[Chimera-users] Regarding blender

Tue Oct 14 09:16:29 PDT 2008

Hi guys,

I saw on the mailing list some information on exporting/importing 3D files.
However, I can't really figure out what would be the best way to export
chimera scene so that blender can import them.

Is the x3d format the best? Which plug-in do you use? Is there another way
better?

Cheers,
JD

-----Mensaje original-----
De: chimera-users-bounces at cgl.ucsf.edu
[mailto:chimera-users-bounces at cgl.ucsf.edu] En nombre de
chimera-users-request at cgl.ucsf.edu
Enviado el: lunes, 13 de octubre de 2008 21:00
Para: chimera-users at cgl.ucsf.edu
Asunto: Chimera-users Digest, Vol 66, Issue 12

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Today's Topics:

   1. Re: Helix-Numbers (skmolugu at miners.utep.edu)
   2. automating ensemble clustering in chimera (Katryna Cisek)
   3. Re: Printing on white background (Elaine Meng)
   4. Re: Helix-Numbers (Elaine Meng)
   5. Re: save reply log from chimera python script (Katryna Cisek)
   6. Re: Pruning pdb graphically (Elaine Meng)
   7. Re: save reply log from chimera python script (Thomas Goddard)

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

Message: 1
Date: Sun, 12 Oct 2008 13:21:53 -0600
From: <skmolugu at miners.utep.edu>
Subject: Re: [Chimera-users] Helix-Numbers
To: chimera users <chimera-users at cgl.ucsf.edu>
Message-ID: <BLU105-W44550A870C50C9AE487BFD85370 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
I was wondering if there is a way in chimera for numbering the helices in
the map fitted with coordinates. I Basically wanted to explain the location
of helix in the map by means of numbering it, so that it will be easy for me
to explain in my paper.
thank you very much for your time,
sudheer.

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

Message: 2
Date: Sun, 12 Oct 2008 15:42:47 -0400
From: "Katryna Cisek" <cisek.2 at osu.edu>
Subject: [Chimera-users] automating ensemble clustering in chimera
To: chimera-users <chimera-users at cgl.ucsf.edu>
Message-ID:
	<1bd6604c0810121242j2c9b4d48kc030b8a225af66d9 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Chimera Users,

How can I automate/import the Ensemble Cluster (Structure Comparison,
MD/Ensemble Analysis; cluster members of a
conformational ensemble, determine cluster representatives) module
into a python script?

Thanks,
Katryna

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

Message: 3
Date: Sun, 12 Oct 2008 13:09:33 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Printing on white background
To: Christian Schudoma <Schudoma at mpimp-golm.mpg.de>,	Francesco Pietra
	<chiendarret at gmail.com>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Message-ID: <350D2312-C5FB-4B46-B6B5-023FE8BA7875 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Thanks, Christian!  Besides the ways you mentioned, there is also the  
"set" command,
for example:

set bg_color white

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

Francesco and others may also be interested in the "tips on preparing  
images" page, which covers background color and other issues:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>

Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Oct 12, 2008, at 8:50 AM, Christian Schudoma wrote:

> Hi Francesco,
> you can change the background colour in Chimera: Actions->Color- 
> >background, then Actions->Color->[choose your colour like you would  
> for colouring atoms etc.].
> Then just save your image as usual and it should be on a white  
> background.
>
> Also, some of the Publication Options in the Presets menu  
> automatically set the background colour to white.
>
> Maybe there is a command line call for changing the background as  
> well? I don't know...
> Cheers,
> Christian
> ________________________________________
> From: chimera-users-bounces at cgl.ucsf.edu
[chimera-users-bounces at cgl.ucsf.edu 
> ] On Behalf Of Francesco Pietra [chiendarret at gmail.com]
> Sent: 12 October 2008 12:44
> To: chimera
> Subject: [Chimera-users] Printing on white background
>
> When mapping protein residues around a ligand I would like to have a
> printout of the enlarged binding site area, so as to put remarks by
> pencil on the printout. However, on a white background, in order to
> save ink. Is that a problem of working out the image (I have Gimp
> only, of which I never gained expertise), or can Chimera provide
> directly?
>
> Thanks
> francesco pietra

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

Message: 4
Date: Sun, 12 Oct 2008 13:26:20 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Helix-Numbers
To: <skmolugu at miners.utep.edu>
Cc: chimera users <chimera-users at cgl.ucsf.edu>
Message-ID: <F5081034-A931-431B-B612-2A930580D98F at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi Sudheer,
Sounds like you want 2D labels (Tools... Utilities... 2D Labels):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.
html 
 >

Since these labels don't move when you rotate the structure, you would  
first find the position you want to show in your figure, and then add  
the labels.

Alternatively, for labels in 3D that move with the structure, you  
could just label one atom in each helix and then manually change what  
is in the label (for example with "Actions... Label... other...").   
However, for figures I think 2D labels are much better, since they  
allow more control over location and can include symbols such as Greek  
letters, and it is easier to change their sizes and colors.

Some example images with 2D labels:
<http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png>
<http://www.cgl.ucsf.edu/chimera/feature_highlights/2fma-density.png>
<http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities-larg
e.png 
 >

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Oct 12, 2008, at 12:21 PM, <skmolugu at miners.utep.edu> wrote:
> Hi,
> I was wondering if there is a way in chimera for numbering the  
> helices in the map fitted with coordinates. I Basically wanted to  
> explain the location of helix in the map by means of numbering it,  
> so that it will be easy for me to explain in my paper.
> thank you very much for your time,
> sudheer.

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

Message: 5
Date: Mon, 13 Oct 2008 12:22:59 -0400
From: "Katryna Cisek" <cisek.2 at osu.edu>
Subject: Re: [Chimera-users] save reply log from chimera python script
To: "Tom Goddard" <goddard at cgl.ucsf.edu>
Cc: chimera-users at cgl.ucsf.edu
Message-ID:
	<1bd6604c0810130922m35b031c4sc4694d7e46f6ce81 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Chimera Users,
Could someone please point out the syntax error in this code:

def save_reply_log("/tmp/tmplog.txt"):    <<--- error should be here
based on error info
    from chimera import dialogs
    r = dialogs.find('reply')
    text = r.text.get('1.0', 'end')
    f = open('/tmp/tmplog.txt', 'w')
    f.write(text)
    f.close()

---------------------------chimera error info from reply
log-------------------------------

<type 'exceptions.SyntaxError'> Exception in Tk callback
  Function: <function command at 0x132d230> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    None
  File "CHIMERA/share/chimera/baseDialog.py", line 244, in command
    None
  File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK
    None
  File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply
    None
  File "CHIMERA/share/SimpleSession/gui.py", line 41, in _openCB
    None
  File "CHIMERA/share/chimera/__init__.py", line 1344, in open
    None
  File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython
    None
<type 'exceptions.SyntaxError'>: invalid syntax
(refalignrotatewholesymmetrysavelog.py, line 58)

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

Thanks,
Katryna

On Wed, Oct 8, 2008 at 10:33 PM, Tom Goddard <goddard at cgl.ucsf.edu> wrote:
> Hi Katryna,
>
>  I don't think there is a command to save the text in the reply log.  In
the
> Python function the variable path is the path to the file, for example
> "/tmp/mylog.txt".
>
>   Tom
>
>
> Katryna Cisek wrote:
>>
>> Hi Chimera users,
>> Is there a new way to save the reply log from a chimera python script,
>> other than below (from Chimera Archive 2006)?
>>
>> def save_reply_log(path):
>>  from chimera import dialogs
>>  r = dialogs.find('reply')
>>  text = r.text.get('1.0', 'end')
>>  f = open(path, 'w')
>>  f.write(text)
>>  f.close()
>>
>> If not, what is the filename given to the reply log in this function?
>> Is it possible to
>> designate the name?
>> Thanks,
>> Katryna
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>

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

Message: 6
Date: Mon, 13 Oct 2008 10:02:10 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Pruning pdb graphically
To: "Francesco Pietra" <chiendarret at gmail.com>
Cc: chimera <chimera-users at cgl.ucsf.edu>
Message-ID: <DD923F0C-8D7F-478E-991A-FD8E054B7E81 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi Francesco,
As usual in Chimera, there are several possible ways to do this, and  
what is "best" depends not only on what you plan to do with the  
result, but also your personal preferences and working style.

I would probably start by using either zones or Find Clashes/Contacts  
with a conservative cutoff to select all the residues you want to  
keep, which would probably also include several extra residues.  If  
you used Find Clashes/Contacts, one option selects the contacting  
atoms, and you would press the keyboard up arrow to promote the  
selection to whole residues.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas
h.html 
 >

Next, invert the selection (for example with Select... Invert (all  
models)) to include the residues you do NOT want, then undisplay them  
(for example with Actions... Atoms/Bonds... hide).

Then you can manually get rid of the few extra residues here and  
there:  Ctrl-click to select one atom or bond in an unwanted residue,  
press keyboard up arrow to promote to whole residue, undisplay as  
before.  Repeat as needed.

I don't know if you meant you wanted to just undisplay atoms or  
actually delete them.

If you wanted to delete them:  you could save PDB(s) and choose the  
option to include only the atoms that are displayed.  Alternatively,  
you could use the approach described above except instead of  
undisplaying atoms, deleting atoms (for example with Actions... Atoms/ 
Bonds... Delete) and then save PDB(s).

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht
ml#deletion 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Oct 12, 2008, at 10:05 AM, Francesco Pietra wrote:

> I would like to remove several parts from a complex protein, just
> leaving the portion where a complex has been created with amberscore.
> Which is the besr way in Chimera, while observing the pruning on the
> screen?
> Thanks
> francesco pietra

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

Message: 7
Date: Mon, 13 Oct 2008 10:49:43 -0700
From: Thomas Goddard <goddard at cgl.ucsf.edu>
Subject: Re: [Chimera-users] save reply log from chimera python script
To: Katryna Cisek <cisek.2 at osu.edu>
Cc: chimera-users at cgl.ucsf.edu
Message-ID: <48F38A37.5080803 at cgl.ucsf.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Katryna,

   The original code defines a function.  You leave it unchanged and add 
a line at the end to call it as follows.

	Tom

def save_reply_log(path):
   from chimera import dialogs
   r = dialogs.find('reply')
   text = r.text.get('1.0', 'end')
   f = open(path, 'w')
   f.write(text)
   f.close()

save_reply_log("/tmp/tmplog.txt")

Katryna Cisek wrote:
> Hi Chimera Users,
> Could someone please point out the syntax error in this code:
> 
> def save_reply_log("/tmp/tmplog.txt"):    <<--- error should be here
> based on error info
>     from chimera import dialogs
>     r = dialogs.find('reply')
>     text = r.text.get('1.0', 'end')
>     f = open('/tmp/tmplog.txt', 'w')
>     f.write(text)
>     f.close()
> 
> ---------------------------chimera error info from reply
> log-------------------------------
> 
> <type 'exceptions.SyntaxError'> Exception in Tk callback
>   Function: <function command at 0x132d230> (type: <type 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
> line 1747, in __call__
>     None
>   File "CHIMERA/share/chimera/baseDialog.py", line 244, in command
>     None
>   File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK
>     None
>   File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply
>     None
>   File "CHIMERA/share/SimpleSession/gui.py", line 41, in _openCB
>     None
>   File "CHIMERA/share/chimera/__init__.py", line 1344, in open
>     None
>   File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython
>     None
> <type 'exceptions.SyntaxError'>: invalid syntax
> (refalignrotatewholesymmetrysavelog.py, line 58)
> 
> --------------
> 
> Thanks,
> Katryna
> 
> 
> On Wed, Oct 8, 2008 at 10:33 PM, Tom Goddard <goddard at cgl.ucsf.edu> wrote:
>> Hi Katryna,
>>
>>  I don't think there is a command to save the text in the reply log.  In
the
>> Python function the variable path is the path to the file, for example
>> "/tmp/mylog.txt".
>>
>>   Tom
>>
>>
>> Katryna Cisek wrote:
>>> Hi Chimera users,
>>> Is there a new way to save the reply log from a chimera python script,
>>> other than below (from Chimera Archive 2006)?
>>>
>>> def save_reply_log(path):
>>>  from chimera import dialogs
>>>  r = dialogs.find('reply')
>>>  text = r.text.get('1.0', 'end')
>>>  f = open(path, 'w')
>>>  f.write(text)
>>>  f.close()
>>>
>>> If not, what is the filename given to the reply log in this function?
>>> Is it possible to
>>> designate the name?
>>> Thanks,
>>> Katryna
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>

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

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