glasgow.ac.uk>
References: <07B430E1-19BB-4619-B190-A8788766C551@glasgow.ac.uk>
Message-ID: <1055ABA3-0FE9-4888-B2DF-DBE18CE84088@cgl.ucsf.edu>

Hi David,
	As per Install macOS 10.14 Mojave on Mac Pro (Mid 2010) and Mac Pro (Mid 2012) - Apple Support <https://support.apple.com/en-us/HT208898>, the Quadro 4000 isn?t a card that ?works with? Mojave, so I don?t know that there?s anything we can do about your problem.  You may have to roll back.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




> On Oct 26, 2018, at 8:05 AM, David Bhella <David.Bhella at glasgow.ac.uk> wrote:
> 
> Dear All
> 
> I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. 
> I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop.
> 
> Chimera throws an error now - complaining about the graphics settings being incorrect:
> "Display misconfiguration.  Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card.  Also see chimera installation instructions."
> Presumably because the graphics driver is not working correctly.
> 
> Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading.
> 
> Thanks,
> D
> 
> 
> Dr David Bhella
> Director - Scottish Centre for Macromolecular Imaging
> 
> MRC-University of Glasgow Centre for Virus Research
> Sir Michael Stoker Building
> Garscube Campus
> 464 Bearsden Road
> Glasgow G61 1QH
> Scotland (UK)
> 
> Telephone:  0141-330-3685
> Skype: d.bhella
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From paristzou at gmail.com  Sat Oct 27 19:31:58 2018
From: paristzou at gmail.com (Paris Tzou)
Date: Sun, 28 Oct 2018 10:31:58 +0800
Subject: [Chimera-users] How can I load a list of residues of protein?
Message-ID: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>

Dear all,
  I want to load a file containing a lit of residues of protein which is
already shown in Chimera. I don't want to manually select the residues
under investigation through "Favorite -- Sequence". Is there a way of doing
this ?  I know I can do it using command line like:select
#0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content
like:

15,C
16,C
17,C
263,A
264,A
265,A

Thank you very much.

Paris Tzou
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From meng at cgl.ucsf.edu  Sun Oct 28 09:12:56 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 28 Oct 2018 09:12:56 -0700
Subject: [Chimera-users] How can I load a list of residues of protein?
In-Reply-To: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>
References: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>
Message-ID: <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>

Hi Paris,
What do you want to do with these  residues, only select them?  You could just make that list into a command file.  E.g.

select :15.c
select :16.c

(etc.) and name this plain text file something.cmd or something.com.  Then opening it will execute the commands. By default each selection command will replace the previous (so that would only select one residue at a time) but if you first choose menu: "Select? Selection mode? append? it will then accumulate the selections instead.

Of course, the command file could do other things like coloring instead of selection.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>

However, I?m guessing you really want to do several different things with this set of residues.  In that case,  just give the set(s) of residues different short names with the ?alias" command.  Then you can keep doing things easily to that set including selecting/deselecting it.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

However, the alias needs all the residues that you want to give a single name to be in a single command, e.g.

alias myres1 :15-17.C,263-265.A

?.and/or multiple sets with multiple names? 

alias cres :15-17.C
alias ares :263-265.A

Then later you can just use them in other commands, 

select myres1
color orange cres
color dodger blue ares

These alias commands can be quite long if your residue list is long, but you?d only have to enter a given alias once, and the alias command itself could be in a command file.  I?ve often done this for making paper figures where I want to easily color certain sets of residues (domains, catalytic sites, mutation hotspots, etc.)

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

> On Oct 27, 2018, at 7:31 PM, Paris Tzou <paristzou at gmail.com> wrote:
> 
> Dear all,
>   I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ?  I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like:
> 
> 15,C
> 16,C
> 17,C
> 263,A
> 264,A
> 265,A
> 
> Thank you very much.
> Paris Tzou




From arne.moeller at biophys.mpg.de  Mon Oct 29 02:21:00 2018
From: arne.moeller at biophys.mpg.de (armoelle)
Date: Mon, 29 Oct 2018 10:21:00 +0100
Subject: [Chimera-users] Split map from command line
Message-ID: <FDCCC94D-EE80-4665-AE5B-3BC5B9FDA26B@biophys.mpg.de>

Dear Chimera Team,

I am trying to call the split map command directly from a script but somehow I don?t seem to be able to get it to run - maybe you can help me?

I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. 
However, generally nothing happens - sometimes though (I don?t know what triggers it - and I am not doing anything different) it runs perfectly fine.
I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. 

Many thanks for your help!

cheers
Arne






________________________________

Dr. Arne Moeller
Independent Research Group Leader
Department of Structural Biology
Max-Planck-Institute of Biophysics

Affiliated Researcher 
DANDRITE, Aarhus University, DK

www.moeller-lab.com
www.biophys.mpg.de/en/moeller.html

Arne.Moeller at biophys.mpg.de
0049 69 63033057
Max-von-Laue-Strasse 3
D-60438 Frankfurt am Main
Office L.1.015




From goddard at sonic.net  Mon Oct 29 10:29:24 2018
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 29 Oct 2018 10:29:24 -0700
Subject: [Chimera-users] Split map from command line
In-Reply-To: <FDCCC94D-EE80-4665-AE5B-3BC5B9FDA26B@biophys.mpg.de>
References: <FDCCC94D-EE80-4665-AE5B-3BC5B9FDA26B@biophys.mpg.de>
Message-ID: <97EA8434-FF68-4BB8-A10E-AD137030DB98@sonic.net>

Hi Arne,

  The keyboard shortcut ?sm? for splitting a map based on the color zone coloring operates on the active volume ? that is the one highlighted in Volume Viewer (it?s title above the histogram has a blue background).  If you are just opening maps then I think the most recent one is the active volume.  Ideally there would be a command and not just a shortcut to do this splitting operation.  I?ll add this to our new program ChimeraX.  You could use Python to do the splitting of say all maps by putting the following code in splitmap.py and using ?open /path/to/script/splitmap.py?

from VolumeViewer import volume_list
from ColorZone import split_volume_by_color_zone
for v in volume_list():
	split_volume_by_color_zone(v)

  Tom



> On Oct 29, 2018, at 2:21 AM, armoelle <arne.moeller at biophys.mpg.de> wrote:
> 
> Dear Chimera Team,
> 
> I am trying to call the split map command directly from a script but somehow I don?t seem to be able to get it to run - maybe you can help me?
> 
> I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. 
> However, generally nothing happens - sometimes though (I don?t know what triggers it - and I am not doing anything different) it runs perfectly fine.
> I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. 
> 
> Many thanks for your help!
> 
> cheers
> Arne
> 
> 
> 
> 
> 
> 
> ________________________________
> 
> Dr. Arne Moeller
> Independent Research Group Leader
> Department of Structural Biology
> Max-Planck-Institute of Biophysics
> 
> Affiliated Researcher 
> DANDRITE, Aarhus University, DK
> 
> www.moeller-lab.com
> www.biophys.mpg.de/en/moeller.html
> 
> Arne.Moeller at biophys.mpg.de
> 0049 69 63033057
> Max-von-Laue-Strasse 3
> D-60438 Frankfurt am Main
> Office L.1.015
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From paristzou at gmail.com  Mon Oct 29 21:15:50 2018
From: paristzou at gmail.com (Paris Tzou)
Date: Tue, 30 Oct 2018 12:15:50 +0800
Subject: [Chimera-users] How can I load a list of residues of protein?
In-Reply-To: <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>
References: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>
 <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>
Message-ID: <CAFd34LytbMOcuHrnbXh5dPG7mUx_iicr69Ud=hYsG2zg-7+LpA@mail.gmail.com>

Thanks, I'll check them out.


Wen-Shyong Tzou



Elaine Meng <meng at cgl.ucsf.edu> ? 2018?10?29? ?? ??12:12???

> Hi Paris,
> What do you want to do with these  residues, only select them?  You could
> just make that list into a command file.  E.g.
>
> select :15.c
> select :16.c
>
> (etc.) and name this plain text file something.cmd or something.com.
> Then opening it will execute the commands. By default each selection
> command will replace the previous (so that would only select one residue at
> a time) but if you first choose menu: "Select? Selection mode? append? it
> will then accumulate the selections instead.
>
> Of course, the command file could do other things like coloring instead of
> selection.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
> >
>
> However, I?m guessing you really want to do several different things with
> this set of residues.  In that case,  just give the set(s) of residues
> different short names with the ?alias" command.  Then you can keep doing
> things easily to that set including selecting/deselecting it.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>
> However, the alias needs all the residues that you want to give a single
> name to be in a single command, e.g.
>
> alias myres1 :15-17.C,263-265.A
>
> ?.and/or multiple sets with multiple names?
>
> alias cres :15-17.C
> alias ares :263-265.A
>
> Then later you can just use them in other commands,
>
> select myres1
> color orange cres
> color dodger blue ares
>
> These alias commands can be quite long if your residue list is long, but
> you?d only have to enter a given alias once, and the alias command itself
> could be in a command file.  I?ve often done this for making paper figures
> where I want to easily color certain sets of residues (domains, catalytic
> sites, mutation hotspots, etc.)
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 27, 2018, at 7:31 PM, Paris Tzou <paristzou at gmail.com> wrote:
> >
> > Dear all,
> >   I want to load a file containing a lit of residues of protein which is
> already shown in Chimera. I don't want to manually select the residues
> under investigation through "Favorite -- Sequence". Is there a way of doing
> this ?  I know I can do it using command line like:select
> #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content
> like:
> >
> > 15,C
> > 16,C
> > 17,C
> > 263,A
> > 264,A
> > 265,A
> >
> > Thank you very much.
> > Paris Tzou
>
>
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From paristzou at gmail.com  Mon Oct 29 21:28:58 2018
From: paristzou at gmail.com (Paris Tzou)
Date: Tue, 30 Oct 2018 12:28:58 +0800
Subject: [Chimera-users] How can I load a list of residues of protein?
In-Reply-To: <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>
References: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>
 <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>
Message-ID: <CAFd34LzF6yGSzQ0LAK5pbNjJtCzkj4S9NwGkfBH_RVkewmyEYQ@mail.gmail.com>

Is it possible to do set operation like
alias common_set set_A & set_B
alias subtract_set set A not set_B
Thanks a lot
Wen-Shyong

Elaine Meng <meng at cgl.ucsf.edu> ? 2018?10?29? ?? ??12:12???

> Hi Paris,
> What do you want to do with these  residues, only select them?  You could
> just make that list into a command file.  E.g.
>
> select :15.c
> select :16.c
>
> (etc.) and name this plain text file something.cmd or something.com.
> Then opening it will execute the commands. By default each selection
> command will replace the previous (so that would only select one residue at
> a time) but if you first choose menu: "Select? Selection mode? append? it
> will then accumulate the selections instead.
>
> Of course, the command file could do other things like coloring instead of
> selection.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
> >
>
> However, I?m guessing you really want to do several different things with
> this set of residues.  In that case,  just give the set(s) of residues
> different short names with the ?alias" command.  Then you can keep doing
> things easily to that set including selecting/deselecting it.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>
> However, the alias needs all the residues that you want to give a single
> name to be in a single command, e.g.
>
> alias myres1 :15-17.C,263-265.A
>
> ?.and/or multiple sets with multiple names?
>
> alias cres :15-17.C
> alias ares :263-265.A
>
> Then later you can just use them in other commands,
>
> select myres1
> color orange cres
> color dodger blue ares
>
> These alias commands can be quite long if your residue list is long, but
> you?d only have to enter a given alias once, and the alias command itself
> could be in a command file.  I?ve often done this for making paper figures
> where I want to easily color certain sets of residues (domains, catalytic
> sites, mutation hotspots, etc.)
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 27, 2018, at 7:31 PM, Paris Tzou <paristzou at gmail.com> wrote:
> >
> > Dear all,
> >   I want to load a file containing a lit of residues of protein which is
> already shown in Chimera. I don't want to manually select the residues
> under investigation through "Favorite -- Sequence". Is there a way of doing
> this ?  I know I can do it using command line like:select
> #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content
> like:
> >
> > 15,C
> > 16,C
> > 17,C
> > 263,A
> > 264,A
> > 265,A
> >
> > Thank you very much.
> > Paris Tzou
>
>
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From arne.moeller at biophys.mpg.de  Mon Oct 29 23:42:46 2018
From: arne.moeller at biophys.mpg.de (armoelle)
Date: Tue, 30 Oct 2018 07:42:46 +0100
Subject: [Chimera-users] Split map from command line
In-Reply-To: <97EA8434-FF68-4BB8-A10E-AD137030DB98@sonic.net>
References: <FDCCC94D-EE80-4665-AE5B-3BC5B9FDA26B@biophys.mpg.de>
 <97EA8434-FF68-4BB8-A10E-AD137030DB98@sonic.net>
Message-ID: <BCC9D8BF-F793-49C8-94B2-0DBACABE0014@biophys.mpg.de>

Dear Tom,
Many thanks for your swift reply - 
Last night I found the problem with my script:

Originally, I first opened several maps and then split them - while color zone does work the ac sm command does not.
However, when I work in sequence - so opening, colorzone and then split it works without a problem. 
I guess this is related to you saying that the volume has to be active in the volume viewer and it might not be after I have opened another map.

Anyways?

Thanks again

cheers
Arne

> On 29. Oct 2018, at 18:29, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Arne,
> 
>  The keyboard shortcut ?sm? for splitting a map based on the color zone coloring operates on the active volume ? that is the one highlighted in Volume Viewer (it?s title above the histogram has a blue background).  If you are just opening maps then I think the most recent one is the active volume.  Ideally there would be a command and not just a shortcut to do this splitting operation.  I?ll add this to our new program ChimeraX.  You could use Python to do the splitting of say all maps by putting the following code in splitmap.py and using ?open /path/to/script/splitmap.py?
> 
> from VolumeViewer import volume_list
> from ColorZone import split_volume_by_color_zone
> for v in volume_list():
> 	split_volume_by_color_zone(v)
> 
>  Tom
> 
> 
> 
>> On Oct 29, 2018, at 2:21 AM, armoelle <arne.moeller at biophys.mpg.de> wrote:
>> 
>> Dear Chimera Team,
>> 
>> I am trying to call the split map command directly from a script but somehow I don?t seem to be able to get it to run - maybe you can help me?
>> 
>> I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. 
>> However, generally nothing happens - sometimes though (I don?t know what triggers it - and I am not doing anything different) it runs perfectly fine.
>> I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. 
>> 
>> Many thanks for your help!
>> 
>> cheers
>> Arne
>> 
>> 
>> 
>> 
>> 
>> 
>> ________________________________
>> 
>> Dr. Arne Moeller
>> Independent Research Group Leader
>> Department of Structural Biology
>> Max-Planck-Institute of Biophysics
>> 
>> Affiliated Researcher 
>> DANDRITE, Aarhus University, DK
>> 
>> www.moeller-lab.com
>> www.biophys.mpg.de/en/moeller.html
>> 
>> Arne.Moeller at biophys.mpg.de
>> 0049 69 63033057
>> Max-von-Laue-Strasse 3
>> D-60438 Frankfurt am Main
>> Office L.1.015
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 




From meng at cgl.ucsf.edu  Tue Oct 30 08:18:06 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 30 Oct 2018 08:18:06 -0700
Subject: [Chimera-users] How can I load a list of residues of protein?
In-Reply-To: <CAFd34LzF6yGSzQ0LAK5pbNjJtCzkj4S9NwGkfBH_RVkewmyEYQ@mail.gmail.com>
References: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>
 <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>
 <CAFd34LzF6yGSzQ0LAK5pbNjJtCzkj4S9NwGkfBH_RVkewmyEYQ@mail.gmail.com>
Message-ID: <DA824606-04E2-49C0-9FDA-1FEE13285FE4@cgl.ucsf.edu>

Hi Wen-Shyong,
Yes, you can do combinations (and/or/not) in command-line atom specifications, see explanation and examples at:

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

Also aliases can be combinations of aliases. If you already defined (with alias) set1 and set2, something similar to your example would be

alias combined set1 | set2
alias intersected set1 & ~ set2

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


> On Oct 29, 2018, at 9:28 PM, Paris Tzou <paristzou at gmail.com> wrote:
> 
> Is it possible to do set operation like
> alias common_set set_A & set_B
> alias subtract_set set A not set_B
> Thanks a lot
> Wen-Shyong
> 
> Elaine Meng <meng at cgl.ucsf.edu> ? 2018?10?29? ?? ??12:12???
> Hi Paris,
> What do you want to do with these  residues, only select them?  You could just make that list into a command file.  E.g.
> 
> select :15.c
> select :16.c
> 
> (etc.) and name this plain text file something.cmd or something.com.  Then opening it will execute the commands. By default each selection command will replace the previous (so that would only select one residue at a time) but if you first choose menu: "Select? Selection mode? append? it will then accumulate the selections instead.
> 
> Of course, the command file could do other things like coloring instead of selection.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
> 
> However, I?m guessing you really want to do several different things with this set of residues.  In that case,  just give the set(s) of residues different short names with the ?alias" command.  Then you can keep doing things easily to that set including selecting/deselecting it.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
> 
> However, the alias needs all the residues that you want to give a single name to be in a single command, e.g.
> 
> alias myres1 :15-17.C,263-265.A
> 
> ?.and/or multiple sets with multiple names? 
> 
> alias cres :15-17.C
> alias ares :263-265.A
> 
> Then later you can just use them in other commands, 
> 
> select myres1
> color orange cres
> color dodger blue ares
> 
> These alias commands can be quite long if your residue list is long, but you?d only have to enter a given alias once, and the alias command itself could be in a command file.  I?ve often done this for making paper figures where I want to easily color certain sets of residues (domains, catalytic sites, mutation hotspots, etc.)
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Oct 27, 2018, at 7:31 PM, Paris Tzou <paristzou at gmail.com> wrote:
> > 
> > Dear all,
> >   I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ?  I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like:
> > 
> > 15,C
> > 16,C
> > 17,C
> > 263,A
> > 264,A
> > 265,A
> > 
> > Thank you very much.
> > Paris Tzou




From paristzou at gmail.com  Tue Oct 30 20:00:36 2018
From: paristzou at gmail.com (Paris Tzou)
Date: Wed, 31 Oct 2018 11:00:36 +0800
Subject: [Chimera-users] How can I load a list of residues of protein?
In-Reply-To: <DA824606-04E2-49C0-9FDA-1FEE13285FE4@cgl.ucsf.edu>
References: <CAFd34LzJdFihS=-P8we21zhucBqVyQ=3CER1F=4wdt6LJ-h_8g@mail.gmail.com>
 <4F446567-C893-4E66-9539-3A15FA36A00F@cgl.ucsf.edu>
 <CAFd34LzF6yGSzQ0LAK5pbNjJtCzkj4S9NwGkfBH_RVkewmyEYQ@mail.gmail.com>
 <DA824606-04E2-49C0-9FDA-1FEE13285FE4@cgl.ucsf.edu>
Message-ID: <CAFd34LwHb-m7MLV+-QmjiVAQHMnra+JgZkif4SN4_mguWZ8NdQ@mail.gmail.com>

Thank you!  It  does help.
Paris


Elaine Meng <meng at cgl.ucsf.edu> ? 2018?10?30? ?? ??11:18???

> Hi Wen-Shyong,
> Yes, you can do combinations (and/or/not) in command-line atom
> specifications, see explanation and examples at:
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations
> >
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
>
> Also aliases can be combinations of aliases. If you already defined (with
> alias) set1 and set2, something similar to your example would be
>
> alias combined set1 | set2
> alias intersected set1 & ~ set2
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Oct 29, 2018, at 9:28 PM, Paris Tzou <paristzou at gmail.com> wrote:
> >
> > Is it possible to do set operation like
> > alias common_set set_A & set_B
> > alias subtract_set set A not set_B
> > Thanks a lot
> > Wen-Shyong
> >
> > Elaine Meng <meng at cgl.ucsf.edu> ? 2018?10?29? ?? ??12:12???
> > Hi Paris,
> > What do you want to do with these  residues, only select them?  You
> could just make that list into a command file.  E.g.
> >
> > select :15.c
> > select :16.c
> >
> > (etc.) and name this plain text file something.cmd or something.com.
> Then opening it will execute the commands. By default each selection
> command will replace the previous (so that would only select one residue at
> a time) but if you first choose menu: "Select? Selection mode? append? it
> will then accumulate the selections instead.
> >
> > Of course, the command file could do other things like coloring instead
> of selection.
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
> >
> >
> > However, I?m guessing you really want to do several different things
> with this set of residues.  In that case,  just give the set(s) of residues
> different short names with the ?alias" command.  Then you can keep doing
> things easily to that set including selecting/deselecting it.
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
> >
> > However, the alias needs all the residues that you want to give a single
> name to be in a single command, e.g.
> >
> > alias myres1 :15-17.C,263-265.A
> >
> > ?.and/or multiple sets with multiple names?
> >
> > alias cres :15-17.C
> > alias ares :263-265.A
> >
> > Then later you can just use them in other commands,
> >
> > select myres1
> > color orange cres
> > color dodger blue ares
> >
> > These alias commands can be quite long if your residue list is long, but
> you?d only have to enter a given alias once, and the alias command itself
> could be in a command file.  I?ve often done this for making paper figures
> where I want to easily color certain sets of residues (domains, catalytic
> sites, mutation hotspots, etc.)
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Oct 27, 2018, at 7:31 PM, Paris Tzou <paristzou at gmail.com> wrote:
> > >
> > > Dear all,
> > >   I want to load a file containing a lit of residues of protein which
> is already shown in Chimera. I don't want to manually select the residues
> under investigation through "Favorite -- Sequence". Is there a way of doing
> this ?  I know I can do it using command line like:select
> #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content
> like:
> > >
> > > 15,C
> > > 16,C
> > > 17,C
> > > 263,A
> > > 264,A
> > > 265,A
> > >
> > > Thank you very much.
> > > Paris Tzou
>
>
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From huim868 at gmail.com  Wed Oct 31 08:00:49 2018
From: huim868 at gmail.com (Hui Min)
Date: Wed, 31 Oct 2018 11:00:49 -0400
Subject: [Chimera-users] Chimera use
Message-ID: <CAApsJcxm2wQHSfo7kpwpE6H1i8RVXKv=3c2bPWDrnDqn-X6KdA@mail.gmail.com>

Hi there,

Sorry to disturb you. I have a question of how to use the Chimera software.
If I've already got a .pdb file and use SMART to predict the domains, how
can
I mark the 3D structure with user defined color? Thank you in advance for
your help


-- 
*Hui Min*
Postdoctoral Scholar Research,
Department of Internal Medicine,
College of Medicine,
University of South Florida, Tampa, FL 33612
minh8 at health.usf.edu
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From meng at cgl.ucsf.edu  Wed Oct 31 09:33:34 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 31 Oct 2018 09:33:34 -0700
Subject: [Chimera-users] coloring domains
In-Reply-To: <CAApsJcxm2wQHSfo7kpwpE6H1i8RVXKv=3c2bPWDrnDqn-X6KdA@mail.gmail.com>
References: <CAApsJcxm2wQHSfo7kpwpE6H1i8RVXKv=3c2bPWDrnDqn-X6KdA@mail.gmail.com>
Message-ID: <6FB9A64F-80BC-4D92-98CD-D9DEB8ED1D6E@cgl.ucsf.edu>

Hi Hui Min,
I don?t know what the SMART output looks like, but I guess it might have residue numbers, or show the domains on the sequence.

If you have residue numbers that go with your structure (pdb file) you can just use them in a ?color? command, or ?select? command and then use menu: Actions? Color? (etc.) to color the selection. For example, to color residues 35-89 and 112-150 in chain A:

command: color red :35-89.A,112-150.A
- or -
command: select :35-89.A,112-150.A
(then use menu: Actions?Color (etc.))

How to specify residues etc. in commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Actions menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuactions>

Actions? Color? all options? allows showing all 60 colors but if you don?t want any of those, you can still define your own by choosing ?from editor? in that dialog.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/coloractions.html>

Or, if you want to look at the sequence and choose from there, first open the pdb, then show its sequence (menu: Favorites? Sequence) and then use the mouse to drag a box to select the residues in the sequence window.  Then you can use the Actions menu to color as described above.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

There are tutorials for learning these basic actions in Chimera for example: 
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

? more tutorials can be opened from the Help menu.  Here?s the copy of the same stuff on our website:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

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

> On Oct 31, 2018, at 8:00 AM, Hui Min <huim868 at gmail.com> wrote:
> 
> Hi there,
> Sorry to disturb you. I have a question of how to use the Chimera software.
> If I've already got a .pdb file and use SMART to predict the domains, how can 
> I mark the 3D structure with user defined color? Thank you in advance for your help
> 



From benjamin.feinsilver at gmail.com  Wed Oct 31 09:15:49 2018
From: benjamin.feinsilver at gmail.com (Benjamin Feinsilver)
Date: Wed, 31 Oct 2018 12:15:49 -0400
Subject: [Chimera-users] Batch Processing of Molecular Attributes
Message-ID: <CAMvLk_TMksA51=6D_vRF2sbodb+x5cB-Khr_BXKZeW9LMPMeGA@mail.gmail.com>

Hello,

Is it possible to pass a CSV file to Chimera containing a list of SMILEs,
then output their molecular attributes in a new CSV file? For example,
volume, surface area, the number of surface points with positive
electrostatic potential, and the energy of the molecule's current 3D
conformation. If so, would you please let me know how I would accomplish
this?

Thanks,

Ben
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From meng at cgl.ucsf.edu  Wed Oct 31 15:32:22 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 31 Oct 2018 15:32:22 -0700
Subject: [Chimera-users] Batch Processing of Molecular Attributes
In-Reply-To: <CAMvLk_TMksA51=6D_vRF2sbodb+x5cB-Khr_BXKZeW9LMPMeGA@mail.gmail.com>
References: <CAMvLk_TMksA51=6D_vRF2sbodb+x5cB-Khr_BXKZeW9LMPMeGA@mail.gmail.com>
Message-ID: <8F0D50C6-3102-4195-A1B0-95DEE11D008A@cgl.ucsf.edu>

Hi Ben,
Chimera may not be the best tool for what you want to do.  I?ll try to briefly explain what it can do and limitations related to your question.

Although in principal some of those measurables could be calculated in Chimera, you?d have to figure out Chimera commands or python, make a script to work on a single SMILES input, and then adapt to looping through a list of multiple SMILES.  Chimera does not read csv files.  Information on scripts and looping, and saving the log (which contains results messages):
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

Some relevant Chimera commands: surface, measure area, measure volume

For individual command manual pages see links here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

Chimera?s electrostatic potential-related features are meant mainly for proteins and not a panoply of small molecules.  Although you could try to calculate ESP for the small molecules (relevant commands: addh, addcharge, coulombic  or  vina ) the charge calculation would be run via antechamber/sqm and is only effective/intended for smallish small molecules without high charge density, metals, uncommon elements or other unusual features.

Chimera has a ?mimimize? command that reports total energy but it is mainly meant for getting reasonable conformations, not reporting conformational energies. It also requires parametrization of the molecule beforehand with addh and addcharge, just like ESP calculations.

There is no command to report number of surface points with positive electrostatic potential, so you?d have to figure out python to do that, which would take fairly advanced understanding of Chimera code.

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

> On Oct 31, 2018, at 9:15 AM, Benjamin Feinsilver <benjamin.feinsilver at gmail.com> wrote:
> 
> Hello,
> Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this?
> Thanks,
> Ben




From Joanne.Williams at ucsf.edu  Wed Oct 31 15:53:55 2018
From: Joanne.Williams at ucsf.edu (Williams, Joanne)
Date: Wed, 31 Oct 2018 22:53:55 +0000
Subject: [Chimera-users] FW: Chimera [viewer] for iOS in the future?
In-Reply-To: <CFE7A4B3-17EF-4ED0-8A51-DCA266DF1283@unb.ca>
References: <CFE7A4B3-17EF-4ED0-8A51-DCA266DF1283@unb.ca>
Message-ID: <D7995DD5-F1CF-409D-BDC5-F717679B821C@ucsf.edu>



From: Bryan Crawford <bryanc at unb.ca>
Date: Wednesday, October 31, 2018 at 3:53 PM
To: "chimera at cgl.ucsf.edu" <chimera at cgl.ucsf.edu>
Subject: Chimera [viewer] for iOS in the future?

Hello,

I use Chimera occasionally in my research, and extensively for teaching (biochemistry, cell biology, developmental biology).  It is now the only remaining piece of software I use that requires me to bring a laptop computer to class.  For everything else (PDFs, animations, Keynote presentations, etc.) I can use my iPad which connects by AirPlay to the projector, and screencast everything using Doceri.  Furthermore, the touch-screen interface of the iPad seems ideally suited for many of the analyses and/or molecular renderings people use Chimera for.

So I?m wondering if there are any plans to produce either a full or partial version (perhaps with only viewing capabilities) of Chimera that runs on iOS?  If there is, I would be very happy to help with beta testing.  If not, can I ask if you can recommend any software that runs on iOS that I might consider?

Cheers

--
Dr. B.D.Crawford
Professor
Matrix Dynamics Lab
Department of Biology
University of New Brunswick
Fredericton, NB, Canada

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