From goddard at cgl.ucsf.edu  Tue Sep  1 11:58:31 2009
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 01 Sep 2009 11:58:31 -0700
Subject: [Chimera-users] Cannot save the labels in Volume trace
In-Reply-To: <4A9C70A0.4050304@cgl.ucsf.edu>
References: <391712D3-29D0-43A0-9DED-569B96685DFC@biochem.uthscsa.edu>	<D5BC07D5-E5C8-40AA-AE3A-2FA52EDFC027@cgl.ucsf.edu>	<002201ca2a5d$fc76a700$f563f500$@edu>
	<4A9C70A0.4050304@cgl.ucsf.edu>
Message-ID: <4A9D6ED7.2030505@cgl.ucsf.edu>

Hi Xing,

   Yes, now I see that if you select a link and use menu Actions / Label 
/ other... and type a text label such as a number for your helices then 
that label is not saved in sessions.  This is a bug, that labels on 
links or bonds are not saved in sessions.  Eric Pettersen says he will 
fix it this week (probably today).

   The marker notes only apply to the markers, not the links. I will fix 
the code so that marker labels created with Actions / Label / other... 
are saved.  Currently having an empty marker note overrides such labels. 
  I expect to fix this later in the week.  Will let you know when it is 
fixed.

	Tom


-------- Original Message --------
Subject: Re: [Chimera-users] Cannot save the labels in Volume trace
From: Xing Zhang
To: 'Thomas Goddard'
Date: 9/1/09 10:09 AM

> Thanks, Tom,
> 
> I just found my mistake. I actually want to label the*_ linker_**_s_* 
> (not markers) between two makers to represent the sequence of each 
> secondary structure. So how can I do that in Chimera which could be 
> saved and restored? Thank you very much.
> 
> Xing
> 


-------- Original Message --------
Subject: Re: [Chimera-users] Cannot save the labels in Volume trace
From: Thomas Goddard
To: Xing Zhang
Date: 8/31/09 5:53 PM

> Hi Xing,
> 
>    If you placed markers with the Volume Tracer dialog and use Features 
> / Marker Note in that dialog to label the markers they will be saved in 
> session files.  I see that if you use Actions / Label / other... to 
> label the markers then that is not saved in Chimera 1.3, and it is saved 
> but not restored in Chimera 1.4, because the empty Marker Note overrides 
> the label.
> 
>    I'll try to fix this for the upcoming Chimera 1.4 release, so that 
> labels set with Actions / Label are treated the same as marker notes. 
> For now, use the Volume Tracer dialog Features / Marker Note and it will 
>   be saved and restored from sessions.
> 
>    Thanks for reporting the problem.
> 
> 	Tom
> 
> 
> -------- Original Message --------
> Subject: [Chimera-users] Cannot save the labels in Volume trace
> From: Xing Zhang
> To: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
> Date: 8/31/09 10:10 AM
> 
>> Dear All,
>>
>> I try to put stickers and balls in my EM density to trace secondary
>> structures of protein. During this process, I put a number to label each of
>> the secondary structures. However, these labels are all lost after I save
>> this session and restore the session. Any suggestion to solve this problem
>> would be greatly appreciated. Thanks.
>>
>> Xing
>>
>>


From pett at cgl.ucsf.edu  Tue Sep  1 17:06:32 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 1 Sep 2009 17:06:32 -0700
Subject: [Chimera-users] menu commands in script
In-Reply-To: <4A9C6BF8.7020704@umontreal.ca>
References: <288df32a0908310156j3a35cd59ief95fc076d1228af@mail.gmail.com>
	<EBDA9116-3CEC-4C2A-8E4E-8B74C1DC19F9@cgl.ucsf.edu>
	<4A9C6BF8.7020704@umontreal.ca>
Message-ID: <EEBDA11B-15A8-412D-A7F0-1BDAAFCE4905@cgl.ucsf.edu>

On Aug 31, 2009, at 5:34 PM, James Fethiere wrote:

> is there a command equivalent to the menu command: coulombic surface  
> coloring. I need to include it in a movie script.

Hi James,
	The short answer is no, there is not.  Probably should be.  I'll try  
to fix that when I can.
	Not a great short answer, so here's a longer answer.  I've attached a  
script that if you open it ("open esp.py") will coulombic-ly color all  
open molecular surfaces.  By default it will color red-white-blue -10  
- 0 - 10, but I think it's fairly easy to modify those values just by  
looking at the script.  Let me know if you have problems.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


-------------- next part --------------
A non-text attachment was scrubbed...
Name: esp.py
Type: text/x-python-script
Size: 301 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090901/a8e14fc4/attachment.bin>

From goddard at cgl.ucsf.edu  Wed Sep  2 10:52:50 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Wed, 02 Sep 2009 10:52:50 -0700
Subject: [Chimera-users] 2D projections
In-Reply-To: <4A9C6903.7070007@cgl.ucsf.edu>
References: <9769b07f0908281508h691c905fj9085ad08c6e7ab75@mail.gmail.com>
	<4A9C6903.7070007@cgl.ucsf.edu>
Message-ID: <4A9EB0F2.5040407@cgl.ucsf.edu>

Hi Ana,

  Can you explain what you mean by "projecting a surface"?  Is the 
result a flat triangulated surface lying entirely in a plane? or a curve 
in a plane that is the projected boundary?  Chimera doesn't do either of 
those but a Python script could easily do the former, the latter being a 
more complex computational geometry problem.  Do you have a file format 
in mind for saving that result?  Will the formats that Chimera can 
export a surface in (x3d, vrml, grasp, ...) be of use to you?

    Tom


-------- Original Message --------
Subject: Re: [Chimera-users] 2D projections
From: Ana Luiza
To: Thomas Goddard
Date: 9/2/09 5:11 AM
> Hi Thomas,
>
> Thanks for the answer.
>
> What I really have to do in my work is:
> - Build a protein surface (only the outside surface, the contour, it 
> doesn?t matter what is inside)
> - Rotate this surface 360o in axis x, y and z
> - Take a 2D projection of the surface in each position during rotation 
> and save it and its specific angle
>
> I'm thinking about develop a Python script to do this with the commands:
> - roll (to rotate the model in axis x, y and z)
> - push (to save each 2D projection)
>
> The problem is that I don?t know how to take the 2D projections during 
> rotation.
>
> Can you help me, please?
>
> Thanks in advance.
>
> Best regards,
> Ana Luiza.


-------- Original Message --------
Subject: Re: [Chimera-users] 2D projections
From: Thomas Goddard
To: chimera-users
Date: 8/31/09 5:21 PM
> Hi Ana,
>
>    Do you want to project volume data or a surface?
>
>    For volume data you can display a projection by using "solid" style 
> rendering and set the transparency to 100% in the volume dialog 
> brightness and transparency panel, and move the nodes on the volume 
> histogram to create a linear ramp.  This just provides an on-screen 
> image that looks like a projection.  Probably good to use orthographic 
> projection too (menu Tools / Viewing Controls / Camera, projection -> 
> orthographic) instead of perspective projection.
>
>    Chimera is not able to create a 2d volume data sets which is the 
> exact projection, but I'd like to add that.  It is on the Chimera 
> request list (entry 58).
>
>      http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests
>
>    Tom
>
> -------- Original Message --------
> Subject: [Chimera-users] 2D projections
> From: Ana Luiza
> To: chimera-users
> Date: 8/28/09 3:08 PM
>
>   
>> Hi,
>>
>> Is it possible to build 2D projections from a 3D surface in Chimera?
>>
>> Thanks,
>> Ana Luiza.
>>
>>
>>     



From kjwu at ucsd.edu  Wed Sep  2 16:08:44 2009
From: kjwu at ucsd.edu (Kevin Wu)
Date: Wed, 2 Sep 2009 16:08:44 -0700
Subject: [Chimera-users] Rendering with nogui
Message-ID: <1571db7a0909021608s7bbd411ap791b2b3309b0ff4d@mail.gmail.com>

Hi,

It seems like it's not possible to render figures or models in Chimera when
using the nogui option. Is there anyway around this? I'd like to use Chimera
in a program to render models to display.

Regards,
Kevin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090902/ad4efff0/attachment.html>

From gregc at cgl.ucsf.edu  Wed Sep  2 17:07:11 2009
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Wed, 2 Sep 2009 17:07:11 -0700 (PDT)
Subject: [Chimera-users] Rendering with nogui
In-Reply-To: <1571db7a0909021608s7bbd411ap791b2b3309b0ff4d@mail.gmail.com>
References: <1571db7a0909021608s7bbd411ap791b2b3309b0ff4d@mail.gmail.com>
Message-ID: <Pine.OSF.4.63.0909021702340.1858452@guanine.cgl.ucsf.edu>

On Wed, 2 Sep 2009, Kevin Wu wrote:

> Hi,
>
> It seems like it's not possible to render figures or models in Chimera when
> using the nogui option. Is there anyway around this? I'd like to use Chimera
> in a program to render models to display.
>
> Regards,
> Kevin

Right now, the only solution is to use a headless version of chimera. 
And those are only available for Linux as daily builds (last two listings 
in the table).  When you find a part of chimera that doesn't work in nogui 
mode (fewer and fewer!), please submit a bug report.

 	- Greg


From miriam.gochin at tu.edu  Tue Sep  1 15:09:44 2009
From: miriam.gochin at tu.edu (Miriam Gochin)
Date: Tue, 1 Sep 2009 15:09:44 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string into structure
Message-ID: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>

I have downloaded the latest build (Aug 30, 2009) and don't seem to be able to input a SMILES string.  I have tried both the Utilities -> Structure Diagram and the Structure Editing -> Build Structure tool, and in both cases I can see a box to input the SMILES string, but the copy and paste mechanism won't work.  I can enter text in the box, but cannot paste it in, which I need to do.  Thanks for your help.


Miriam Gochin
Touro University - CA
miriam.gochin at tu.edu
707-638-5463


From marzi at titus.u-strasbg.fr  Thu Sep  3 06:15:00 2009
From: marzi at titus.u-strasbg.fr (Stefano Marzi)
Date: Thu, 03 Sep 2009 15:15:00 +0200
Subject: [Chimera-users] wglMakeCurrent failed
Message-ID: <4A9FC154.5070904@igbmc.u-strasbg.fr>

Hi,

With the new production releases, from 1.2540 to the very last one 
1.4_b28596, for windows, I am keeping getting the wglMakeCurrent failure.

This happens when I try to make a movie.

I have searched in the Chimera-user mailing list archive but I have 
found only a thread by Greg Couch saying that this bug has been fixed 
already one year ago, September 2008.

Could anyone please help me with that?


Thank you,

Best

Stefano Marzi


From gregc at cgl.ucsf.edu  Thu Sep  3 10:09:38 2009
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 3 Sep 2009 10:09:38 -0700 (PDT)
Subject: [Chimera-users] wglMakeCurrent failed
In-Reply-To: <4A9FC154.5070904@igbmc.u-strasbg.fr>
References: <4A9FC154.5070904@igbmc.u-strasbg.fr>
Message-ID: <Pine.OSF.4.63.0909031002510.1720348@guanine.cgl.ucsf.edu>

On Thu, 3 Sep 2009, Stefano Marzi wrote:

> Hi,
>
> With the new production releases, from 1.2540 to the very last one
> 1.4_b28596, for windows, I am keeping getting the wglMakeCurrent failure.
>
> This happens when I try to make a movie.
>
> I have searched in the Chimera-user mailing list archive but I have
> found only a thread by Greg Couch saying that this bug has been fixed
> already one year ago, September 2008.
>
> Could anyone please help me with that?
>
>
> Thank you,
>
> Best
>
> Stefano Marzi

Hello Stefano,

Please use chimera's Help / Report a Bug dialog to report this bug so we 
will have a record of what graphics card and driver you're using, so we 
can try to reproduce the bug locally.  Next, update your graphics driver 
to the latest version.  With the information in your bug report, I can 
help you with that if need be.  Chances are that the problem will 
disappear with a newer graphics driver, but maybe there's a code path in 
the movie making code that needs to be fixed.

 	- Greg


From meng at cgl.ucsf.edu  Thu Sep  3 10:46:25 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 3 Sep 2009 10:46:25 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string into
	structure
In-Reply-To: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>
Message-ID: <719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>

Hi Miriam,
Are you on a Mac?  I'm using a Mac and was able to copy text from  
Terminal and paste it into both those places.  The copy/paste  
procedure depends on your platform.  Using the Mac aqua version, I  
highlighted text in Terminal and pressed command-c to copy, then to  
paste, I clicked into the blank dialog text area and pressed command- 
v.  Using the Mac X11 version, I used the same copying procedure but  
then to paste, clicked into the blank dialog text area and then  
clicked middle mouse button.  On Windows, copy and paste may be Ctrl-c  
and Ctrl-v.

You can also get SMILES->3D from the Chimera command line, e.g.

open smiles:C1CCC(O)CC1

and the copy/paste procedure there is the same, but again platform- 
dependent.

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

On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:

> I have downloaded the latest build (Aug 30, 2009) and don't seem to  
> be able to input a SMILES string.  I have tried both the Utilities - 
> > Structure Diagram and the Structure Editing -> Build Structure  
> tool, and in both cases I can see a box to input the SMILES string,  
> but the copy and paste mechanism won't work.  I can enter text in  
> the box, but cannot paste it in, which I need to do.  Thanks for  
> your help.



From miriam.gochin at tu.edu  Thu Sep  3 11:16:51 2009
From: miriam.gochin at tu.edu (Miriam Gochin)
Date: Thu, 3 Sep 2009 11:16:51 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string into
 structure
In-Reply-To: <719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>,
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
Message-ID: <8F37ABB227136A48A611B3BA213DF7F02C5D691A79@TUMAIL.tuca.touro.edu>

Hi Elaine,

I can see that the problem is that I can't copy and paste anything at all, eg. I can't copy a command from a file using command-c and paste it using command-v on the Chimera command line.  It gives an error (a sound).  But I can copy and paste into text files etc.  I'm using Mac-OSX-10.4.11 on a PowerPC.

Miriam Gochin
Touro University - CA
miriam.gochin at tu.edu
707-638-5463
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, September 03, 2009 10:46 AM
To: Miriam Gochin
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Using Chimera to read SMILES string into structure

Hi Miriam,
Are you on a Mac?  I'm using a Mac and was able to copy text from
Terminal and paste it into both those places.  The copy/paste
procedure depends on your platform.  Using the Mac aqua version, I
highlighted text in Terminal and pressed command-c to copy, then to
paste, I clicked into the blank dialog text area and pressed command-
v.  Using the Mac X11 version, I used the same copying procedure but
then to paste, clicked into the blank dialog text area and then
clicked middle mouse button.  On Windows, copy and paste may be Ctrl-c
and Ctrl-v.

You can also get SMILES->3D from the Chimera command line, e.g.

open smiles:C1CCC(O)CC1

and the copy/paste procedure there is the same, but again platform-
dependent.

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

On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:

> I have downloaded the latest build (Aug 30, 2009) and don't seem to
> be able to input a SMILES string.  I have tried both the Utilities -
> > Structure Diagram and the Structure Editing -> Build Structure
> tool, and in both cases I can see a box to input the SMILES string,
> but the copy and paste mechanism won't work.  I can enter text in
> the box, but cannot paste it in, which I need to do.  Thanks for
> your help.


--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From meng at cgl.ucsf.edu  Thu Sep  3 12:58:13 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 3 Sep 2009 12:58:13 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string into
	structure
In-Reply-To: <8F37ABB227136A48A611B3BA213DF7F02C5D691A79@TUMAIL.tuca.touro.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>,
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
	<8F37ABB227136A48A611B3BA213DF7F02C5D691A79@TUMAIL.tuca.touro.edu>
Message-ID: <8AC71A55-47E9-45D7-96F4-0C97CC024109@cgl.ucsf.edu>

Hi Miriam,
Are you using X11 Chimera or Aqua Chimera?  In the X11 one I had to  
click middle mouse button instead of using command-v.  Maybe it would  
be better if you used "Help... Report a Bug" instead of sending mail  
to chimera-users, since that bug dialog automatically includes  
information on which Chimera you are using and your system.  We  
probably can't offer advice unless we can reproduce the problem.

You would need to describe the problem again and include your e-mail  
address on the report.  Also explain what you mean by "I can copy and  
paste into text files" (how did you do it? menu? command-c and command- 
v?  are you using Word, Text-edit, or Terminal?).
Elaine

On Sep 3, 2009, at 11:16 AM, Miriam Gochin wrote:

> Hi Elaine,
>
> I can see that the problem is that I can't copy and paste anything  
> at all, eg. I can't copy a command from a file using command-c and  
> paste it using command-v on the Chimera command line.  It gives an  
> error (a sound).  But I can copy and paste into text files etc.  I'm  
> using Mac-OSX-10.4.11 on a PowerPC.
>
> Miriam Gochin
> Touro University - CA
> miriam.gochin at tu.edu
> 707-638-5463
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Thursday, September 03, 2009 10:46 AM
> To: Miriam Gochin
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Using Chimera to read SMILES string  
> into structure
>
> Hi Miriam,
> Are you on a Mac?  I'm using a Mac and was able to copy text from
> Terminal and paste it into both those places.  The copy/paste
> procedure depends on your platform.  Using the Mac aqua version, I
> highlighted text in Terminal and pressed command-c to copy, then to
> paste, I clicked into the blank dialog text area and pressed command-
> v.  Using the Mac X11 version, I used the same copying procedure but
> then to paste, clicked into the blank dialog text area and then
> clicked middle mouse button.  On Windows, copy and paste may be Ctrl-c
> and Ctrl-v.
>
> You can also get SMILES->3D from the Chimera command line, e.g.
>
> open smiles:C1CCC(O)CC1
>
> and the copy/paste procedure there is the same, but again platform-
> dependent.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:
>
>> I have downloaded the latest build (Aug 30, 2009) and don't seem to
>> be able to input a SMILES string.  I have tried both the Utilities -
>>> Structure Diagram and the Structure Editing -> Build Structure
>> tool, and in both cases I can see a box to input the SMILES string,
>> but the copy and paste mechanism won't work.  I can enter text in
>> the box, but cannot paste it in, which I need to do.  Thanks for
>> your help.
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From miriam.gochin at tu.edu  Thu Sep  3 13:54:03 2009
From: miriam.gochin at tu.edu (Miriam Gochin)
Date: Thu, 3 Sep 2009 13:54:03 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string into
 structure
In-Reply-To: <8AC71A55-47E9-45D7-96F4-0C97CC024109@cgl.ucsf.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>,
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
	<8F37ABB227136A48A611B3BA213DF7F02C5D691A79@TUMAIL.tuca.touro.edu>,
	<8AC71A55-47E9-45D7-96F4-0C97CC024109@cgl.ucsf.edu>
Message-ID: <8F37ABB227136A48A611B3BA213DF7F02C5D691A7D@TUMAIL.tuca.touro.edu>

You have solved my problem!  If I use CONTROL-APPLE-v it works!!!  (no middle mouse on a Mac).

Thank you so much.

I wonder if you could suggest how to fix this problem:
I am registered on chimera-users, because I have a profile and always get the chimera-users e-mails, but when I sent this request, it told me it would be held for the moderator (~ 24h) because I am not a member of the group.  How do I become a member?

Miriam Gochin
Touro University - CA
miriam.gochin at tu.edu
707-638-5463
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, September 03, 2009 12:58 PM
To: Miriam Gochin
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Using Chimera to read SMILES string into structure

Hi Miriam,
Are you using X11 Chimera or Aqua Chimera?  In the X11 one I had to
click middle mouse button instead of using command-v.  Maybe it would
be better if you used "Help... Report a Bug" instead of sending mail
to chimera-users, since that bug dialog automatically includes
information on which Chimera you are using and your system.  We
probably can't offer advice unless we can reproduce the problem.

You would need to describe the problem again and include your e-mail
address on the report.  Also explain what you mean by "I can copy and
paste into text files" (how did you do it? menu? command-c and command-
v?  are you using Word, Text-edit, or Terminal?).
Elaine

On Sep 3, 2009, at 11:16 AM, Miriam Gochin wrote:

> Hi Elaine,
>
> I can see that the problem is that I can't copy and paste anything
> at all, eg. I can't copy a command from a file using command-c and
> paste it using command-v on the Chimera command line.  It gives an
> error (a sound).  But I can copy and paste into text files etc.  I'm
> using Mac-OSX-10.4.11 on a PowerPC.
>
> Miriam Gochin
> Touro University - CA
> miriam.gochin at tu.edu
> 707-638-5463
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Thursday, September 03, 2009 10:46 AM
> To: Miriam Gochin
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Using Chimera to read SMILES string
> into structure
>
> Hi Miriam,
> Are you on a Mac?  I'm using a Mac and was able to copy text from
> Terminal and paste it into both those places.  The copy/paste
> procedure depends on your platform.  Using the Mac aqua version, I
> highlighted text in Terminal and pressed command-c to copy, then to
> paste, I clicked into the blank dialog text area and pressed command-
> v.  Using the Mac X11 version, I used the same copying procedure but
> then to paste, clicked into the blank dialog text area and then
> clicked middle mouse button.  On Windows, copy and paste may be Ctrl-c
> and Ctrl-v.
>
> You can also get SMILES->3D from the Chimera command line, e.g.
>
> open smiles:C1CCC(O)CC1
>
> and the copy/paste procedure there is the same, but again platform-
> dependent.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:
>
>> I have downloaded the latest build (Aug 30, 2009) and don't seem to
>> be able to input a SMILES string.  I have tried both the Utilities -
>>> Structure Diagram and the Structure Editing -> Build Structure
>> tool, and in both cases I can see a box to input the SMILES string,
>> but the copy and paste mechanism won't work.  I can enter text in
>> the box, but cannot paste it in, which I need to do.  Thanks for
>> your help.
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From meng at cgl.ucsf.edu  Thu Sep  3 14:26:07 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 3 Sep 2009 14:26:07 -0700
Subject: [Chimera-users] chimera-users membership
In-Reply-To: <8F37ABB227136A48A611B3BA213DF7F02C5D691A7D@TUMAIL.tuca.touro.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>,
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
	<8F37ABB227136A48A611B3BA213DF7F02C5D691A79@TUMAIL.tuca.touro.edu>,
	<8AC71A55-47E9-45D7-96F4-0C97CC024109@cgl.ucsf.edu>
	<8F37ABB227136A48A611B3BA213DF7F02C5D691A7D@TUMAIL.tuca.touro.edu>
Message-ID: <B9956FE3-C2BD-4FA7-A173-A8C5F098C6C2@cgl.ucsf.edu>

Hi Miriam,
Glad you can paste now!

Now for the other problem...
My guess is that the email address that your sent messages are marked  
with is slightly different than the one given when you first signed up  
for chimera-users.  For example, the messages you sent could be marked  
as sent by name at school.edu whereas the initial signup could have been  
something like name at machine.school.edu, or vice versa.  In that case,  
messages sent to either would still reach you, but on one address  
would be recognized as already belonging to the chimera-users list.

That is only a guess, however.  If I'm right, the way to fix it would  
be to either

(a) unsubscribe the existing subscription and sign up again with  
address that matches your outgoing signatures
(these can be done at <http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users 
 > )

(b) change your mail setup so that your sent mail is marked with the  
other version of your email address

Perhaps others who know more about this (Conrad?) can pipe up if my  
guess and/or suggestions are wrong...
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco






On Sep 3, 2009, at 1:54 PM, Miriam Gochin wrote:

> You have solved my problem!  If I use CONTROL-APPLE-v it works!!!   
> (no middle mouse on a Mac).
>
> Thank you so much.
>
> I wonder if you could suggest how to fix this problem:
> I am registered on chimera-users, because I have a profile and  
> always get the chimera-users e-mails, but when I sent this request,  
> it told me it would be held for the moderator (~ 24h) because I am  
> not a member of the group.  How do I become a member?
>
> Miriam Gochin
> Touro University - CA
> miriam.gochin at tu.edu
> 707-638-5463



From goddard at cgl.ucsf.edu  Thu Sep  3 17:09:15 2009
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 03 Sep 2009 17:09:15 -0700
Subject: [Chimera-users] 2D projections
In-Reply-To: <4A9C6903.7070007@cgl.ucsf.edu>
References: <9769b07f0908281508h691c905fj9085ad08c6e7ab75@mail.gmail.com>
	<4A9C6903.7070007@cgl.ucsf.edu>
Message-ID: <4AA05AAB.9040801@cgl.ucsf.edu>

Hi Alex,

   I've added a Python script surfsilhouette.py to make silhouette 
images of orthographically projected surfaces to the Chimera scripts web 
page

	http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts

Edit it to meet your needs.  There is an option called "multilayer" that 
will show multiple layers of the surface using different gray levels.

   Tom

-------- Original Message --------
Subject: Re: Fwd: [Chimera-users] 2D projections
From: Alexandre Cunha
To: goddard
Date: 9/2/09 4:55 PM

> Dear Thomas,
> 
> Ana has forwarded me the emails you have recently exchanged. Please find 
> attached a picture showing an example of what the initial goal is: to 
> construct silhouettes/masks of orthographic projections of protein 
> isosurfaces. The mask you see in the right picture was formed by 
> replacing everything that was not black (background) in the left image 
> (produced using Chimera) by white and inverting the colors (some math 
> morphology was used to remove spurious salt & pepper data that appears 
> away from the surface).
> 
> Ana started investigating how we could use Chimera to create such 
> projection masks for a particular protein from a given set of Euler 
> angles. Does Chimera has something already built in for that that we 
> could take advantage of ?
> 
> Another interest is to use ortographic projections of proteins rendered 
> with translucent isosurfaces. In this case the projection is not a black 
> and white mask anymore but a gray image where the intensity of projected 
> pixels depends on how many hits the projection ray encounters before 
> reaching the projection plane. The higher the hits the lower the 
> intensity. Is Chimera capable of creating such projections or we would 
> need to create our own projection scripts  ? Please advise.
> 
> Best regards,
> - Alex.
> 
> 
> Ana Luiza wrote:
>>
>>
>> ---------- Forwarded message ----------
>> From: *Tom Goddard* <goddard at cgl.ucsf.edu <mailto:goddard at cgl.ucsf.edu>>
>> Date: 2009/9/2
>> Subject: Re: [Chimera-users] 2D projections
>> To: analuiza
>> Cc: chimera-users
>>
>>
>> Hi Ana,
>>
>>  Can you explain what you mean by "projecting a surface"?  Is the 
>> result a flat triangulated surface lying entirely in a plane? or a 
>> curve in a plane that is the projected boundary?  Chimera doesn't do 
>> either of those but a Python script could easily do the former, the 
>> latter being a more complex computational geometry problem.  Do you 
>> have a file format in mind for saving that result?  Will the formats 
>> that Chimera can export a surface in (x3d, vrml, grasp, ...) be of use 
>> to you?
>>
>>   Tom
>>
>>
>>
>> -------- Original Message --------
>> Subject: Re: [Chimera-users] 2D projections
>> From: Ana Luiza
>> To: Thomas Goddard
>> Date: 9/2/09 5:11 AM
>>
>>     Hi Thomas,
>>
>>     Thanks for the answer.
>>
>>     What I really have to do in my work is:
>>     - Build a protein surface (only the outside surface, the contour, it
>>     doesn?t matter what is inside)
>>     - Rotate this surface 360o in axis x, y and z
>>     - Take a 2D projection of the surface in each position during
>>     rotation and save it and its specific angle
>>
>>     I'm thinking about develop a Python script to do this with the 
>> commands:
>>     - roll (to rotate the model in axis x, y and z)
>>     - push (to save each 2D projection)
>>
>>     The problem is that I don?t know how to take the 2D projections
>>     during rotation.
>>
>>     Can you help me?
>>
>>     Thanks in advance.
>>
>>     Best regards,
>>     Ana Luiza.
>>
>>
>>
>> -------- Original Message --------
>> Subject: Re: [Chimera-users] 2D projections
>> From: Thomas Goddard
>> To: chimera-users
>> Date: 8/31/09 5:21 PM
>>
>>     Hi Ana,
>>
>>       Do you want to project volume data or a surface?
>>
>>       For volume data you can display a projection by using "solid"
>>     style rendering and set the transparency to 100% in the volume
>>     dialog brightness and transparency panel, and move the nodes on the
>>     volume histogram to create a linear ramp.  This just provides an
>>     on-screen image that looks like a projection.  Probably good to use
>>     orthographic projection too (menu Tools / Viewing Controls / Camera,
>>     projection -> orthographic) instead of perspective projection.
>>
>>       Chimera is not able to create a 2d volume data sets which is the
>>     exact projection, but I'd like to add that.  It is on the Chimera
>>     request list (entry 58).
>>
>>         http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests
>>
>>       Tom
>>
>>     -------- Original Message --------
>>     Subject: [Chimera-users] 2D projections
>>     From: Ana Luiza
>>     To: chimera-users
>>     Date: 8/28/09 3:08 PM
>>
>>     
>>         Hi,
>>
>>         Is it possible to build 2D projections from a 3D surface in 
>> Chimera?
>>
>>         Thanks,
>>         Ana Luiza.
>>
>>
>>           
>>
>>
> 
> ------------------------------------------------------------------------
> 

-------------- next part --------------
A non-text attachment was scrubbed...
Name: silhouettes.png
Type: image/png
Size: 59558 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090903/37605e08/attachment.png>

From bala.biophysics at gmail.com  Fri Sep  4 08:33:52 2009
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Fri, 4 Sep 2009 21:03:52 +0530
Subject: [Chimera-users] hydrogen bond representation
Message-ID: <288df32a0909040833v3186d9ecr5ac3ec41f372669d@mail.gmail.com>

Friends,

Is there any way to represent hydrogen bonds as dotted lines instead of a
solid line in Chimera. Sometimes hbond analysis in chimera shows same atom
to be involved in two hydrogen bonds, why is it so ?

Thanks,
Bala
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/771859ce/attachment.html>

From meng at cgl.ucsf.edu  Fri Sep  4 08:56:34 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 4 Sep 2009 08:56:34 -0700
Subject: [Chimera-users] hydrogen bond representation
In-Reply-To: <288df32a0909040833v3186d9ecr5ac3ec41f372669d@mail.gmail.com>
References: <288df32a0909040833v3186d9ecr5ac3ec41f372669d@mail.gmail.com>
Message-ID: <5FFF96D9-C8C2-42DB-9925-4F94725D164D@cgl.ucsf.edu>

Hi Bala,
As mentioned in the FindHBond page,
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ 
findhbond.html>

"All potential H-bonding interactions fulfilling the criteria are  
shown." In other words, each is possible taken individually based on  
distances and angles, but it will not necessarily be possible to form  
all of them at the same time.  If the structure does not include  
hydrogens, for example, the H-bonds possible from a hydroxyl oxygen  
might require the OH hydrogen to be in different places.

The H-bonds are shown with pseudobonds, and there are several ways to  
change their appearance.  The line style is actually an attribute of  
the pseudobond group.  Ways to change this:

(a) Ctrl-click to select one H-bond, press up arrow to expand  
selection to all H-bonds, open Selection Inspector, inspect  
"Pseudobond group" and change the "line style"

(b) start Pseudobond Panel (under Tools... General Controls), click  
on group name "hydrogen bonds" on the left and then "attributes" on  
the right, change "line style"

(c) use command "setattr" e.g. something like:
setattr g lineType 3
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

The attribute name (e.g. lineType) and what values mean what (e.g. 3  
= dotted, which just looks like shorter dashes to me) are shown in  
the balloon help when you put the mouse over the attribute dialogs  
mentioned in (a) and (b).

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

On Sep 4, 2009, at 8:33 AM, Bala subramanian wrote:

> Friends,
> Is there any way to represent hydrogen bonds as dotted lines  
> instead of a solid line in Chimera. Sometimes hbond analysis in  
> chimera shows same atom to be involved in two hydrogen bonds, why  
> is it so ?
> Thanks,
> Bala



From goddard at cgl.ucsf.edu  Fri Sep  4 13:42:01 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 04 Sep 2009 13:42:01 -0700
Subject: [Chimera-users] Problem with benzenes split across crystal unit cell
In-Reply-To: <37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>
References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu>	<4A985D1E.300@cgl.ucsf.edu>
	<4A9C6A12.2090307@cgl.ucsf.edu> <4A9C7574.5080600@cgl.ucsf.edu>
	<5A13371E-67D1-46D1-8873-D6AF970662F3@caltech.edu>
	<4A9D4B74.2090908@cgl.ucsf.edu>
	<9AE9942C-32E2-48F5-A7D8-B5B90C38B3C5@caltech.edu>
	<4A9F13B9.1010300@cgl.ucsf.edu>
	<37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>
Message-ID: <4AA17B99.8000700@cgl.ucsf.edu>

Hi Mike,

  The Chimera unit cell dialog is behaving as expected in the cases 
where the asymmetric unit contains half of a benzene ring.  First, parts 
of the asymmetric unit are not moved relative to other parts of the 
asymmetric unit, so as you observe the half benzenes in asymmetric unit 
copies sometimes lie outside the unit cell.  All unit cell dialog
just puts the center of the asymmetric unit in the unit cell box.  A 
second problem is that a half benzene ring from one asymmetric unit will 
not be joined to a half benzene ring from another asymmetric unit.  They 
will line up perfectly but Chimera does not see bonds between the two 
halfs so for instance, selecting aromatic rings won't pick those up.

  I guess the first problem could be handled by moving each connected 
group of atoms so its center lies in the unit cell.  I think it could 
lead to undesired results.  For example a protein with a bound ligand 
might have the ligand outside the unit cell causing it to be moved to 
some other asymmetric unit's binding site.  The trouble with that is 
that the protein and ligand are part of one molecule model in Chimera, 
so now you have taken the ligand in that molecule and placed it with the 
protein of another copy of the molecule.  That may not be what you want.

  Another answer to the first problem, is that I added to the unit cell 
dialog the ability to make multiple asymmetric unit copies to fill 
multiple unit cells.  If you make several unit cells, then the half 
benzenes lying outside one unit cell do join up with the half benzenes 
from a different unit cell.

  If you were trying to make a figure and you didn't want half-benzenes 
floating around -- you could simply select them and delete them (Actions 
/ Atoms / Delete).

  The second problem is harder.  Chimera could guess that the 
half-benzenes should be joined since they have exactly coincident 
atoms.  (This relies on the strange inconsistency that the half-benzenes 
in the PDB files you sent contain 4 atoms instead of the expected 3 
atoms.  So it doesn't actually represent an asymmetric unit since there 
is an extra atom that will be duplicated in other asymmetric units.)  
But Chimera can't join them because covalent bonds can't be formed 
between different molecule objects -- it would require making a new 
molecule to contain all the atoms.  Creating extra molecule models to 
join the half benzenes is possible but weird.

    Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Centro-symmetric space groups
From: Michael Day
To: Tom Goddard
Date: 9/4/09 12:41 PM
> Hi Tom,
>
> Thanks. It looks like the issue is mostly resolved. 
>
> The is a problem with molecular units sitting at symmetry element in 
> non-primitive cells, for now I've found it in C2/c (iat03.pdb) and 
> Fdd2 (ta21.pdb) which I've attached. As far as I can tell this is not 
> unique to chimera, some programs handle this okay, many don't. You'll 
> see that in these two cases benzene molecules land outside of the cell 
> or fail to complete a pair.
>
> If I had to lobby for any particular ticket on your list it would be 
> #201. What I would add in way of description on that ticket is that 
> I'm not talking about using SHELX in Chimera. What I meant to say is 
> for Chimera to read a standard format CIF file containing the 
> reciprocal space transform of the real space electron density. The fft 
> routines to transform back to real space have been around forever and 
> are in most all modern languages. 
>
> All crystallography packages can write this type of file containing 
> h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in 
> degrees). This the preferred format for sending data to the PDB.
>
> I'm not looking to add a bunch of "stuff" to your already huge pile 
> but I thought most of this was already in the public domain. After 
> all, nothing is impossible for the guy that doesn't have to do it. 
> It's all easy and straightforward, right? ;0)
>
> As for the issue of reading the CIF, P21/n is a very common alternate 
> setting of P21/c and the PDB symmetry list does not contain it.
>
> Thanks again!!
> Cheers,
> Mike
>
> <<< 
> ------------------------------------------------------------------------>>>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
>
> <<< 
> ------------------------------------------------------------------------>>>
>
> On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote:
>
> Hi Mike,
>
>   I've fixed the unit cell dialog to handle inverting symmetries.  It 
> was a simple change.  Will be in tonight's daily builds.
>
>   We could have Unit Cell work with CIF files but that is an 
> enhancement that will have to compete for time with the hundreds of 
> other feature requests we're looking at.  My list of requests is here
>
>     http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests
>
> and Eric and other developer maintain their own off-line lists.  So 
> you need to make a good case.  It could be an easy task if our 
> third-party CIF file reader already parses the needed symmetry 
> operators.  If it does not provide those then it could be a 
> significant bit of work.
>
>     Tom
>
>
> -------- Original Message --------
> Subject: Re: [Chimera-users] Centro-symmetric space groups
> From: Michael Day
> To: Thomas Goddard
> Date: 9/1/09 1:19 PM
>> Hi Tom,
>>
>> Thanks.
>>
>> Another option you might consider is to have the Unit Cell tool work 
>> also with CIF files then only coordinate transformations are needed 
>> as the symmetry operators are included. An advantage is that if 
>> someone uses a non-standard setting of a space group the symmetry 
>> operators are still valid for the coordinates.
>>
>> Thanks for all your work. All of you on the Chimera team (Elaine, 
>> Eric and Greg) set the bar pretty high! My hats off to you.
>>
>> Cheers,
>> Mike
>>
>> <<< 
>> ------------------------------------------------------------------------>>>
>> Dr. Michael W. Day
>> Director - X-ray Crystallography Lab & Molecular Observatory
>> California Institute of Technology
>> Mail Code 139-74
>> Pasadena, CA 91125
>>
>> <<< 
>> ------------------------------------------------------------------------>>>
>>
>> On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote:
>>
>> Hi Mike,
>>
>>  Thanks for the suggestions.  The coordinate transformations are 
>> routine.  The trouble is that the Chimera Molecule C++ code takes the 
>> transformation matrix and orthonormalizes it to a proper rotation. 
>>  So the inversion operator of "P -1" gets changed to inverting x and 
>> y axes but not the z axis.  The orthonormalization is supposed to 
>> just fix tiny round-off transformation problems, like matrices read 
>> from a PDB file that have only 5 digits of precision.  Really we 
>> should be warning if a transformation is very far from a proper rotation.
>>
>>  I'll let you know when the problem is fixed in the daily builds.
>>
>> Tom
>>
>>
>> -------- Original Message --------
>> Subject: Re: [Chimera-users] Centro-symmetric space groups
>> From: Michael Day
>> To: Thomas Goddard
>> Date: 8/31/09 7:54 PM
>>
>>> Tom,
>>> Thanks again. Awesome!
>>> I suspect mirrors and therefore glide planes could be an issue as 
>>> you don't see them in proteins.
>>> I don't know what your overall strategy is for applying space group 
>>> operators but to avoid issues I would suggest;
>>> 1) deorthogonalize into crystallographic coordinates as fractions of 
>>> cell edge
>>> 2) apply symmetry operators in turn to the original set (x,y,z) to 
>>> get (x',y',z') for each operator
>>> 3) calculate the centroid for each equivalent set of coordinates 
>>> (x',y',z')
>>> 4) move centroids into unit cell as needed so they are x=0,1 y=0,1 
>>> and z=0,1
>>> I suspect you already know this but it never hurts to say it. My 
>>> students think I overstate the basics at times but it sure helps all 
>>> of us get on the same page.
>>> Cheers,
>>> Mike
>>> <<< 
>>> ------------------------------------------------------------------------>>>
>>> Dr. Michael W. Day
>>> Director - X-ray Crystallography Lab & Molecular Observatory
>>> California Institute of Technology
>>> Mail Code 139-74
>>> Pasadena, CA 91125
>>> >
>>> <<< 
>>> ------------------------------------------------------------------------>>>
>>> On 31 Aug, 2009, at 6:14 PM, Thomas Goddard wrote:
>>>> Hi Mike,
>>>>
>>>> Oops. The symmetries that invert coordinates don't work in the Unit 
>>>> Cell tool.  This is because it sets the transformation matrix 
>>>> (rotation and shift) for the asymmetric unit copies but it can only 
>>>> handle proper rotations.  Chimera is generally used for proteins 
>>>> which are handed (not symmetric under inversion) so such space 
>>>> groups generally don't occur for proteins.  But of course for small 
>>>> molecules they can.
>>>>
>>>> I'll fix this soon, maybe later this week.  I'll have to change 
>>>> atom coordinates instead of setting the transform matrix for the 
>>>> asymmetric unit copies.
>>>>
>>>> Tom

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/e3f48cab/attachment.html>

From goddard at cgl.ucsf.edu  Fri Sep  4 13:55:46 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 04 Sep 2009 13:55:46 -0700
Subject: [Chimera-users] Computing xray density from structure factors
In-Reply-To: <37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>
References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu>	<4A985D1E.300@cgl.ucsf.edu>
	<4A9C6A12.2090307@cgl.ucsf.edu> <4A9C7574.5080600@cgl.ucsf.edu>
	<5A13371E-67D1-46D1-8873-D6AF970662F3@caltech.edu>
	<4A9D4B74.2090908@cgl.ucsf.edu>
	<9AE9942C-32E2-48F5-A7D8-B5B90C38B3C5@caltech.edu>
	<4A9F13B9.1010300@cgl.ucsf.edu>
	<37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>
Message-ID: <4AA17ED2.5040900@cgl.ucsf.edu>

Hi Mike,

  If it is just a matter of computing a Fourier transform that is easy.  
Chimera already has libraries that does that.  The trouble will be 
parsing the CIF file.  Chimera reads molecular structure CIF and mmCIF 
files using a third party library called mmLib.  I don't know if mmLib 
will read the structure factors.  If you send me an example CIF file 
with structure factors I'll give it a try.

    Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Centro-symmetric space groups
From: Michael Day
To: Tom Goddard
Date: 9/4/09 12:41 PM
> Hi Tom,
>
> ...
>
> If I had to lobby for any particular ticket on your list it would be 
> #201. What I would add in way of description on that ticket is that 
> I'm not talking about using SHELX in Chimera. What I meant to say is 
> for Chimera to read a standard format CIF file containing the 
> reciprocal space transform of the real space electron density. The fft 
> routines to transform back to real space have been around forever and 
> are in most all modern languages. 
>
> All crystallography packages can write this type of file containing 
> h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in 
> degrees). This the preferred format for sending data to the PDB.
>
> I'm not looking to add a bunch of "stuff" to your already huge pile 
> but I thought most of this was already in the public domain. After 
> all, nothing is impossible for the guy that doesn't have to do it. 
> It's all easy and straightforward, right? ;0)
>
> As for the issue of reading the CIF, P21/n is a very common alternate 
> setting of P21/c and the PDB symmetry list does not contain it.
>
> Thanks again!!
> Cheers,
> Mike
>
> <<< 
> ------------------------------------------------------------------------>>>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
>
> <<< 
> ------------------------------------------------------------------------>>>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/8faa2d0c/attachment.html>

From mikeday at caltech.edu  Fri Sep  4 14:57:53 2009
From: mikeday at caltech.edu (Michael Day)
Date: Fri, 4 Sep 2009 14:57:53 -0700
Subject: [Chimera-users] Problem with benzenes split across crystal unit
	cell
In-Reply-To: <4AA17B99.8000700@cgl.ucsf.edu>
References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu>	<4A985D1E.300@cgl.ucsf.edu>
	<4A9C6A12.2090307@cgl.ucsf.edu> <4A9C7574.5080600@cgl.ucsf.edu>
	<5A13371E-67D1-46D1-8873-D6AF970662F3@caltech.edu>
	<4A9D4B74.2090908@cgl.ucsf.edu>
	<9AE9942C-32E2-48F5-A7D8-B5B90C38B3C5@caltech.edu>
	<4A9F13B9.1010300@cgl.ucsf.edu>
	<37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>
	<4AA17B99.8000700@cgl.ucsf.edu>
Message-ID: <D04E0D69-9ECD-4A5F-9555-A2CDCE3AAA2D@caltech.edu>

Hi Tom,

I've attached three screen shots corresponding to iat03.pdb, solvent  
only, no solvent and everything. If solvent is the only thing it gives  
different results than for the whole asymmetric unit.

I assume the change in unit cell will be in the next daily build?

The second problem is not really an issue because it helps force the  
idea that these half molecules really are half molecules. I didn't  
really expect Chimera to draw the bonds. The reason there are four  
atoms is that two of them sit on the 2-fold (through 0,y,1/4 or 0,-y, 
3/4 or 1/2, 1/2+y, 1/4 or 1/2, 1/2-y, 3/4). If the benzene sat on an  
inversion center then there would only be three of them.

Cheers,
Mike

<<<  
------------------------------------------------------------------------> 
 >>
Dr. Michael W. Day
Director - X-ray Crystallography Lab & Molecular Observatory
California Institute of Technology
Mail Code 139-74
Pasadena, CA 91125

<>< <>< <>< <>< <>< <>< <>< <>< <>< <><

Beckman Institute, Room 116
Phone: (626) 395-2734
Fax: (626) 449-4159
e-mail: mikeday at caltech.edu
<<<  
------------------------------------------------------------------------> 
 >>

On Sep 4, 2009, at 1:42 PM, Tom Goddard wrote:

Hi Mike,

   The Chimera unit cell dialog is behaving as expected in the cases  
where the asymmetric unit contains half of a benzene ring.  First,  
parts of the asymmetric unit are not moved relative to other parts of  
the asymmetric unit, so as you observe the half benzenes in asymmetric  
unit copies sometimes lie outside the unit cell.  All unit cell dialog
just puts the center of the asymmetric unit in the unit cell box.  A  
second problem is that a half benzene ring from one asymmetric unit  
will not be joined to a half benzene ring from another asymmetric  
unit.  They will line up perfectly but Chimera does not see bonds  
between the two halfs so for instance, selecting aromatic rings won't  
pick those up.

   I guess the first problem could be handled by moving each connected  
group of atoms so its center lies in the unit cell.  I think it could  
lead to undesired results.  For example a protein with a bound ligand  
might have the ligand outside the unit cell causing it to be moved to  
some other asymmetric unit's binding site.  The trouble with that is  
that the protein and ligand are part of one molecule model in Chimera,  
so now you have taken the ligand in that molecule and placed it with  
the protein of another copy of the molecule.  That may not be what you  
want.

   Another answer to the first problem, is that I added to the unit  
cell dialog the ability to make multiple asymmetric unit copies to  
fill multiple unit cells.  If you make several unit cells, then the  
half benzenes lying outside one unit cell do join up with the half  
benzenes from a different unit cell.

   If you were trying to make a figure and you didn't want half- 
benzenes floating around -- you could simply select them and delete  
them (Actions / Atoms / Delete).

   The second problem is harder.  Chimera could guess that the half- 
benzenes should be joined since they have exactly coincident atoms.   
(This relies on the strange inconsistency that the half-benzenes in  
the PDB files you sent contain 4 atoms instead of the expected 3  
atoms.  So it doesn't actually represent an asymmetric unit since  
there is an extra atom that will be duplicated in other asymmetric  
units.)  But Chimera can't join them because covalent bonds can't be  
formed between different molecule objects -- it would require making a  
new molecule to contain all the atoms.  Creating extra molecule models  
to join the half benzenes is possible but weird.

     Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Centro-symmetric space groups
From: Michael Day
To: Tom Goddard
Date: 9/4/09 12:41 PM
> Hi Tom,
>
> Thanks. It looks like the issue is mostly resolved.
>
> The is a problem with molecular units sitting at symmetry element in  
> non-primitive cells, for now I've found it in C2/c (iat03.pdb) and  
> Fdd2 (ta21.pdb) which I've attached. As far as I can tell this is  
> not unique to chimera, some programs handle this okay, many don't.  
> You'll see that in these two cases benzene molecules land outside of  
> the cell or fail to complete a pair.
>
> If I had to lobby for any particular ticket on your list it would be  
> #201. What I would add in way of description on that ticket is that  
> I'm not talking about using SHELX in Chimera. What I meant to say is  
> for Chimera to read a standard format CIF file containing the  
> reciprocal space transform of the real space electron density. The  
> fft routines to transform back to real space have been around  
> forever and are in most all modern languages.
>
> All crystallography packages can write this type of file containing  
> h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in  
> degrees). This the preferred format for sending data to the PDB.
>
> I'm not looking to add a bunch of "stuff" to your already huge pile  
> but I thought most of this was already in the public domain. After  
> all, nothing is impossible for the guy that doesn't have to do it.  
> It's all easy and straightforward, right? ;0)
>
> As for the issue of reading the CIF, P21/n is a very common  
> alternate setting of P21/c and the PDB symmetry list does not  
> contain it.
>
> Thanks again!!
> Cheers,
> Mike
>
> <<<  
> ------------------------------------------------------------------------> 
> >>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
>
> <<<  
> ------------------------------------------------------------------------> 
> >>
>
> On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote:
>
> Hi Mike,
>
>   I've fixed the unit cell dialog to handle inverting symmetries.   
> It was a simple change.  Will be in tonight's daily builds.
>
>   We could have Unit Cell work with CIF files but that is an  
> enhancement that will have to compete for time with the hundreds of  
> other feature requests we're looking at.  My list of requests is here
>
>     http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests
>
> and Eric and other developer maintain their own off-line lists.  So  
> you need to make a good case.  It could be an easy task if our third- 
> party CIF file reader already parses the needed symmetry operators.   
> If it does not provide those then it could be a significant bit of  
> work.
>
>     Tom
>
>
> -------- Original Message --------
> Subject: Re: [Chimera-users] Centro-symmetric space groups
> From: Michael Day
> To: Thomas Goddard
> Date: 9/1/09 1:19 PM
>> Hi Tom,
>>
>> Thanks.
>>
>> Another option you might consider is to have the Unit Cell tool  
>> work also with CIF files then only coordinate transformations are  
>> needed as the symmetry operators are included. An advantage is that  
>> if someone uses a non-standard setting of a space group the  
>> symmetry operators are still valid for the coordinates.
>>
>> Thanks for all your work. All of you on the Chimera team (Elaine,  
>> Eric and Greg) set the bar pretty high! My hats off to you.
>>
>> Cheers,
>> Mike
>>
>> <<<  
>> ------------------------------------------------------------------------> 
>> >>
>> Dr. Michael W. Day
>> Director - X-ray Crystallography Lab & Molecular Observatory
>> California Institute of Technology
>> Mail Code 139-74
>> Pasadena, CA 91125
>>
>> <<<  
>> ------------------------------------------------------------------------> 
>> >>
>>
>> On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote:
>>
>> Hi Mike,
>>
>>  Thanks for the suggestions.  The coordinate transformations are  
>> routine.  The trouble is that the Chimera Molecule C++ code takes  
>> the transformation matrix and orthonormalizes it to a proper  
>> rotation.  So the inversion operator of "P -1" gets changed to  
>> inverting x and y axes but not the z axis.  The orthonormalization  
>> is supposed to just fix tiny round-off transformation problems,  
>> like matrices read from a PDB file that have only 5 digits of  
>> precision.  Really we should be warning if a transformation is very  
>> far from a proper rotation.
>>
>>  I'll let you know when the problem is fixed in the daily builds.
>>
>>  Tom
>>
>>
>> -------- Original Message --------
>> Subject: Re: [Chimera-users] Centro-symmetric space groups
>> From: Michael Day
>> To: Thomas Goddard
>> Date: 8/31/09 7:54 PM
>>
>>> Tom,
>>> Thanks again. Awesome!
>>> I suspect mirrors and therefore glide planes could be an issue as  
>>> you don't see them in proteins.
>>> I don't know what your overall strategy is for applying space  
>>> group operators but to avoid issues I would suggest;
>>> 1) deorthogonalize into crystallographic coordinates as fractions  
>>> of cell edge
>>> 2) apply symmetry operators in turn to the original set (x,y,z) to  
>>> get (x',y',z') for each operator
>>> 3) calculate the centroid for each equivalent set of coordinates  
>>> (x',y',z')
>>> 4) move centroids into unit cell as needed so they are x=0,1 y=0,1  
>>> and z=0,1
>>> I suspect you already know this but it never hurts to say it. My  
>>> students think I overstate the basics at times but it sure helps  
>>> all of us get on the same page.
>>> Cheers,
>>> Mike
>>> <<<  
>>> ------------------------------------------------------------------------> 
>>> >>
>>> Dr. Michael W. Day
>>> Director - X-ray Crystallography Lab & Molecular Observatory
>>> California Institute of Technology
>>> Mail Code 139-74
>>> Pasadena, CA 91125
>>> >
>>> <<<  
>>> ------------------------------------------------------------------------> 
>>> >>
>>> On 31 Aug, 2009, at 6:14 PM, Thomas Goddard wrote:
>>>> Hi Mike,
>>>>
>>>> Oops. The symmetries that invert coordinates don't work in the  
>>>> Unit Cell tool.  This is because it sets the transformation  
>>>> matrix (rotation and shift) for the asymmetric unit copies but it  
>>>> can only handle proper rotations.  Chimera is generally used for  
>>>> proteins which are handed (not symmetric under inversion) so such  
>>>> space groups generally don't occur for proteins.  But of course  
>>>> for small molecules they can.
>>>>
>>>> I'll fix this soon, maybe later this week.  I'll have to change  
>>>> atom coordinates instead of setting the transform matrix for the  
>>>> asymmetric unit copies.
>>>>
>>>> Tom


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/11c9db19/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: iat03_withsolvent.jpg
Type: image/jpeg
Size: 63441 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/11c9db19/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: iat03_solventonly.jpg
Type: image/jpeg
Size: 14209 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/11c9db19/attachment-0001.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: iat03_nosolvent.jpg
Type: image/jpeg
Size: 53268 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/11c9db19/attachment-0002.jpg>

From mikeday at caltech.edu  Fri Sep  4 15:07:30 2009
From: mikeday at caltech.edu (Michael Day)
Date: Fri, 4 Sep 2009 15:07:30 -0700
Subject: [Chimera-users] Computing xray density from structure factors
In-Reply-To: <4AA17ED2.5040900@cgl.ucsf.edu>
References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu>	<4A985D1E.300@cgl.ucsf.edu>
	<4A9C6A12.2090307@cgl.ucsf.edu> <4A9C7574.5080600@cgl.ucsf.edu>
	<5A13371E-67D1-46D1-8873-D6AF970662F3@caltech.edu>
	<4A9D4B74.2090908@cgl.ucsf.edu>
	<9AE9942C-32E2-48F5-A7D8-B5B90C38B3C5@caltech.edu>
	<4A9F13B9.1010300@cgl.ucsf.edu>
	<37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>
	<4AA17ED2.5040900@cgl.ucsf.edu>
Message-ID: <3ABD3E6E-72C1-436B-A364-12E50D4D619C@caltech.edu>

Hi Tom,

Attached is the structure factor file corresponding to iat03.

Cheers,
Mike

<<<  
------------------------------------------------------------------------> 
 >>
Dr. Michael W. Day
Director - X-ray Crystallography Lab & Molecular Observatory
California Institute of Technology
Mail Code 139-74
Pasadena, CA 91125

<>< <>< <>< <>< <>< <>< <>< <>< <>< <><

Beckman Institute, Room 116
Phone: (626) 395-2734
Fax: (626) 449-4159
e-mail: mikeday at caltech.edu
<<<  
------------------------------------------------------------------------> 
 >>

On Sep 4, 2009, at 1:55 PM, Tom Goddard wrote:

Hi Mike,

   If it is just a matter of computing a Fourier transform that is  
easy.  Chimera already has libraries that does that.  The trouble will  
be parsing the CIF file.  Chimera reads molecular structure CIF and  
mmCIF files using a third party library called mmLib.  I don't know if  
mmLib will read the structure factors.  If you send me an example CIF  
file with structure factors I'll give it a try.

     Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Centro-symmetric space groups
From: Michael Day
To: Tom Goddard
Date: 9/4/09 12:41 PM
> Hi Tom,
>
> ...
>
> If I had to lobby for any particular ticket on your list it would be  
> #201. What I would add in way of description on that ticket is that  
> I'm not talking about using SHELX in Chimera. What I meant to say is  
> for Chimera to read a standard format CIF file containing the  
> reciprocal space transform of the real space electron density. The  
> fft routines to transform back to real space have been around  
> forever and are in most all modern languages.
>
> All crystallography packages can write this type of file containing  
> h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in  
> degrees). This the preferred format for sending data to the PDB.
>
> I'm not looking to add a bunch of "stuff" to your already huge pile  
> but I thought most of this was already in the public domain. After  
> all, nothing is impossible for the guy that doesn't have to do it.  
> It's all easy and straightforward, right? ;0)
>
> As for the issue of reading the CIF, P21/n is a very common  
> alternate setting of P21/c and the PDB symmetry list does not  
> contain it.
>
> Thanks again!!
> Cheers,
> Mike
>
> <<<  
> ------------------------------------------------------------------------> 
> >>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
>
> <<<  
> ------------------------------------------------------------------------> 
> >>


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/a6a5e978/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: iat03.fcf
Type: application/octet-stream
Size: 1358098 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/a6a5e978/attachment.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/a6a5e978/attachment-0001.html>

From goddard at cgl.ucsf.edu  Fri Sep  4 15:17:30 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 04 Sep 2009 15:17:30 -0700
Subject: [Chimera-users] Problem with benzenes split across crystal unit
 cell
In-Reply-To: <D04E0D69-9ECD-4A5F-9555-A2CDCE3AAA2D@caltech.edu>
References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu>	<4A985D1E.300@cgl.ucsf.edu>	<4A9C6A12.2090307@cgl.ucsf.edu>
	<4A9C7574.5080600@cgl.ucsf.edu>	<5A13371E-67D1-46D1-8873-D6AF970662F3@caltech.edu>	<4A9D4B74.2090908@cgl.ucsf.edu>	<9AE9942C-32E2-48F5-A7D8-B5B90C38B3C5@caltech.edu>	<4A9F13B9.1010300@cgl.ucsf.edu>	<37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu>	<4AA17B99.8000700@cgl.ucsf.edu>
	<D04E0D69-9ECD-4A5F-9555-A2CDCE3AAA2D@caltech.edu>
Message-ID: <4AA191FA.6030403@cgl.ucsf.edu>

Hi Mike,

  The reason the unit cell for the solvent-only model looks different is 
because the asymmetric units are positioned so that their geometric 
center (i.e. unweighted average atom position) lies within the unit cell 
box.  If you remove the non-solvent that changes the geometric center 
quite a bit for this structure and the translations to put the centers 
of the asymmetric units in the unit cell come out differently than for 
the all-atom model.

  My understanding of the term "asymmetric unit" is that copies will 
produce exactly the crystal lattice with no duplicate atoms.  The "half 
benzenes" having 4 atoms doesn't conform to this definition.  It is not 
important as you are not interested in joining the half benzenes.

  The unit cell dialog with the option to specify the number of cells 
along each axis will be in tonight's builds.

    Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Problem with benzenes split across crystal 
unit    cell
From: Michael Day
To: 'Chimera BB'
Date: 9/4/09 2:57 PM
> Hi Tom,
>
> I've attached three screen shots corresponding to iat03.pdb, solvent 
> only, no solvent and everything. If solvent is the only thing it gives 
> different results than for the whole asymmetric unit.
>
> I assume the change in unit cell will be in the next daily build?
>
> The second problem is not really an issue because it helps force the 
> idea that these half molecules really are half molecules. I didn't 
> really expect Chimera to draw the bonds. The reason there are four 
> atoms is that two of them sit on the 2-fold (through 0,y,1/4 or 
> 0,-y,3/4 or 1/2, 1/2+y, 1/4 or 1/2, 1/2-y, 3/4). If the benzene sat on 
> an inversion center then there would only be three of them.
>  
> Cheers,
> Mike
>
> <<< 
> ------------------------------------------------------------------------>>>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
>
> <<< 
> ------------------------------------------------------------------------>>>
>
> On Sep 4, 2009, at 1:42 PM, Tom Goddard wrote:
>
> Hi Mike,
>
>   The Chimera unit cell dialog is behaving as expected in the cases 
> where the asymmetric unit contains half of a benzene ring.  First, 
> parts of the asymmetric unit are not moved relative to other parts of 
> the asymmetric unit, so as you observe the half benzenes in asymmetric 
> unit copies sometimes lie outside the unit cell.  All unit cell dialog
> just puts the center of the asymmetric unit in the unit cell box.  A 
> second problem is that a half benzene ring from one asymmetric unit 
> will not be joined to a half benzene ring from another asymmetric 
> unit.  They will line up perfectly but Chimera does not see bonds 
> between the two halfs so for instance, selecting aromatic rings won't 
> pick those up.
>
>   I guess the first problem could be handled by moving each connected 
> group of atoms so its center lies in the unit cell.  I think it could 
> lead to undesired results.  For example a protein with a bound ligand 
> might have the ligand outside the unit cell causing it to be moved to 
> some other asymmetric unit's binding site.  The trouble with that is 
> that the protein and ligand are part of one molecule model in Chimera, 
> so now you have taken the ligand in that molecule and placed it with 
> the protein of another copy of the molecule.  That may not be what you 
> want.
>
>   Another answer to the first problem, is that I added to the unit 
> cell dialog the ability to make multiple asymmetric unit copies to 
> fill multiple unit cells.  If you make several unit cells, then the 
> half benzenes lying outside one unit cell do join up with the half 
> benzenes from a different unit cell.
>
>   If you were trying to make a figure and you didn't want 
> half-benzenes floating around -- you could simply select them and 
> delete them (Actions / Atoms / Delete).
>
>   The second problem is harder.  Chimera could guess that the 
> half-benzenes should be joined since they have exactly coincident 
> atoms.  (This relies on the strange inconsistency that the 
> half-benzenes in the PDB files you sent contain 4 atoms instead of the 
> expected 3 atoms.  So it doesn't actually represent an asymmetric unit 
> since there is an extra atom that will be duplicated in other 
> asymmetric units.)  But Chimera can't join them because covalent bonds 
> can't be formed between different molecule objects -- it would require 
> making a new molecule to contain all the atoms.  Creating extra 
> molecule models to join the half benzenes is possible but weird.
>
>     Tom
>
> -------- Original Message --------
> Subject: Re: [Chimera-users] Centro-symmetric space groups
> From: Michael Day
> To: Tom Goddard
> Date: 9/4/09 12:41 PM
>> Hi Tom,
>>
>> Thanks. It looks like the issue is mostly resolved. 
>>
>> The is a problem with molecular units sitting at symmetry element in 
>> non-primitive cells, for now I've found it in C2/c (iat03.pdb) and 
>> Fdd2 (ta21.pdb) which I've attached. As far as I can tell this is not 
>> unique to chimera, some programs handle this okay, many don't. You'll 
>> see that in these two cases benzene molecules land outside of the 
>> cell or fail to complete a pair.
>>
>> If I had to lobby for any particular ticket on your list it would be 
>> #201. What I would add in way of description on that ticket is that 
>> I'm not talking about using SHELX in Chimera. What I meant to say is 
>> for Chimera to read a standard format CIF file containing the 
>> reciprocal space transform of the real space electron density. The 
>> fft routines to transform back to real space have been around forever 
>> and are in most all modern languages. 
>>
>> All crystallography packages can write this type of file containing 
>> h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in 
>> degrees). This the preferred format for sending data to the PDB.
>>
>> I'm not looking to add a bunch of "stuff" to your already huge pile 
>> but I thought most of this was already in the public domain. After 
>> all, nothing is impossible for the guy that doesn't have to do it. 
>> It's all easy and straightforward, right? ;0)
>>
>> As for the issue of reading the CIF, P21/n is a very common alternate 
>> setting of P21/c and the PDB symmetry list does not contain it.
>>
>> Thanks again!!
>> Cheers,
>> Mike
>>
>> <<< 
>> ------------------------------------------------------------------------>>>
>> Dr. Michael W. Day
>> Director - X-ray Crystallography Lab & Molecular Observatory
>> California Institute of Technology
>> Mail Code 139-74
>> Pasadena, CA 91125
>>
>> <<< 
>> ------------------------------------------------------------------------>>>
>>
>> On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote:
>>
>> Hi Mike,
>>
>>   I've fixed the unit cell dialog to handle inverting symmetries.  It 
>> was a simple change.  Will be in tonight's daily builds.
>>
>>   We could have Unit Cell work with CIF files but that is an 
>> enhancement that will have to compete for time with the hundreds of 
>> other feature requests we're looking at.  My list of requests is here
>>
>>     http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests
>>
>> and Eric and other developer maintain their own off-line lists.  So 
>> you need to make a good case.  It could be an easy task if our 
>> third-party CIF file reader already parses the needed symmetry 
>> operators.  If it does not provide those then it could be a 
>> significant bit of work.
>>
>>     Tom
>>
>>
>> -------- Original Message --------
>> Subject: Re: [Chimera-users] Centro-symmetric space groups
>> From: Michael Day
>> To: Thomas Goddard
>> Date: 9/1/09 1:19 PM
>>> Hi Tom,
>>>
>>> Thanks.
>>>
>>> Another option you might consider is to have the Unit Cell tool work 
>>> also with CIF files then only coordinate transformations are needed 
>>> as the symmetry operators are included. An advantage is that if 
>>> someone uses a non-standard setting of a space group the symmetry 
>>> operators are still valid for the coordinates.
>>>
>>> Thanks for all your work. All of you on the Chimera team (Elaine, 
>>> Eric and Greg) set the bar pretty high! My hats off to you.
>>>
>>> Cheers,
>>> Mike
>>>
>>> <<< 
>>> ------------------------------------------------------------------------>>>
>>> Dr. Michael W. Day
>>> Director - X-ray Crystallography Lab & Molecular Observatory
>>> California Institute of Technology
>>> Mail Code 139-74
>>> Pasadena, CA 91125
>>>
>>> <<< 
>>> ------------------------------------------------------------------------>>>
>>>
>>> On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote:
>>>
>>> Hi Mike,
>>>
>>>  Thanks for the suggestions.  The coordinate transformations are 
>>> routine.  The trouble is that the Chimera Molecule C++ code takes 
>>> the transformation matrix and orthonormalizes it to a proper 
>>> rotation.  So the inversion operator of "P -1" gets changed to 
>>> inverting x and y axes but not the z axis.  The orthonormalization 
>>> is supposed to just fix tiny round-off transformation problems, like 
>>> matrices read from a PDB file that have only 5 digits of precision. 
>>>  Really we should be warning if a transformation is very far from a 
>>> proper rotation.
>>>
>>>  I'll let you know when the problem is fixed in the daily builds.
>>>
>>> Tom
>>>
>>>
>>> -------- Original Message --------
>>> Subject: Re: [Chimera-users] Centro-symmetric space groups
>>> From: Michael Day
>>> To: Thomas Goddard
>>> Date: 8/31/09 7:54 PM
>>>
>>>> Tom,
>>>> Thanks again. Awesome!
>>>> I suspect mirrors and therefore glide planes could be an issue as 
>>>> you don't see them in proteins.
>>>> I don't know what your overall strategy is for applying space group 
>>>> operators but to avoid issues I would suggest;
>>>> 1) deorthogonalize into crystallographic coordinates as fractions 
>>>> of cell edge
>>>> 2) apply symmetry operators in turn to the original set (x,y,z) to 
>>>> get (x',y',z') for each operator
>>>> 3) calculate the centroid for each equivalent set of coordinates 
>>>> (x',y',z')
>>>> 4) move centroids into unit cell as needed so they are x=0,1 y=0,1 
>>>> and z=0,1
>>>> I suspect you already know this but it never hurts to say it. My 
>>>> students think I overstate the basics at times but it sure helps 
>>>> all of us get on the same page.
>>>> Cheers,
>>>> Mike
>>>> <<< 
>>>> ------------------------------------------------------------------------>>>
>>>> Dr. Michael W. Day
>>>> Director - X-ray Crystallography Lab & Molecular Observatory
>>>> California Institute of Technology
>>>> Mail Code 139-74
>>>> Pasadena, CA 91125
>>>> >
>>>> <<< 
>>>> ------------------------------------------------------------------------>>>
>>>> On 31 Aug, 2009, at 6:14 PM, Thomas Goddard wrote:
>>>>> Hi Mike,
>>>>>
>>>>> Oops. The symmetries that invert coordinates don't work in the 
>>>>> Unit Cell tool.  This is because it sets the transformation matrix 
>>>>> (rotation and shift) for the asymmetric unit copies but it can 
>>>>> only handle proper rotations.  Chimera is generally used for 
>>>>> proteins which are handed (not symmetric under inversion) so such 
>>>>> space groups generally don't occur for proteins.  But of course 
>>>>> for small molecules they can.
>>>>>
>>>>> I'll fix this soon, maybe later this week.  I'll have to change 
>>>>> atom coordinates instead of setting the transform matrix for the 
>>>>> asymmetric unit copies.
>>>>>
>>>>> Tom
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>   

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/bc2a05de/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 63441 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/bc2a05de/attachment.jpe>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 14209 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/bc2a05de/attachment-0001.jpe>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 53268 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090904/bc2a05de/attachment-0002.jpe>

From bala.biophysics at gmail.com  Wed Sep  9 01:45:37 2009
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Wed, 9 Sep 2009 14:15:37 +0530
Subject: [Chimera-users] label
Message-ID: <288df32a0909090145t26194931ucd2c852460ea7f3a@mail.gmail.com>

Friends,

Is there any possiblity to move a 3D label along a particular axis in
chimera 1.4. I labelled the residues of a DNA molecule using rlabel command.
Some residue labels are displayed behind the base of the DNA. I tried to
change the lighting also but it vain.

Thanks,
Bala
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090909/a5e5126a/attachment.html>

From meng at cgl.ucsf.edu  Wed Sep  9 08:45:26 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 9 Sep 2009 08:45:26 -0700
Subject: [Chimera-users] label
In-Reply-To: <288df32a0909090145t26194931ucd2c852460ea7f3a@mail.gmail.com>
References: <288df32a0909090145t26194931ucd2c852460ea7f3a@mail.gmail.com>
Message-ID: <DBDF7E39-306E-4DA8-9744-878CED76143A@cgl.ucsf.edu>

Hi Bala,
Yes, in recent daily builds you can move the regular (3D) labels by  
specifying "offset" along with the command "label" or "rlabel," or by  
dragging the label with the mouse (default Ctrl-right button).   
Example command:

rlabel offset 0.5,1,2.2 nucleic acid

The numbers are x,y,z distances, so that command would offset the  
labels 0.5 angstrom to the right, 1 angstrom up, and 2.2 angstroms  
toward the viewer.

Documentation for the commands:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/label.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rlabel.html>

For using the mouse:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#othermouse>

I don't understand what you are saying about the lighting -- in my  
tests that is working fine, although it may not affect the labels very  
much.  If you think there is a problem, you should use "Help... Report  
a Bug" and include much more information, such as all the steps you  
tried, what happened, and how that was different than what you expected.

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

On Sep 9, 2009, at 1:45 AM, Bala subramanian wrote:

> Friends,
> Is there any possiblity to move a 3D label along a particular axis  
> in chimera 1.4. I labelled the residues of a DNA molecule using  
> rlabel command. Some residue labels are displayed behind the base of  
> the DNA. I tried to change the lighting also but it vain.
> Thanks,
> Bala


From pett at cgl.ucsf.edu  Wed Sep  9 11:46:10 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 9 Sep 2009 11:46:10 -0700
Subject: [Chimera-users] [chimera-dev] Suggestion: define selection name
	for startup chimera
In-Reply-To: <4291ada55fa5.4aa6b114@uab.es>
References: <4291ada55fa5.4aa6b114@uab.es>
Message-ID: <7D0242FD-77F7-40D1-902E-58A261CE562F@cgl.ucsf.edu>

On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote:

> In the new builts of chimera, you have change the initial  
> representation of the protein so that binding sites immediately  
> appear and the rest of the protein is in ribbon (which is a great  
> idea by the way). That means that you have a automatic analysis of  
> binding site recognition. I wonder if you couldn't include a  
> selection named "binding site" (or something similar), that would  
> appear as a named selection and that we could call at the early  
> beginning of the session.

Hi JD,
	I could.  I definitely wouldn't want to call it "binding site" since  
it includes waters and residues not necessarily involved in binding,  
not to mention the entire structure for small-molecule structures.   
It's also a misleading name for structures without ligand present --  
since their binding sites won't be selected by it.  FInally, it's also  
somewhat confusing as to what should happen if you open multiple  
structures over the course of a session.
	So it could be called "smart display atoms" I suppose.  If some other  
users thought it'd be useful I'd do that (anyone?).  In the interim,  
you can pretty easily create the selection yourself with these  
commands after opening the structure:

	sel @/display; namesel smart atoms; ~sel

You could alias that to something snappier. :-)

--Eric

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090909/8508dedd/attachment.html>

From waltfast at mail.utexas.edu  Wed Sep  9 11:50:16 2009
From: waltfast at mail.utexas.edu (Walter Fast)
Date: Wed, 09 Sep 2009 13:50:16 -0500
Subject: [Chimera-users] Can you morph a ligand
Message-ID: <C6CD6318.E77C%waltfast@mail.utexas.edu>

Hi!

Chimera is great - thanks again!  I use it all the time for research and
teaching.  I have a quick question:

We have two different product-bound structures, but when I morph between the
two we loose the active site metal ions and the active-site ligands.  Is
there a way to include these as well?

Thanks,

Walt

-- 
Walter Fast, Ph.D.
Associate Professor

The University of Texas at Austin
College of Pharmacy
The Division of Medicinal Chemistry
Phone:  (512) 232-4000
Fax:    (512) 232-2606
Lab:    (512) 471-5839
Email:  WaltFast at mail.utexas.edu
http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html





From meng at cgl.ucsf.edu  Wed Sep  9 12:47:11 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 9 Sep 2009 12:47:11 -0700
Subject: [Chimera-users] Can you morph a ligand
In-Reply-To: <C6CD6318.E77C%waltfast@mail.utexas.edu>
References: <C6CD6318.E77C%waltfast@mail.utexas.edu>
Message-ID: <8BFAD09D-4336-4E16-A409-05067D66E13F@cgl.ucsf.edu>

Hi Walt,
Thanks for the compliments -- and (even without the compliments) nice  
to hear from you!

The morph trajectory will only include the atoms that are in both  
input conformations.  They would have to be recognized as "atoms in  
common" in order to be retained.  I was going to say that perhaps this  
could be done with tricky renaming if the numbers of atoms were the  
same, but on second thought, that may not work.  I haven't tried it.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html 
 >

However, you can certainly still display those unique parts from the  
input models along with the trajectory, they just won't morph.   
Morphing with "hide conformations" turns off the model display of the  
input structures.  You could turn them back on with the "modeldisplay"  
command or by checking the "Shown" boxes in the Model Panel.   You  
would probably want to ~ribbon, ~disp the other parts of those input  
structures.

Say your input structures were models 0 and 1 and the morph trajectory  
is model 2.  To show (for example) the ligand and ions from model 1  
you could use the commands:

modeldisp #1
~ribbon #1
~disp #1
disp #1 & ligand
disp #1 & ions

In MD Movie, the tool that shows the morph trajectory, you could  
script it so that these atoms would appear at a certain frame.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame 
 >

If you are displaying ribbons, another thing you may want to include  
in a per-frame script is re-evaluating the secondary structure at each  
frame with the "ksdssp" command.  For default settings the command  
would simply be "ksdssp" without arguments.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

Other than using the MD Movie dialog, another option for playing back  
the trajectory is the "coordset" command.  This is not integrated with  
the scripting in the MD Movie dialog, however.  Basically the same  
things could be done, just in a different way, possibly with some  
combination of the "coordset" and "perframe" commands:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>

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

On Sep 9, 2009, at 11:50 AM, Walter Fast wrote:

> Hi!
> Chimera is great - thanks again!  I use it all the time for research  
> and
> teaching.  I have a quick question:
>
> We have two different product-bound structures, but when I morph  
> between the
> two we loose the active site metal ions and the active-site  
> ligands.  Is
> there a way to include these as well?
>
> Thanks,
> Walt
>


From JeanDidier.Marechal at uab.cat  Wed Sep  9 12:12:58 2009
From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal)
Date: Wed, 09 Sep 2009 21:12:58 +0200
Subject: [Chimera-users] [chimera-dev] Suggestion: define selection name
	for startup	chimera
Message-ID: <597694235cdb.4aa81a5a@uab.es>

Hi Eric,

"binding site" was an idea more than anything else but I realize from your e-mail that we don't really need. Strangely, though using @/display frequently I never thought about using it for selecting. 

Think I can do without the shortcut...
Sorry!

Cheers
JD


Dr. Jean-Didier Mar?chal
Lecturer
Computational Biotechnological Chemistry @ Transmet
Unitat de Qu?mica F?sica
Departament de Qu?mica
Universitat Aut?noma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: Eric Pettersen <pett at cgl.ucsf.edu>
Data: Dimecres, Setembre 9, 2009 8:46 pm
Assumpte: Re: [chimera-dev] Suggestion: define selection name for startup	chimera

> On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote:
> 
> > In the new builts of chimera, you have change the initial  
> > representation of the protein so that binding sites immediately  
> > appear and the rest of the protein is in ribbon (which is a 
> great  
> > idea by the way). That means that you have a automatic analysis 
> of  
> > binding site recognition. I wonder if you couldn't include a  
> > selection named "binding site" (or something similar), that 
> would  
> > appear as a named selection and that we could call at the early  
> > beginning of the session.
> 
> Hi JD,
> 	I could.  I definitely wouldn't want to call it "binding site" 
> since  
> it includes waters and residues not necessarily involved in 
> binding,  
> not to mention the entire structure for small-molecule structures. 
>  
> It's also a misleading name for structures without ligand present -
> -  
> since their binding sites won't be selected by it.  FInally, it's 
> also  
> somewhat confusing as to what should happen if you open multiple  
> structures over the course of a session.
> 	So it could be called "smart display atoms" I suppose.  If some 
> other  
> users thought it'd be useful I'd do that (anyone?).  In the 
> interim,  
> you can pretty easily create the selection yourself with these  
> commands after opening the structure:
> 
> 	sel @/display; namesel smart atoms; ~sel
> 
> You could alias that to something snappier. :-)
> 
> --Eric
> 
> 



From waltfast at mail.utexas.edu  Wed Sep  9 13:06:34 2009
From: waltfast at mail.utexas.edu (Walter Fast)
Date: Wed, 09 Sep 2009 15:06:34 -0500
Subject: [Chimera-users] Can you morph a ligand
In-Reply-To: <8BFAD09D-4336-4E16-A409-05067D66E13F@cgl.ucsf.edu>
Message-ID: <C6CD74FA.E787%waltfast@mail.utexas.edu>

Thanks Elaine, we'll give it a try.

For teaching, this Friday I'll use Chimera in lecture with red/cyan glasses
for everyone - from my view it looks just like an old 50s 3D movie audience!

You are always so helpful - Thanks!

Best,

Walt

-- 
Walter Fast, Ph.D.
Associate Professor

The University of Texas at Austin
College of Pharmacy
The Division of Medicinal Chemistry
Phone:  (512) 232-4000
Fax:    (512) 232-2606
Lab:    (512) 471-5839
Email:  WaltFast at mail.utexas.edu
http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html





On 9/9/09 2:47 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Hi Walt,
> Thanks for the compliments -- and (even without the compliments) nice
> to hear from you!
> 
> The morph trajectory will only include the atoms that are in both
> input conformations.  They would have to be recognized as "atoms in
> common" in order to be retained.  I was going to say that perhaps this
> could be done with tricky renaming if the numbers of atoms were the
> same, but on second thought, that may not work.  I haven't tried it.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
>> 
> 
> However, you can certainly still display those unique parts from the
> input models along with the trajectory, they just won't morph.
> Morphing with "hide conformations" turns off the model display of the
> input structures.  You could turn them back on with the "modeldisplay"
> command or by checking the "Shown" boxes in the Model Panel.   You
> would probably want to ~ribbon, ~disp the other parts of those input
> structures.
> 
> Say your input structures were models 0 and 1 and the morph trajectory
> is model 2.  To show (for example) the ligand and ions from model 1
> you could use the commands:
> 
> modeldisp #1
> ~ribbon #1
> ~disp #1
> disp #1 & ligand
> disp #1 & ions
> 
> In MD Movie, the tool that shows the morph trajectory, you could
> script it so that these atoms would appear at a certain frame.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per
> -frame 
>> 
> 
> If you are displaying ribbons, another thing you may want to include
> in a per-frame script is re-evaluating the secondary structure at each
> frame with the "ksdssp" command.  For default settings the command
> would simply be "ksdssp" without arguments.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> 
> Other than using the MD Movie dialog, another option for playing back
> the trajectory is the "coordset" command.  This is not integrated with
> the scripting in the MD Movie dialog, however.  Basically the same
> things could be done, just in a different way, possibly with some
> combination of the "coordset" and "perframe" commands:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Sep 9, 2009, at 11:50 AM, Walter Fast wrote:
> 
>> Hi!
>> Chimera is great - thanks again!  I use it all the time for research
>> and
>> teaching.  I have a quick question:
>> 
>> We have two different product-bound structures, but when I morph
>> between the
>> two we loose the active site metal ions and the active-site
>> ligands.  Is
>> there a way to include these as well?
>> 
>> Thanks,
>> Walt
>> 




From pett at cgl.ucsf.edu  Wed Sep  9 13:53:14 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 9 Sep 2009 13:53:14 -0700
Subject: [Chimera-users] [chimera-dev] suggestion for feature addition
	to chimera
In-Reply-To: <4ac540000909041709u4b02234av2006965d3605144a@mail.gmail.com>
References: <4ac540000909041709u4b02234av2006965d3605144a@mail.gmail.com>
Message-ID: <FD3D832F-1AAD-45C5-B6E3-D2C99E763E75@cgl.ucsf.edu>

On Sep 4, 2009, at 5:09 PM, Rocco Varela wrote:

> Hello,
>
> I have a small suggestion for an additional feature for Chimera that  
> I think would be useful.  I often look at structures of multiple  
> small molecules, some artificial and some real, and I noticed  
> something interesting with the way Chimera writes mol2 files.
>
> Here is Scenario 1:
>
> 1) I open a mol2 file that contains multiple molecules flagged as  
> "separate" MOLECULEs.
>
> 2) I save the loaded file as mol2 and select "a single file  
> [combined @MOLECULE section]" for the "Save multiple models in"  
> option.
>
>
> 3) After saving and reloading this new mol2 file that now has a  
> single MOLECULE section, all the "names" of the previous molecules  
> have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the  
> SUBSTRUCTURE section "UNK0" is used.
>
> It would useful if Chimera could name the components of the new  
> single molecule with the proper names.  I could easily write a  
> script to fix this after the fact but I thought it might be a useful  
> option for other people too?

Okay, I changed the Mol2 writer to use the model name instead of the  
residue type under the following conditions (only):

1) Combining models into a single @MOLECULE
2) All models are a single residue
3) Model names are unique and residue types are not

This change will be in tonight's build.

> Scenario 2:
>
> 1) Same as 1 above.
> 2) Now I want to save all the MOLECULEs in the file as separate mol2  
> files but with the proper "names" that are listed in the original  
> file loaded.  Currently the only option is to provide a common name  
> and to append the "model number".  It would be nice if we were  
> allowed to NOT provide a common name and allow it to name all the  
> files according to the molecule "names" not model numbers.

This seems like a reasonable enough request.  I will open a ticket in  
our Trac database for it, with you on the recipient list so you'll  
know when it gets done.  It's a tad more work than the preceding  
change because aside from adding code to support it, the interface has  
to be changed to allow for the option and the documentation has to be  
updated to describe it -- whereas the other change can sneak in under  
the radar. :-)

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090909/acae6e49/attachment.html>

From matthewd at bcm.tmc.edu  Thu Sep 10 20:33:04 2009
From: matthewd at bcm.tmc.edu (Dougherty, Matthew T.)
Date: Thu, 10 Sep 2009 22:33:04 -0500
Subject: [Chimera-users] Zalman 3D/stereo monitors
References: <web-20314134@cmpmail.ucsf.edu> <4A79C84C.9040201@cgl.ucsf.edu>
	<4A79DBFB.3060905@cgl.ucsf.edu>
Message-ID: <B5CA7C88183F884CB316B04DCD34384901346C12@BCMEVS13.ad.bcm.edu>

For stereo on the Mac I have been using the nvidia 4500 quadro card with a view sonic CRT, chimera with sequential stereo page flipped with an stereo graphics IR & glasses.  In this scenario I was under the impression that the video page flip rate is 100-120Hz

The new 3D LCDs (e.g., Zalman, Hyundai) create stereo through circular polarization that require passive glasses.  But these monitors are working at no greater than 75hz.

The bottom line question is: if I buy one of these units to replace my view sonic CRT, will it work on my Mac?
I get the impression reading the technical specs that it might only work with vista and directX.

Thanks, Matt
 
Matthew Dougherty
713-433-3849 
National Center for Macromolecular Imaging
Baylor College of Medicine/Houston Texas USA
=========================================================================
=========================================================================




-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu on behalf of Tom Ferrin
Sent: Wed 8/5/2009 2:22 PM
To: Miles Pufall
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Zalman 3D
 
Miles,
The other obvious thing is that you need a newer version of Chimera than 
the 1.3 production release.  Just grab any of the daily builds from 
www.cgl.ucsf.edu/chimera/download.html.  If you still have problems 
after trying Conrad's suggestion come on down to GH-N456 and check the 
graphics settings we are using with our Zalman 3D display.

--tom



Conrad Huang wrote:
> Do you have multisampling turned on?  Multisampling on different 
> graphics cards work differently.  Some cards use values from adjacent 
> rows for computing pixel values, and this really doesn't work when using 
>   row-interleaved stereo mode.
> 
> To check if multisampling is on, use the Tools->Viewing Control->Effects 
> menu item to bring up the Viewing panel; the multisampling option should 
> be the bottom-most one on the right.
> 
> Conrad
> 
> Miles Pufall wrote:
>> Hi Guys -
>>
>> I got a Zalman 3D - it's pretty cool with Coot and Pymol. 
>>  Your site says the row-interleaved stereo view under 
>> camera will work with this monitor, but I wasn't having 
>> much success.  Do you have some more detailed instructions 
>> for this particular monitor?
>>
>> I can drop by and visit with it, or you can come see me if 
>> you's like.  Thanks!
>> Miles in Yamamoto Lab
>> S574 Genentech Hall
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090910/04d32679/attachment.html>

From gregc at cgl.ucsf.edu  Fri Sep 11 10:38:52 2009
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 11 Sep 2009 10:38:52 -0700
Subject: [Chimera-users] Zalman 3D/stereo monitors
In-Reply-To: <B5CA7C88183F884CB316B04DCD34384901346C12@BCMEVS13.ad.bcm.edu>
References: <web-20314134@cmpmail.ucsf.edu> <4A79C84C.9040201@cgl.ucsf.edu>
	<4A79DBFB.3060905@cgl.ucsf.edu>
	<B5CA7C88183F884CB316B04DCD34384901346C12@BCMEVS13.ad.bcm.edu>
Message-ID: <Pine.CYG.4.58.0909110953350.4420@retief>

The bottom line is that the stereo on the new 3D LCDs will work with
chimera on newer and some older Macs (and almost all PCs).

Chimera has a special camera mode, "row interleaved stereo", that chimera
uses to generate an interlaced image that the Zalman (Hyundai, Miracube,
etc.) 3D LCD monitor displays in stereo, and the technique should work
with any graphics card on OS X, Windows, or Linux.  However, some older
Macs have a buggy graphics driver that Apple hasn't fixed (maybe won't
ever fix), so depending on what graphics card you have, it may or may not
work.  We are still in the process of figuring out what the exact bug is
and might have a workaround for the 1.4 release.

To see if it will work without buying a 3D LCD monitor, display a model in
chimera that has some depth, and switch the camera to "row interleaved
stereo".  Then on the left and right edges (where the left and right eye
images diverge the most), you should see a feathering effect where
alternating rows do not match up.  IF you see the effect, your setup will
work.

For completeness, if you have a workstation graphics card (ATI
FireGL/FirePro, NVidia Quadro FX) on your Windows or Linux computer, then
you can configure the graphics driver to do the row interleaving, and use
chimera's "sequential stereo" camera mode.  That will ensure that all of
chimera's graphical features work, in particular, silhouette edges don't
work in the "row interleaved stereo" camera mode.

	- Greg

On Thu, 10 Sep 2009, Dougherty, Matthew T. wrote:

> The new 3D LCDs (e.g., Zalman, Hyundai) create stereo through circular
> polarization that require passive glasses.  But these monitors are
> working at no greater than 75hz.
>
> The bottom line question is: if I buy one of these units to replace my
> view sonic CRT, will it work on my Mac? I get the impression reading the
> technical specs that it might only work with vista and directX.
>
> Thanks, Matt
>
> Matthew Dougherty
> 713-433-3849
> National Center for Macromolecular Imaging
> Baylor College of Medicine/Houston Texas USA
> =========================================================================
> =========================================================================
>
>
>
>
> -----Original Message-----
> From: chimera-users-bounces at cgl.ucsf.edu on behalf of Tom Ferrin
> Sent: Wed 8/5/2009 2:22 PM
> To: Miles Pufall
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Zalman 3D
>
> Miles,
> The other obvious thing is that you need a newer version of Chimera than
> the 1.3 production release.  Just grab any of the daily builds from
> www.cgl.ucsf.edu/chimera/download.html.  If you still have problems
> after trying Conrad's suggestion come on down to GH-N456 and check the
> graphics settings we are using with our Zalman 3D display.
>
> --tom
>
>
>
> Conrad Huang wrote:
> > Do you have multisampling turned on?  Multisampling on different
> > graphics cards work differently.  Some cards use values from adjacent
> > rows for computing pixel values, and this really doesn't work when using
> >   row-interleaved stereo mode.
> >
> > To check if multisampling is on, use the Tools->Viewing Control->Effects
> > menu item to bring up the Viewing panel; the multisampling option should
> > be the bottom-most one on the right.
> >
> > Conrad
> >
> > Miles Pufall wrote:
> >> Hi Guys -
> >>
> >> I got a Zalman 3D - it's pretty cool with Coot and Pymol.
> >>  Your site says the row-interleaved stereo view under
> >> camera will work with this monitor, but I wasn't having
> >> much success.  Do you have some more detailed instructions
> >> for this particular monitor?
> >>
> >> I can drop by and visit with it, or you can come see me if
> >> you's like.  Thanks!
> >> Miles in Yamamoto Lab
> >> S574 Genentech Hall
> >> _______________________________________________
> >> Chimera-users mailing list
> >> Chimera-users at cgl.ucsf.edu
> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
>


From kjwu at ucsd.edu  Fri Sep 11 16:04:34 2009
From: kjwu at ucsd.edu (Kevin Wu)
Date: Fri, 11 Sep 2009 16:04:34 -0700
Subject: [Chimera-users] RMSD supports symmetry?
Message-ID: <1571db7a0909111604n4b17e4e9tb2483276784ed452@mail.gmail.com>

Hi all,

I'm wondering if the RMSD function in Chimera will correctly calculate RMSD
when two molecules are compared. For example, if a benzene ring is flipped,
will the RMSD stay the same? Furthermore, how does Chimera do this
comparison?

Thanks!
Kevin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090911/591bfdbb/attachment.html>

From meng at cgl.ucsf.edu  Fri Sep 11 16:59:51 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 11 Sep 2009 16:59:51 -0700
Subject: [Chimera-users] RMSD supports symmetry?
In-Reply-To: <1571db7a0909111604n4b17e4e9tb2483276784ed452@mail.gmail.com>
References: <1571db7a0909111604n4b17e4e9tb2483276784ed452@mail.gmail.com>
Message-ID: <24964C2F-868E-4855-9844-174EF6B32D52@cgl.ucsf.edu>

Hi Kevin,
The "rmsd" and "match" commands do not figure out which atoms are  
chemically equivalent or symmetrically arranged and try all of the  
possibilities.  If the atoms are not specified by name in the command,  
they will be sorted by name and the sorted lists used for pairing.   
You can explicitly give the atom names in the command in whatever  
order you like, however.  For a ring that could be flipped, for  
example, you could issue two "rmsd" commands and then take the lower  
of the resulting RMSD values.  The commands including all the atom  
names could be rather ugly and long, but you could possibly minimize  
the pain with aliases if the names are stereotyped (say within  
standard PDB residues PHE and TYR).

More details on how these commands work:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

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


On Sep 11, 2009, at 4:04 PM, Kevin Wu wrote:

> Hi all,
> I'm wondering if the RMSD function in Chimera will correctly  
> calculate RMSD when two molecules are compared. For example, if a  
> benzene ring is flipped, will the RMSD stay the same? Furthermore,  
> how does Chimera do this comparison?
> Thanks!
> Kevin



From meng at cgl.ucsf.edu  Fri Sep 11 17:21:23 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 11 Sep 2009 17:21:23 -0700
Subject: [Chimera-users] RMSD supports symmetry?
In-Reply-To: <24964C2F-868E-4855-9844-174EF6B32D52@cgl.ucsf.edu>
References: <1571db7a0909111604n4b17e4e9tb2483276784ed452@mail.gmail.com>
	<24964C2F-868E-4855-9844-174EF6B32D52@cgl.ucsf.edu>
Message-ID: <B1DDE046-C2EA-4B93-96F4-548CEC444E5F@cgl.ucsf.edu>

I forgot to mention that I recommend using the Chimera snapshot from  
Aug 20, or even a newer daily build, because now commas in command- 
line atom specifications imply ordering -- in version 1.3, comma- 
separated models, residues, or atoms are not necessarily used in the  
order typed.  To specify atoms in a particular order in those older  
versions it is necessary to enter something like @ca at cb@cd1 at ce1  
whereas in the newer versions, @ca,cb,cd1,ce1 also specifies order.
Elaine

On Sep 11, 2009, at 4:59 PM, Elaine Meng wrote:

> Hi Kevin,
> The "rmsd" and "match" commands do not figure out which atoms are
> chemically equivalent or symmetrically arranged and try all of the
> possibilities.  If the atoms are not specified by name in the command,
> they will be sorted by name and the sorted lists used for pairing.
> You can explicitly give the atom names in the command in whatever
> order you like, however.  For a ring that could be flipped, for
> example, you could issue two "rmsd" commands and then take the lower
> of the resulting RMSD values.  The commands including all the atom
> names could be rather ugly and long, but you could possibly minimize
> the pain with aliases if the names are stereotyped (say within
> standard PDB residues PHE and TYR).
>
> More details on how these commands work:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Sep 11, 2009, at 4:04 PM, Kevin Wu wrote:
>
>> Hi all,
>> I'm wondering if the RMSD function in Chimera will correctly
>> calculate RMSD when two molecules are compared. For example, if a
>> benzene ring is flipped, will the RMSD stay the same? Furthermore,
>> how does Chimera do this comparison?
>> Thanks!
>> Kevin
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From jxc100+ at pitt.edu  Fri Sep 11 12:45:28 2009
From: jxc100+ at pitt.edu (James Conway)
Date: Fri, 11 Sep 2009 15:45:28 -0400
Subject: [Chimera-users] Zooming and orthographic projection mode
Message-ID: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>

I am struggling a bit and would be interested in any pointers from the  
knowledgeable folk here. It seems that I cannot use the mouse to get  
arbitrarily close to a surface in orthographic mode, but I can in  
perspective mode. In orthographic mode (Viewing -> Camera ->  
Projection) if I try to zoom in, the camera instead moves in until the  
front surface clips, but without much actually zooming. (True for the  
different "Center of Rotation" methods). In the Viewing -> Side View  
panel, the width of the field is represented by red lines that I  
cannot control but which I really want to move close together.

According to the help for the Viewing -> Camera panel:

     horizontal field of view (allowed range 1.0-179.0?) - how much
        perspective is used; does not affect the orthographic
        projection. The vertical field of view will change along
        with the horizontal field of view, but their exact
        relationship depends on the aspect ratio of the graphics
        window.

In fact, with the nightly builds of 1.4 this parameter *does* affect  
the orthographic projection, and does zoom in (or out) without  
clipping. Is there an updated explanation of how this works, and if it  
has changed since 1.3 as I seem to find? Am I looking in the wrong  
place for help on nightly builds?

Thanks,

James Conway

From goddard at cgl.ucsf.edu  Mon Sep 14 11:24:47 2009
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 14 Sep 2009 11:24:47 -0700
Subject: [Chimera-users] Zooming and orthographic projection mode
In-Reply-To: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
References: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
Message-ID: <4AAE8A6F.1070401@cgl.ucsf.edu>

Hi James,

   I see sometimes zooming in close in orthographic projection is not 
possible while it works fine in perspective in the current daily build. 
      That is a bug and I'll create a bug report.

   Zooming behavior has changed between Chimera 1.3 and 1.4.  Here are 
some details that may help you.  Zooming moves your view closer to a 
point at a certain depth in the center of the screen.  What depth?  In 
Chimera 1.3 the point to zoom in on was a hidden parameter (called 
"center") not shown in the Camera panel.  It was set when you used the 
focus, window, or center commands and when you first opened a model to 
the center of the bounding sphere.  In 1.4 I changed this to zoom in 
towards the center of rotation.  The default location for the center of 
rotation also changed from 1.3 to 1.4.  In 1.3 it was the center of the 
bounding sphere of the displayed models.  In 1.4 if you are zoomed in it 
rotates about the closest visible object in the center of the screen and 
if you are zoomed out it uses the older center of bounding sphere.  By 
"zoomed in" I mean that the bounding sphere of the displayed models is 
at least twice as big as the window width.  The result is that in 1.4 
daily builds you should zoom in on the closest visible object in the 
center of the window.  In 1.3 you would zoom in on a point that may be 
in front of the closest visible object (so you could never get close) or 
  may be behind the closest visible object (so you would collide with 
the object when zooming).  What I've described seems to be working 
correctly for perspective projection (the default projection mode). 
Something seems slightly wrong (but not too far wrong) for orthographic 
projection where you can't get as close as you want.

   Last week I fixed a bug that may be causing your problem.  It was a 
bug where the center of rotation point was not calculated correctly but 
was put in front of the closest visible object in the center.  That 
would prevent zooming in (in both perspective and orthographic 
projection).  It only occurred when multiple models were shown in 
certain spatial arrangements (a model in front had no object in center 
of window, but its center of bounding box was in front of closest 
visible object).  That was fixed September 8.

	Tom



-------- Original Message --------
Subject: [Chimera-users] Zooming and orthographic projection mode
From: James Conway
To: chimera-users
Date: 9/11/09 12:45 PM

> I am struggling a bit and would be interested in any pointers from the  
> knowledgeable folk here. It seems that I cannot use the mouse to get  
> arbitrarily close to a surface in orthographic mode, but I can in  
> perspective mode. In orthographic mode (Viewing -> Camera ->  
> Projection) if I try to zoom in, the camera instead moves in until the  
> front surface clips, but without much actually zooming. (True for the  
> different "Center of Rotation" methods). In the Viewing -> Side View  
> panel, the width of the field is represented by red lines that I  
> cannot control but which I really want to move close together.
> 
> According to the help for the Viewing -> Camera panel:
> 
>      horizontal field of view (allowed range 1.0-179.0?) - how much
>         perspective is used; does not affect the orthographic
>         projection. The vertical field of view will change along
>         with the horizontal field of view, but their exact
>         relationship depends on the aspect ratio of the graphics
>         window.
> 
> In fact, with the nightly builds of 1.4 this parameter *does* affect  
> the orthographic projection, and does zoom in (or out) without  
> clipping. Is there an updated explanation of how this works, and if it  
> has changed since 1.3 as I seem to find? Am I looking in the wrong  
> place for help on nightly builds?
> 
> Thanks,
> 
> James Conway
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


From Andrew.Waight at med.nyu.edu  Tue Sep 15 10:31:19 2009
From: Andrew.Waight at med.nyu.edu (Waight, Andrew)
Date: Tue, 15 Sep 2009 13:31:19 -0400
Subject: [Chimera-users] Exporting from Chimera to Blender - basic questions.
In-Reply-To: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
References: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
Message-ID: <3760BF13083CBF4F94D34D000ACFB3AB4FEBDCF1@MSGWSDCPMB04.nyumc.org>

Hello all, 

       I have recently solved the structure of a novel membrane protein, and have been using chimera quite a bit for my figures and analysis. In my free time I have been playing around with the 3D animation package Blender which I must say is a total blast, and makes fantastic movies and animations. However exporting from Chimera to Blender is a little tricky, in that when using VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well, the colors are not imported, and imported items such as cartoon helices seem to have totally random materials assigned to nonsensical segments (instead of materials assigned by chain for example) . Ideally I would like to perform and export the coloring operations using chimera because it's obviously an order of magnitude easier to select residues, chains and monomers with chimera. Or at least have the grouping of objects imported correctly. This is really just for fun so I'd thought I'd ask if anyone here has any experience with importing Chimera models into Blender. Of course I have no idea how VRML2 actually works. Thanks all.

                                                Andrew Waight	
                                                     Wang Lab
                    Skirball Institute of Biomedical Sciences
                                       NYU School of Medicine

P.S. Extra Credit: Does anyone have any idea how to export the calculated electrostatic surface into UV mapping for a Blender Object (the surface mesh obviously)? 

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================



From goddard at cgl.ucsf.edu  Tue Sep 15 23:03:03 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 15 Sep 2009 23:03:03 -0700
Subject: [Chimera-users] Exporting from Chimera to Blender - basic
	questions.
In-Reply-To: <3760BF13083CBF4F94D34D000ACFB3AB4FEBDCF1@MSGWSDCPMB04.nyumc.org>
References: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
	<3760BF13083CBF4F94D34D000ACFB3AB4FEBDCF1@MSGWSDCPMB04.nyumc.org>
Message-ID: <4AB07F97.6080108@cgl.ucsf.edu>

Hi Andrew,

  Chimera exports the surface vertex and individual atom and ribbon 
residue colors in the X3D and VRML output.   If you raytrace a scene 
with Chimera File / Save Image... it first exports X3D and then converts 
that X3D to input for POVray which does get all the colors right.  So I 
think your question calls for some expertise with Blender, to find out 
what color information it can handle when importing those files.  I 
don't know anything about Blender.

    Tom


-------- Original Message --------
Subject: [Chimera-users] Exporting from Chimera to Blender - basic 
questions.
From: Waight, Andrew <Andrew.Waight at med.nyu.edu>
To: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Date: 9/15/09 10:31 AM
> Hello all, 
>
>        I have recently solved the structure of a novel membrane protein, and have been using chimera quite a bit for my figures and analysis. In my free time I have been playing around with the 3D animation package Blender which I must say is a total blast, and makes fantastic movies and animations. However exporting from Chimera to Blender is a little tricky, in that when using VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well, the colors are not imported, and imported items such as cartoon helices seem to have totally random materials assigned to nonsensical segments (instead of materials assigned by chain for example) . Ideally I would like to perform and export the coloring operations using chimera because it's obviously an order of magnitude easier to select residues, chains and monomers with chimera. Or at least have the grouping of objects imported correctly. This is really just for fun so I'd thought I'd ask if anyone here has any experience !
>  with importing Chimera models into Blender. Of course I have no idea how VRML2 actually works. Thanks all.
>
>                                                 Andrew Waight	
>                                                      Wang Lab
>                     Skirball Institute of Biomedical Sciences
>                                        NYU School of Medicine
>
> P.S. Extra Credit: Does anyone have any idea how to export the calculated electrostatic surface into UV mapping for a Blender Object (the surface mesh obviously)? 
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>   




From mcgill at digizyme.com  Wed Sep 16 12:17:05 2009
From: mcgill at digizyme.com (Ga=?ISO-8859-1?B?6w==?=l McGill)
Date: Wed, 16 Sep 2009 15:17:05 -0400
Subject: [Chimera-users] Chimera-users Digest, Vol 77, Issue 16
In-Reply-To: <mailman.1.1253127602.1856005.chimera-users@cgl.ucsf.edu>
Message-ID: <C6D6B1F1.6E360%mcgill@digizyme.com>

Hi Andrew,

You might try contacting Monica Zoppe (in Pisa, Italy) - she has experience
importing PDB data into Blender.

Here is her site:
http://www.scivis.ifc.cnr.it/

Her e-mail:
Monica Zopp? <mzoppe at ifc.cnr.it>

Hope this is helpful,
-Gael.

-------------------------
Ga?l McGill, Ph.D.

Director of Molecular Visualization
Center for Molecular & Cellular Dynamics
Harvard Medical School
www.molecularmovies.org

President & CEO
Digizyme, Inc.
P.O. Box 1921
Brookline, MA 02446-1921

(617) 232-7676 (phone)
(617) 232-5623 (fax)
mcgill at digizyme.com
www.digizyme.com






On 9/16/09 3:00 PM, "chimera-users-request at cgl.ucsf.edu"
<chimera-users-request at cgl.ucsf.edu> wrote:

> Send Chimera-users mailing list submissions to
> chimera-users at cgl.ucsf.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> or, via email, send a message with subject or body 'help' to
> chimera-users-request at cgl.ucsf.edu
> 
> You can reach the person managing the list at
> chimera-users-owner at cgl.ucsf.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Exporting from Chimera to Blender - basic questions.
>       (Tom Goddard)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 15 Sep 2009 23:03:03 -0700
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Exporting from Chimera to Blender - basic
> questions.
> To: "Waight, Andrew" <Andrew.Waight at med.nyu.edu>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <4AB07F97.6080108 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi Andrew,
> 
>   Chimera exports the surface vertex and individual atom and ribbon
> residue colors in the X3D and VRML output.   If you raytrace a scene
> with Chimera File / Save Image... it first exports X3D and then converts
> that X3D to input for POVray which does get all the colors right.  So I
> think your question calls for some expertise with Blender, to find out
> what color information it can handle when importing those files.  I
> don't know anything about Blender.
> 
>     Tom
> 
> 
> -------- Original Message --------
> Subject: [Chimera-users] Exporting from Chimera to Blender - basic
> questions.
> From: Waight, Andrew <Andrew.Waight at med.nyu.edu>
> To: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Date: 9/15/09 10:31 AM
>> Hello all, 
>> 
>>        I have recently solved the structure of a novel membrane protein, and
>> have been using chimera quite a bit for my figures and analysis. In my free
>> time I have been playing around with the 3D animation package Blender which I
>> must say is a total blast, and makes fantastic movies and animations. However
>> exporting from Chimera to Blender is a little tricky, in that when using
>> VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well,
>> the colors are not imported, and imported items such as cartoon helices seem
>> to have totally random materials assigned to nonsensical segments (instead of
>> materials assigned by chain for example) . Ideally I would like to perform
>> and export the coloring operations using chimera because it's obviously an
>> order of magnitude easier to select residues, chains and monomers with
>> chimera. Or at least have the grouping of objects imported correctly. This is
>> really just for fun so I'd thought I'd ask if anyone here has any experienc!
>  e !
>>  with importing Chimera models into Blender. Of course I have no idea how
>> VRML2 actually works. Thanks all.
>> 
>>                                                 Andrew Waight 
>>                                                      Wang Lab
>>                     Skirball Institute of Biomedical Sciences
>>                                        NYU School of Medicine
>> 
>> P.S. Extra Credit: Does anyone have any idea how to export the calculated
>> electrostatic surface into UV mapping for a Blender Object (the surface mesh
>> obviously)? 
>> 
>> ------------------------------------------------------------
>> This email message, including any attachments, is for the sole use of the
>> intended recipient(s) and may contain information that is proprietary,
>> confidential, and exempt from disclosure under applicable law. Any
>> unauthorized review, use, disclosure, or distribution is prohibited. If you
>> have received this email in error please notify the sender by return email
>> and delete the original message. Please note, the recipient should check this
>> email and any attachments for the presence of viruses. The organization
>> accepts no liability for any damage caused by any virus transmitted by this
>> email.
>> =================================
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>   
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> End of Chimera-users Digest, Vol 77, Issue 16
> *********************************************




From gregc at cgl.ucsf.edu  Wed Sep 16 16:25:36 2009
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Wed, 16 Sep 2009 16:25:36 -0700 (PDT)
Subject: [Chimera-users] Exporting from Chimera to Blender - basic
 questions.
In-Reply-To: <3760BF13083CBF4F94D34D000ACFB3AB4FEBDCF1@MSGWSDCPMB04.nyumc.org>
References: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
	<3760BF13083CBF4F94D34D000ACFB3AB4FEBDCF1@MSGWSDCPMB04.nyumc.org>
Message-ID: <Pine.OSF.4.63.0909161425230.1681608@guanine.cgl.ucsf.edu>

On Tue, 15 Sep 2009, Waight, Andrew wrote:

> Hello all,
>
>       I have recently solved the structure of a novel membrane protein, 
> and have been using chimera quite a bit for my figures and analysis. In 
> my free time I have been playing around with the 3D animation package 
> Blender which I must say is a total blast, and makes fantastic movies 
> and animations. However exporting from Chimera to Blender is a little 
> tricky, in that when using VRML2 or X3D formats while the actual 3D 
> "mesh vertices" import quite well, the colors are not imported, and 
> imported items such as cartoon helices seem to have totally random 
> materials assigned to nonsensical segments (instead of materials 
> assigned by chain for example) . Ideally I would like to perform and 
> export the coloring operations using chimera because it's obviously an 
> order of magnitude easier to select residues, chains and monomers with 
> chimera. Or at least have the grouping of objects imported correctly. 
> This is really just for fun so I'd thought I'd ask if anyone here has 
> any experience ! with importing Chimera models into Blender. Of course I 
> have no idea how VRML2 actually works. Thanks all.
>
>                                                Andrew Waight
>                                                     Wang Lab
>                    Skirball Institute of Biomedical Sciences
>                                       NYU School of Medicine

This is more of a Blender question than a chimera question, in the sense 
that it is failing when you import the file into Blender, rather than when 
it is exported from chimera.  So normally, I would recommend that you ask 
in a Blender discussion group something like "Why does blender fail to 
import this VRML2/X3D file when it displays just fine in my browser?"

But the X3D importing that Blender 2.46b does is really bad.  It only 
tries to do the subset of X3D that corresponds to VRML97.  I can't tell 
why the surface colors are lost.

Matthieu Delanoe has a much much better X3D importer at 
<http://matthieu.delanoe.googlepages.com/blenderX3D.html>.  It needs to be 
updated for Python 2.6 by adding "# -*- coding: latin-1 -*-" as the second 
line to get it to work.  And again, the colors are lost even though there 
is code for them in the import script.

> P.S. Extra Credit: Does anyone have any idea how to export the 
> calculated electrostatic surface into UV mapping for a Blender Object 
> (the surface mesh obviously)?

If the surface has no holes (not true in general for molecular surfaces), 
then the mapping would be possible.  Not knowing Blender, can you say why 
you want the UV mapping?

 	-- Greg


From mschmid at bcm.edu  Wed Sep 16 13:27:21 2009
From: mschmid at bcm.edu (Michael Schmid)
Date: Wed, 16 Sep 2009 15:27:21 -0500
Subject: [Chimera-users] Fit MAP to MODEL
Message-ID: <C6D6B459.DE1F%mschmid@bcm.edu>

HI-
We are using chimera to fit xxx model into rho map. I'd like to fit rho map
into xxx model. That is, rotate and translate my map to coincide with a
fixed orientation of the model. Of course, then I can average rho1, rho2
etc. We can get around the "map" part of the "fit (button1) to map
(button2)" by running pdb2mrc to turn xxx model into xxx map. No problem.
But how do we write out the new rotated version of the rho map when we are
done fitting? Thanks.



From nhiroshi at berkeley.edu  Thu Sep 17 14:34:14 2009
From: nhiroshi at berkeley.edu (Hiroshi Nikaido)
Date: Thu, 17 Sep 2009 14:34:14 -0700
Subject: [Chimera-users] Cannot open pdb files with older versions of Chimera
Message-ID: <4AB2AB56.2010200@berkeley.edu>

Hello,
I sometimes have to use older versions of Chimera (1.2350 or 1.2422) 
because the more recent versions refuse to calculate surfaces for my 
protein.  They used to work fine in my old computer running windows xp, 
but with my new computer (still running xp) an attempt to try any pdb 
files on my hard disk produces an error message (TypeError: argument 1 
should be a str.).  How could this problem be fixed?  Your help will be 
greatly appreciated.
Hiroshi


From meng at cgl.ucsf.edu  Thu Sep 17 14:51:01 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 17 Sep 2009 14:51:01 -0700
Subject: [Chimera-users] Fit MAP to MODEL
In-Reply-To: <C6D6B459.DE1F%mschmid@bcm.edu>
References: <C6D6B459.DE1F%mschmid@bcm.edu>
Message-ID: <AC083DD1-A29B-442F-A0EA-608C75923283@cgl.ucsf.edu>

Hi Michael,
Saving a rotated map requires resampling it at new grid positions  
because none of the map formats include an option for specifying a  
rotation in the header.  However, with resampling there is some loss  
of resolution because interpolation is required to get the values at  
the new grid point locations.  That is why we normally recommend  
saving the rotated PDB instead when the goal is to have a PDB and map  
that fit together.

However, if you are going to average maps they may need to be  
resampled onto a consistent grid anyway.  Resampling a map onto the  
grid of another map can be done with "vop resample" as described here:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
vop.html#resample>

For example,
vop resample #0 onGrid #1 [other-options]

You would want to figure out which map's grid you want to do the final  
averaging on and use the fewest resamplings as possible to achieve  
that, for minimal loss of data quality.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:

> HI-
> We are using chimera to fit xxx model into rho map. I'd like to fit  
> rho map
> into xxx model. That is, rotate and translate my map to coincide  
> with a
> fixed orientation of the model. Of course, then I can average rho1,  
> rho2
> etc. We can get around the "map" part of the "fit (button1) to map
> (button2)" by running pdb2mrc to turn xxx model into xxx map. No  
> problem.
> But how do we write out the new rotated version of the rho map when  
> we are
> done fitting? Thanks.



From goddard at cgl.ucsf.edu  Thu Sep 17 15:47:31 2009
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 17 Sep 2009 15:47:31 -0700
Subject: [Chimera-users] Fit MAP to MODEL
In-Reply-To: <C6D6B459.DE1F%mschmid@bcm.edu>
References: <C6D6B459.DE1F%mschmid@bcm.edu>
Message-ID: <4AB2BC83.7020900@cgl.ucsf.edu>

Hi Michael,

   Elaine's suggestion to use the "vop resample" command is just what 
you need.  You can also create the map from the model using the Chimera 
molmap command which is equivalent to the EMAN pdb2mrc program (I looked 
at how the pdb2mrc code defines the parameters when I implemented 
molmap).  For example

	molmap #0 5

will create a 5 Angstrom resolution map from atomic model #0.

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html

You can also add different maps in Chimera using the "vop add" command 
and then if you want an average you can divide by the number of maps 
with the "vop scale" command.

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html

   Tom


-------- Original Message --------
Subject: [Chimera-users] Fit MAP to MODEL
From: Michael Schmid
To: chimera-users
Date: 9/16/09 1:27 PM

> HI-
> We are using chimera to fit xxx model into rho map. I'd like to fit rho map
> into xxx model. That is, rotate and translate my map to coincide with a
> fixed orientation of the model. Of course, then I can average rho1, rho2
> etc. We can get around the "map" part of the "fit (button1) to map
> (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem.
> But how do we write out the new rotated version of the rho map when we are
> done fitting? Thanks.
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


From pett at cgl.ucsf.edu  Thu Sep 17 15:47:51 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 17 Sep 2009 15:47:51 -0700
Subject: [Chimera-users] Cannot open pdb files with older versions of
	Chimera
In-Reply-To: <4AB2AB56.2010200@berkeley.edu>
References: <4AB2AB56.2010200@berkeley.edu>
Message-ID: <AB895E76-00B1-4001-9088-6846E7BDB85D@cgl.ucsf.edu>

Hi Hiroshi,
	It's too bad that you can't use a newer version since the handling of  
files/folders with non-ASCII characters in their names is much  
improved compared with old versions.  Also, I'm surprised that  
surfacing works in an old version but not a newer version.  For the  
most part surfacing is more robust in newer versions.  Also, we expect  
to have a new surface library available in a release Real Soon Now.
	My advice is to make sure that your file name has only ASCII  
characters in it, the folder it's in has only ASCII characters, as  
well as the folder above that, etc.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Sep 17, 2009, at 2:34 PM, Hiroshi Nikaido wrote:

> Hello,
> I sometimes have to use older versions of Chimera (1.2350 or 1.2422)
> because the more recent versions refuse to calculate surfaces for my
> protein.  They used to work fine in my old computer running windows  
> xp,
> but with my new computer (still running xp) an attempt to try any pdb
> files on my hard disk produces an error message (TypeError: argument 1
> should be a str.).  How could this problem be fixed?  Your help will  
> be
> greatly appreciated.
> Hiroshi
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090917/0f4a098a/attachment.html>

From meng at cgl.ucsf.edu  Thu Sep 17 15:53:54 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 17 Sep 2009 15:53:54 -0700
Subject: [Chimera-users] measurements to planes
In-Reply-To: <961ADDF1-B7B8-4D97-986A-95BFF7DAF18D@cgl.ucsf.edu>
References: <b5db3ac10809050911x5abc801bkc33667b975919939@mail.gmail.com>
	<961ADDF1-B7B8-4D97-986A-95BFF7DAF18D@cgl.ucsf.edu>
Message-ID: <77B9DCE5-1EA0-4EAF-B4E8-104A2952244D@cgl.ucsf.edu>

Hi Serge, Dave, Jim, et al.,

In recent daily builds of Chimera, you can now define planes and  
measure distances and angles to these objects.  The planes are shown  
as disks, and you can perform plane-plane, axis-plane, and atom-plane  
measurements, in addition to the axis-axis and atom-axis measurements  
we had earlier.

The tool formerly known as Axes is now "Axes/Planes," and we  
anticipate it will eventually include centroids.  The updated  
documentation isn't there today but should show up tomorrow at
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes 
 >
and the interface is mostly self-explanatory anyway.

Each of you had asked about planes at some point (possibly a while  
ago), in case you are wondering why I addressed this message to you. 8-)
Enjoy!
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



From smeliga at gmail.com  Mon Sep 21 07:02:10 2009
From: smeliga at gmail.com (Stefano Meliga)
Date: Mon, 21 Sep 2009 15:02:10 +0100
Subject: [Chimera-users] select many atoms by serial number
Message-ID: <4AB78762.6030209@gmail.com>

Hello,

I use a clustering algorithm to find partitions of proteins.
The output is the list of node indexes belonging to each cluster.

I would like to plot the clusters in different colours.

I successfully managed to select one atom in the graphical interface using:
 Select > Atom Specifier and typing @\serialNumber=n

Nevertheless, I need to select many atoms from a list of serial numbers, 
what can I do?

Cheers,

Stefano


From meng at cgl.ucsf.edu  Mon Sep 21 09:06:31 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 21 Sep 2009 09:06:31 -0700
Subject: [Chimera-users] select many atoms by serial number
In-Reply-To: <4AB78762.6030209@gmail.com>
References: <4AB78762.6030209@gmail.com>
Message-ID: <6EC7968E-C537-4410-A50A-DFD365647198@cgl.ucsf.edu>

Hi Stefano,
If you really want to specify atoms by serial number, and do it many  
times, you could do that with a Chimera command script, e.g.

color red @/serialNumber=4 or serialNumber=8 or serialNumber=10
color red @/serialNumber=20
label @/serialNumber=20
color goldenrod @/serialNumber<100 and serialNumber>20
color dodger blue @/serialNumber>100

These are the same commands that could be entered at the Command Line  
(show using Favorites... Command Line) -- you can test them there.   
Then just put all the commands you want into a text file, the Chimera  
command script.  Just opening the script (named *.com or *.cmd) would  
execute the commands.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors 
 >

However, there are many other ways to specify atoms besides serial  
number that might be easier:  atom name, residue name and number,  
values of other attributes such as element or bfactor, etc.

color red :25.a,43-57.a at ca
   (alpha-carbons of residues 25 and 43-57 in chain A)
color red @/bfactor>50
   (all atoms with B-factor >50)

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

Some other approaches that would give you more flexibility in coloring:

- create your own aliases, for example

alias clust1 :25.a,43-57.a
alias clust2 :1-24.a,1-40.b
color red clust1
color dodger blue clust2

- create your own new attribute, for example named "clusterNumber" and  
assign values 1,2, ... then just use commands like

color red @/clusterNumber=1

More on how to create your own attribute:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html 
 >

You can still use serial numbers when creating the aliases or defining  
a new attribute if that is the most convenient specifier.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 21, 2009, at 7:02 AM, Stefano Meliga wrote:

> Hello,
> I use a clustering algorithm to find partitions of proteins.
> The output is the list of node indexes belonging to each cluster.
>
> I would like to plot the clusters in different colours.
>
> I successfully managed to select one atom in the graphical interface  
> using:
> Select > Atom Specifier and typing @\serialNumber=n
>
> Nevertheless, I need to select many atoms from a list of serial  
> numbers,
> what can I do?
> Cheers,
> Stefano



From mschmid at bcm.edu  Thu Sep 17 15:35:41 2009
From: mschmid at bcm.edu (Michael Schmid)
Date: Thu, 17 Sep 2009 17:35:41 -0500
Subject: [Chimera-users] Fit MAP to MODEL
In-Reply-To: <AC083DD1-A29B-442F-A0EA-608C75923283@cgl.ucsf.edu>
Message-ID: <C6D823ED.DE89%mschmid@bcm.edu>

Hi-
We tried this 
vop resample #0 onGrid #14

And got 
Invalid model specifier syntax:"resample"

On 9/17/09 4:51 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Hi Michael,
> Saving a rotated map requires resampling it at new grid positions
> because none of the map formats include an option for specifying a
> rotation in the header.  However, with resampling there is some loss
> of resolution because interpolation is required to get the values at
> the new grid point locations.  That is why we normally recommend
> saving the rotated PDB instead when the goal is to have a PDB and map
> that fit together.
> 
> However, if you are going to average maps they may need to be
> resampled onto a consistent grid anyway.  Resampling a map onto the
> grid of another map can be done with "vop resample" as described here:
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
> vop.html#resample>
> 
> For example,
> vop resample #0 onGrid #1 [other-options]
> 
> You would want to figure out which map's grid you want to do the final
> averaging on and use the fewest resamplings as possible to achieve
> that, for minimal loss of data quality.  I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> On Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:
> 
>> HI-
>> We are using chimera to fit xxx model into rho map. I'd like to fit
>> rho map
>> into xxx model. That is, rotate and translate my map to coincide
>> with a
>> fixed orientation of the model. Of course, then I can average rho1,
>> rho2
>> etc. We can get around the "map" part of the "fit (button1) to map
>> (button2)" by running pdb2mrc to turn xxx model into xxx map. No
>> problem.
>> But how do we write out the new rotated version of the rho map when
>> we are
>> done fitting? Thanks.
> 



From sgorelsk at uottawa.ca  Fri Sep 18 08:38:14 2009
From: sgorelsk at uottawa.ca (Serge Gorelsky)
Date: Fri, 18 Sep 2009 11:38:14 -0400
Subject: [Chimera-users] measurements to planes
In-Reply-To: <77B9DCE5-1EA0-4EAF-B4E8-104A2952244D@cgl.ucsf.edu>
References: <b5db3ac10809050911x5abc801bkc33667b975919939@mail.gmail.com>
	<961ADDF1-B7B8-4D97-986A-95BFF7DAF18D@cgl.ucsf.edu>
	<77B9DCE5-1EA0-4EAF-B4E8-104A2952244D@cgl.ucsf.edu>
Message-ID: <b5db3ac10909180838r17911ca3h9f8cc19f9da30c31@mail.gmail.com>

Hello Elaine, thank you very much for the update! Serge

On Thu, Sep 17, 2009 at 6:53 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Serge, Dave, Jim, et al.,
>
> In recent daily builds of Chimera, you can now define planes and measure
> distances and angles to these objects. ?The planes are shown as disks, and
> you can perform plane-plane, axis-plane, and atom-plane measurements, in
> addition to the axis-axis and atom-axis measurements we had earlier.
>
> The tool formerly known as Axes is now "Axes/Planes," and we anticipate it
> will eventually include centroids. ?The updated documentation isn't there
> today but should show up tomorrow at
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> and the interface is mostly self-explanatory anyway.
>
> Each of you had asked about planes at some point (possibly a while ago), in
> case you are wondering why I addressed this message to you. 8-)
> Enjoy!
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>



-- 
Best regards,
  Serge Gorelsky


From meng at cgl.ucsf.edu  Mon Sep 21 10:21:37 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 21 Sep 2009 10:21:37 -0700
Subject: [Chimera-users] Fit MAP to MODEL
In-Reply-To: <C6D823ED.DE89%mschmid@bcm.edu>
References: <C6D823ED.DE89%mschmid@bcm.edu>
Message-ID: <9AD40F07-E495-4115-87BE-54770C4AED36@cgl.ucsf.edu>

Hi Michael,
It depends on what version you are using.  What I showed was for newer  
versions.  If you are using an older version the "resample" goes after  
the model number.  To see the documentation for the version you are  
using, use the command

help vop

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

On Sep 17, 2009, at 3:35 PM, Michael Schmid wrote:

> Hi-
> We tried this
> vop resample #0 onGrid #14
>
> And got
> Invalid model specifier syntax:"resample"
>
> On 9/17/09 4:51 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>
>> Hi Michael,
>> Saving a rotated map requires resampling it at new grid positions
>> because none of the map formats include an option for specifying a
>> rotation in the header.  However, with resampling there is some loss
>> of resolution because interpolation is required to get the values at
>> the new grid point locations.  That is why we normally recommend
>> saving the rotated PDB instead when the goal is to have a PDB and map
>> that fit together.
>>
>> However, if you are going to average maps they may need to be
>> resampled onto a consistent grid anyway.  Resampling a map onto the
>> grid of another map can be done with "vop resample" as described  
>> here:
>>
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
>> vop.html#resample>
>>
>> For example,
>> vop resample #0 onGrid #1 [other-options]
>>
>> You would want to figure out which map's grid you want to do the  
>> final
>> averaging on and use the fewest resamplings as possible to achieve
>> that, for minimal loss of data quality.  I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>> On Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:
>>
>>> HI-
>>> We are using chimera to fit xxx model into rho map. I'd like to fit
>>> rho map
>>> into xxx model. That is, rotate and translate my map to coincide
>>> with a
>>> fixed orientation of the model. Of course, then I can average rho1,
>>> rho2
>>> etc. We can get around the "map" part of the "fit (button1) to map
>>> (button2)" by running pdb2mrc to turn xxx model into xxx map. No
>>> problem.
>>> But how do we write out the new rotated version of the rho map when
>>> we are
>>> done fitting? Thanks.
>>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From xarana at gmx.net  Mon Sep 21 10:34:08 2009
From: xarana at gmx.net (Xarana)
Date: Mon, 21 Sep 2009 19:34:08 +0200
Subject: [Chimera-users] .sld (MOLCAD,
	Sybyl 8.0) file import or visualisation of an inner surface (of a
	protein) in Chimera
Message-ID: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>

Hi,

My interest is a 4 helix protein which has a cavity inside. A colleague
generated with a 1,4 Angstr?m probe this ?inner surface? with Sybyl for me
and exported the surface as .sld file. Can I import this file into chimera
somehow? Alternatively, can I generate such a surface with chimera? 

My knowledge of protein visualization is limited and I am very thankful for
any help

Thank you very much in advance.

Best Wishes

Natalie

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090921/2368688d/attachment.html>

From meng at cgl.ucsf.edu  Mon Sep 21 13:27:42 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 21 Sep 2009 13:27:42 -0700
Subject: [Chimera-users] .sld (MOLCAD,
	Sybyl 8.0) file import or visualisation of an inner surface (of a
	protein) in Chimera
In-Reply-To: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>
References: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>
Message-ID: <3AE4EBAE-67B9-4F25-A757-D4938BAF705B@cgl.ucsf.edu>

Hi Natalie,
Chimera does not know the *.sld file type.  Can SYBYL save this file  
in a format Chimera knows, such as VRML?
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>

If not, you could try opening the structure (PDB or Mol2 file) in  
Chimera, instead of the surface file, and have Chimera calculate the  
surface.

In Chimera, you can display the surface with "Actions... Surface...  
show".  The default in Chimera is also to use a 1.4 Angstrom probe.   
That would generate both the inner and outer surfaces, which you could  
see by slicing the structure in the Side View (under Favorites menu).  
There will probably be differences in the surface due to the different  
default atomic radii in Chimera and SYBYL, but I would not expect them  
to be large.

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


On Sep 21, 2009, at 10:34 AM, Xarana wrote:

> Hi,
> My interest is a 4 helix protein which has a cavity inside. A  
> colleague generated with a 1,4 Angstr?m probe this ?inner surface?  
> with Sybyl for me and exported the surface as .sld file. Can I  
> import this file into chimera somehow? Alternatively, can I generate  
> such a surface with chimera?
> My knowledge of protein visualization is limited and I am very  
> thankful for any help
> Thank you very much in advance.
> Best Wishes
> Natalie


From pett at cgl.ucsf.edu  Mon Sep 21 14:11:03 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 21 Sep 2009 14:11:03 -0700
Subject: [Chimera-users] [chimera-dev] select opt
In-Reply-To: <20090921142516.M40592@klingon.uab.es>
References: <20090921142516.M40592@klingon.uab.es>
Message-ID: <1C257263-D84D-4670-B605-07683AA2D08C@cgl.ucsf.edu>

On Sep 21, 2009, at 7:27 AM, Victor Mu??oz wrote:

> I'd like to know if there's a way to select the select mode "append"  
> using the
> command line instead of the visual interface.

Hi Victor,
	There isn't a way to do that, but it typically isn't necessary.  The  
"|" and "&" characters perform union and intersection operations  
respectively.  So for example you can add all LYS residues to the  
current selection with:

	sel sel | : LYS

or you could intersect the current selection with LYS residues with:

	sel sel & :LYS

If you really need to change the mode for some reason, let me know  
what that reason is and maybe we can add something.

--Eric
                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

P.S. The "|" character is a vertical bar, not a capital i, in case  
that's not clear in the font you're using.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090921/119cfbb2/attachment.html>

From gregc at cgl.ucsf.edu  Mon Sep 21 16:06:13 2009
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 21 Sep 2009 16:06:13 -0700 (PDT)
Subject: [Chimera-users] Exporting from Chimera to Blender - basic
 questions.
In-Reply-To: <Pine.OSF.4.63.0909161425230.1681608@guanine.cgl.ucsf.edu>
References: <8DC852AC-FA61-4117-8F55-F1E16CA4B0BB@pitt.edu>
	<3760BF13083CBF4F94D34D000ACFB3AB4FEBDCF1@MSGWSDCPMB04.nyumc.org>
	<Pine.OSF.4.63.0909161425230.1681608@guanine.cgl.ucsf.edu>
Message-ID: <Pine.OSF.4.63.0909211601570.2059698@guanine.cgl.ucsf.edu>

Turns out Matthieu Delanoe's X3D importer for Blender does get the correct 
colors from chimera.  Not being a Blender user, I didn't realize I had to 
switch the Viewport Shading mode from Solid to Textured to see the colors.

 	- Greg

On Wed, 16 Sep 2009, Greg Couch wrote:

> On Tue, 15 Sep 2009, Waight, Andrew wrote:
>
>> Hello all,
>>
>>       I have recently solved the structure of a novel membrane protein,
>> and have been using chimera quite a bit for my figures and analysis. In
>> my free time I have been playing around with the 3D animation package
>> Blender which I must say is a total blast, and makes fantastic movies
>> and animations. However exporting from Chimera to Blender is a little
>> tricky, in that when using VRML2 or X3D formats while the actual 3D
>> "mesh vertices" import quite well, the colors are not imported, and
>> imported items such as cartoon helices seem to have totally random
>> materials assigned to nonsensical segments (instead of materials
>> assigned by chain for example) . Ideally I would like to perform and
>> export the coloring operations using chimera because it's obviously an
>> order of magnitude easier to select residues, chains and monomers with
>> chimera. Or at least have the grouping of objects imported correctly.
>> This is really just for fun so I'd thought I'd ask if anyone here has
>> any experience ! with importing Chimera models into Blender. Of course I
>> have no idea how VRML2 actually works. Thanks all.
>>
>>                                                Andrew Waight
>>                                                     Wang Lab
>>                    Skirball Institute of Biomedical Sciences
>>                                       NYU School of Medicine
>
> This is more of a Blender question than a chimera question, in the sense
> that it is failing when you import the file into Blender, rather than when
> it is exported from chimera.  So normally, I would recommend that you ask
> in a Blender discussion group something like "Why does blender fail to
> import this VRML2/X3D file when it displays just fine in my browser?"
>
> But the X3D importing that Blender 2.46b does is really bad.  It only
> tries to do the subset of X3D that corresponds to VRML97.  I can't tell
> why the surface colors are lost.
>
> Matthieu Delanoe has a much much better X3D importer at
> <http://matthieu.delanoe.googlepages.com/blenderX3D.html>.  It needs to be
> updated for Python 2.6 by adding "# -*- coding: latin-1 -*-" as the second
> line to get it to work.  And again, the colors are lost even though there
> is code for them in the import script.
>
>> P.S. Extra Credit: Does anyone have any idea how to export the
>> calculated electrostatic surface into UV mapping for a Blender Object
>> (the surface mesh obviously)?
>
> If the surface has no holes (not true in general for molecular surfaces),
> then the mapping would be possible.  Not knowing Blender, can you say why
> you want the UV mapping?
>
> 	-- Greg
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


From David_Belnap at byu.edu  Mon Sep 21 16:07:48 2009
From: David_Belnap at byu.edu (David Belnap)
Date: Mon, 21 Sep 2009 17:07:48 -0600
Subject: [Chimera-users] Write out phi/psi angles
Message-ID: <1F33FAD1-4935-444F-B9DA-EEB10835BA47@byu.edu>

I've read on the archived lists that Chimera does not have a  
Ramachandran plot viewer.  I found phi/psi angles by selecting  
"Actions", "Inspect", then inspecting "Residue".  Can I output the phi/ 
psi angles to a text file?  If so, how do I write out that information?

Thanks.

David

============================================
  David M. Belnap
  Department of Chemistry and Biochemistry
  Brigham Young University
  Provo, Utah 84602  USA

  Phone:  801-422-9163
  FAX:      801-422-0153
  David.Belnap at byu.edu
============================================





From pett at cgl.ucsf.edu  Mon Sep 21 16:16:55 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 21 Sep 2009 16:16:55 -0700
Subject: [Chimera-users] Write out phi/psi angles
In-Reply-To: <1F33FAD1-4935-444F-B9DA-EEB10835BA47@byu.edu>
References: <1F33FAD1-4935-444F-B9DA-EEB10835BA47@byu.edu>
Message-ID: <1A7BD37A-7D43-4893-AB60-8B7DC8389161@cgl.ucsf.edu>

On Sep 21, 2009, at 4:07 PM, David Belnap wrote:

> I've read on the archived lists that Chimera does not have a
> Ramachandran plot viewer.  I found phi/psi angles by selecting
> "Actions", "Inspect", then inspecting "Residue".  Can I output the  
> phi/
> psi angles to a text file?  If so, how do I write out that  
> information?

Hi David,
	Using the Render By Attribute tool, you can write out any attribute  
value (in Chimera phi/psi angles are treated as attributes of  
residues) using that tool's File->Save Attributes menu entry.  You  
need to select the attribute in the tool first.  The save dialog will  
allow you to restrict the save to the current selection if you like.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090921/0d59b564/attachment.html>

From xarana at gmx.net  Tue Sep 22 02:07:12 2009
From: xarana at gmx.net (Xarana)
Date: Tue, 22 Sep 2009 11:07:12 +0200
Subject: [Chimera-users] Thanks for the help,
	Is it possible to only show the "inner surface"?
In-Reply-To: <3AE4EBAE-67B9-4F25-A757-D4938BAF705B@cgl.ucsf.edu>
References: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>
	<3AE4EBAE-67B9-4F25-A757-D4938BAF705B@cgl.ucsf.edu>
Message-ID: <FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4>

Hi Elaine,
Thank you very much for your quick help. That really helped a lot and the
differences are small. One last question: 

Is there a possibility to only show this "inner surface" without the outer
one for more clarity? I have to compare in 10 different structures (NMR
solved) the extent of this cavities. And sadly SYBYL is not able to save as
any other file format. 

Best wishes,
Natalie Bordag
PhD student

-----Urspr?ngliche Nachricht-----
Von: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Gesendet: Montag, 21. September 2009 22:28
An: Xarana
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or
visualisation of an inner surface (of a protein) in Chimera

Hi Natalie,
Chimera does not know the *.sld file type.  Can SYBYL save this file  
in a format Chimera knows, such as VRML?
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>

If not, you could try opening the structure (PDB or Mol2 file) in  
Chimera, instead of the surface file, and have Chimera calculate the  
surface.

In Chimera, you can display the surface with "Actions... Surface...  
show".  The default in Chimera is also to use a 1.4 Angstrom probe.   
That would generate both the inner and outer surfaces, which you could  
see by slicing the structure in the Side View (under Favorites menu).  
There will probably be differences in the surface due to the different  
default atomic radii in Chimera and SYBYL, but I would not expect them  
to be large.

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


On Sep 21, 2009, at 10:34 AM, Xarana wrote:

> Hi,
> My interest is a 4 helix protein which has a cavity inside. A  
> colleague generated with a 1,4 Angstr?m probe this ?inner surface?  
> with Sybyl for me and exported the surface as .sld file. Can I  
> import this file into chimera somehow? Alternatively, can I generate  
> such a surface with chimera?
> My knowledge of protein visualization is limited and I am very  
> thankful for any help
> Thank you very much in advance.
> Best Wishes
> Natalie
No virus found in this incoming message.
Checked by AVG - www.avg.com 
Version: 8.5.409 / Virus Database: 270.13.110/2385 - Release Date: 09/20/09
17:51:00



From wuxue at nankai.edu.cn  Tue Sep 22 04:18:56 2009
From: wuxue at nankai.edu.cn (=?gb2312?B?zuLRqQ==?=)
Date: Tue, 22 Sep 2009 19:18:56 +0800
Subject: [Chimera-users] question about Chimera
Message-ID: <PZKKJOTJDIRSKZXHZLPEQAONCMKF.wuxue@nankai.edu.cn>

Dear colleague:
    I have  a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree".
   I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. 
The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond.
  If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction?
   Sincerly Yours
   WU Xue
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090922/a70f5d2b/attachment.html>

From goddard at cgl.ucsf.edu  Tue Sep 22 09:51:06 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 22 Sep 2009 09:51:06 -0700
Subject: [Chimera-users] Grouping models
In-Reply-To: <A2098225-3D9F-4105-9111-9AA5A5AF8F2F@imp.ac.at>
References: <200711221814.lAMIEKoV1997174@guanine.cgl.ucsf.edu>
	<60d48882a9db6f3e7021da308572fbe8@cgl.ucsf.edu>
	<7ACB4DFC-6924-4007-9173-49EA649B8DFD@imp.univie.ac.at>
	<544FE106-F794-4DEA-9C3E-C5586B80A19B@cgl.ucsf.edu>
	<1E6148FED8920445AC79AEB51579E5230576DF2B@EXCHSRV.imp.univie.ac.at>
	<49402860.1010509@cgl.ucsf.edu>
	<A2098225-3D9F-4105-9111-9AA5A5AF8F2F@imp.ac.at>
Message-ID: <4AB9007A.2060403@cgl.ucsf.edu>

-------- Original Message --------
From: Thomas C. Marlovits
To: Tom Goddard
Date: 9/22/09 2:04 AM
> HI Tom,
>
> I was wondering, whether one can "group" a few models in chimera.  At 
> the moment, I have more than 40 models open simultaneously,  some of 
> which I would like to group in order to make coloring, selection, etc 
> ... more easily.   It might be that the feature is present, but 
> couldn't spot it so far.
> The other thing that I would appreciate, if there is a simple way to 
> assign the model nr manually (at the moment it is done automatically, 
> and it appears that the order is somewhat random ...)
> Best,
> Tx,
> -T.
>
Hi Thomas,

  You can used "named selections" to give a short name to several models 
or to any combination of selected items.  Use menu entry

    Select / Name Selection...

You can use the names in Chimera commands or use the "Select / Named 
Selection / name" menu entry.  I don't know of a command to name a 
selection.  Is there such a command (other Chimera developers)?

  You can set the model number if you open your models with a command, 
for example,

    open 5 twisty.pdb

to open a model as model number 5.  After the model number has been 
assigned it unfortunately cannot be changed.

    Tom




From goddard at cgl.ucsf.edu  Tue Sep 22 10:10:32 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 22 Sep 2009 10:10:32 -0700
Subject: [Chimera-users] Show only molecular pocket surfaces
In-Reply-To: <FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4>
References: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>	<3AE4EBAE-67B9-4F25-A757-D4938BAF705B@cgl.ucsf.edu>
	<FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4>
Message-ID: <4AB90508.20603@cgl.ucsf.edu>

Hi Natalie,

  It is unfortunately a bit tricky to show just the inner pocket surface 
of a molecule in Chimera.  Here's one way.  Create the surface then use 
the following command to make it possible to select the separate 
connected pieces of the surface:

    ac Sc

(This runs the keyboard shortcut "Sc" - split connected pieces of 
selected surface.)  Now select the outer surface with the mouse 
(ctrl-click) and use a command to delete it:

    ac Ds

(Keyboard shortcut "Ds" - delete selected surface pieces.)

  These steps that change the molecular confuse Chimera and the Actions 
/ Surface menu then doesn't work on the inner piece.  The problem is 
that the molecular surface no longer matches the atomic coordinates in 
the way Chimera expects. To get those menu entries to work delete the 
atomic model and reload another copy.  A drawback of all this is that it 
will no longer color the surface to match the atoms.

    Tom

-------- Original Message --------
Subject: [Chimera-users] Thanks for the help,    Is it possible to only 
show the "inner surface"?
From: Xarana
To: chimera-users
Date: 9/22/09 2:07 AM
> Hi Elaine,
> Thank you very much for your quick help. That really helped a lot and the
> differences are small. One last question: 
>
> Is there a possibility to only show this "inner surface" without the outer
> one for more clarity? I have to compare in 10 different structures (NMR
> solved) the extent of this cavities. And sadly SYBYL is not able to save as
> any other file format. 
>
> Best wishes,
> Natalie Bordag
> PhD student
>
> -----Urspr?ngliche Nachricht-----
> Von: Elaine Meng
> Gesendet: Montag, 21. September 2009 22:28
> An: Xarana
> Cc: chimera-users at cgl.ucsf.edu
> Betreff: Re: [Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or
> visualisation of an inner surface (of a protein) in Chimera
>
> Hi Natalie,
> Chimera does not know the *.sld file type.  Can SYBYL save this file  
> in a format Chimera knows, such as VRML?
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
>
> If not, you could try opening the structure (PDB or Mol2 file) in  
> Chimera, instead of the surface file, and have Chimera calculate the  
> surface.
>
> In Chimera, you can display the surface with "Actions... Surface...  
> show".  The default in Chimera is also to use a 1.4 Angstrom probe.   
> That would generate both the inner and outer surfaces, which you could  
> see by slicing the structure in the Side View (under Favorites menu).  
> There will probably be differences in the surface due to the different  
> default atomic radii in Chimera and SYBYL, but I would not expect them  
> to be large.
>
> I hope this helps,
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Sep 21, 2009, at 10:34 AM, Xarana wrote:
>
>   
>> Hi,
>> My interest is a 4 helix protein which has a cavity inside. A  
>> colleague generated with a 1,4 Angstr?m probe this "inner surface"  
>> with Sybyl for me and exported the surface as .sld file. Can I  
>> import this file into chimera somehow? Alternatively, can I generate  
>> such a surface with chimera?
>> My knowledge of protein visualization is limited and I am very  
>> thankful for any help
>> Thank you very much in advance.
>> Best Wishes
>> Natalie
>>     
> No virus found in this incoming message.
> Checked by AVG - www.avg.com 
> Version: 8.5.409 / Virus Database: 270.13.110/2385 - Release Date: 09/20/09
> 17:51:00
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>   

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090922/2b6d1a03/attachment.html>

From meng at cgl.ucsf.edu  Tue Sep 22 10:43:09 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 22 Sep 2009 10:43:09 -0700
Subject: [Chimera-users] Grouping models
In-Reply-To: <4AB9007A.2060403@cgl.ucsf.edu>
References: <200711221814.lAMIEKoV1997174@guanine.cgl.ucsf.edu>
	<60d48882a9db6f3e7021da308572fbe8@cgl.ucsf.edu>
	<7ACB4DFC-6924-4007-9173-49EA649B8DFD@imp.univie.ac.at>
	<544FE106-F794-4DEA-9C3E-C5586B80A19B@cgl.ucsf.edu>
	<1E6148FED8920445AC79AEB51579E5230576DF2B@EXCHSRV.imp.univie.ac.at>
	<49402860.1010509@cgl.ucsf.edu>
	<A2098225-3D9F-4105-9111-9AA5A5AF8F2F@imp.ac.at>
	<4AB9007A.2060403@cgl.ucsf.edu>
Message-ID: <73D17CB6-F015-4606-99E9-52A0B1BD5505@cgl.ucsf.edu>

Hi Thomas,
The command to name a selection is "namesel":
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>

You might also want to take a look at "alias" which I find to be more  
powerful and flexible:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

One reason to use named selections instead, however, is to have their  
names appear in the Select menu.  If that is not important, I  
recommend using "alias."
Best,
Elaine

On Sep 22, 2009, at 9:51 AM, Tom Goddard wrote:

> -------- Original Message --------
> From: Thomas C. Marlovits
> To: Tom Goddard
> Date: 9/22/09 2:04 AM
>> HI Tom,
>>
>> I was wondering, whether one can "group" a few models in chimera.  At
>> the moment, I have more than 40 models open simultaneously,  some of
>> which I would like to group in order to make coloring, selection, etc
>> ... more easily.   It might be that the feature is present, but
>> couldn't spot it so far.
>> The other thing that I would appreciate, if there is a simple way to
>> assign the model nr manually (at the moment it is done automatically,
>> and it appears that the order is somewhat random ...)
>> Best,
>> Tx,
>> -T.
>>
> Hi Thomas,
>
>   You can used "named selections" to give a short name to several  
> models
> or to any combination of selected items.  Use menu entry
>
>     Select / Name Selection...
>
> You can use the names in Chimera commands or use the "Select / Named
> Selection / name" menu entry.  I don't know of a command to name a
> selection.  Is there such a command (other Chimera developers)?
>
>   You can set the model number if you open your models with a command,
> for example,
>
>     open 5 twisty.pdb
>
> to open a model as model number 5.  After the model number has been
> assigned it unfortunately cannot be changed.
>
>     Tom



From meng at cgl.ucsf.edu  Tue Sep 22 11:00:11 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 22 Sep 2009 11:00:11 -0700
Subject: [Chimera-users] question about Chimera
In-Reply-To: <PZKKJOTJDIRSKZXHZLPEQAONCMKF.wuxue@nankai.edu.cn>
References: <PZKKJOTJDIRSKZXHZLPEQAONCMKF.wuxue@nankai.edu.cn>
Message-ID: <9B5D7F73-88C4-43D0-BB83-A0023726CE11@cgl.ucsf.edu>

Dear Wu Xue,
There are several different distance and angle cutoffs that depend on  
the donor and acceptor atom types.  For example, the distance and  
angle cutoffs for finding a H-bond donated from hydroxyl -OH to  
carbonyl =O will be different than from amine -NH3 to carbonyl =O.   
The cutoff values are taken from tables in this paper:

     Three-dimensional hydrogen-bond geometry and probability  
information from a crystal survey. Mills JE, Dean PM. J Comput Aided  
Mol Des. 1996 Dec;10(6):607-22.

As discussed in the FindHBond documentation,
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ 
findhbond.html#criteria>

the criteria in this paper were based on very high resolution crystal  
structures of small molecules.  Typically the structures in the PDB  
are not so high resolution and so the criteria are relaxed.  For  
example, if a strict criterion from the paper is 2.8 Angstroms  
cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms.   
We set the default relaxation amounts to what we felt gives  
reasonable results on most PDB structures.  However, we made them  
user-adjustable so that if you don't like them, you can change the  
values to whatever you want.

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

On Sep 22, 2009, at 4:18 AM, ?? wrote:

> Dear colleague:
>     I have  a question about the "find hydrongen bond" in Chimera.  
> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree".
>    I don't understand the meaning of the parameter. 20 degree may  
> means the angle bias the line,but I can't figure out what is the  
> 0.04nm.
> The cutoff of the hydrogen is 0.4nm, and the angle is about 90  
> degree or some other parameters depending on the strength of the  
> hydrogen bond.
>   If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds  
> are found. I don't know the criteria. Can you give me some advice  
> so that I can follow your instruction?
>    Sincerly Yours
>    WU Xue



From meng at cgl.ucsf.edu  Tue Sep 22 11:23:15 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 22 Sep 2009 11:23:15 -0700
Subject: [Chimera-users] Thanks for the help,
	Is it possible to only show the "inner surface"?
In-Reply-To: <FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4>
References: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>
	<3AE4EBAE-67B9-4F25-A757-D4938BAF705B@cgl.ucsf.edu>
	<FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4>
Message-ID: <4731859F-A861-4522-A105-26BFD9E74CB6@cgl.ucsf.edu>

Hi Natalie,
If the inner surface is totally disconnected from the outer surface  
(like an inside "bubble"), it is fairly easy:

- Ctrl-click to select the surface
- use command: ac Sc
(this makes the disconnected parts into separate "surface pieces"  
that can be controlled separately; choose "Favorites... Command Line"  
from the menu to get the command line)
- Ctrl-click empty space to clear selection
- Ctrl-click outer surface to select it (now the inner surface will  
not be selected)
- choose "Actions... Inspect" from the menu to open the Selection  
Inspector.  In that dialog, Inspect "Surface Piece" and set  
"displayed" to "false."  That will undisplay the outer surface,  
leaving the inner surface.  If there are other pieces to turn off,  
repeat by selecting them and using the Selection Inspector to  
undisplay them.

If inner and outer surfaces are connected, however, it may be  
difficult to just show the part you want.  You can select sets of  
atoms and use "Actions.... Surface... hide/show" to hide or show  
their surface patches, but the problem is that it can be hard to  
figure out which atoms go with which surface patches, and some atoms  
might even form parts of both the inner and outer surfaces.

A third possibility is to use the Surface Zone tool (under Tools...  
Surface/Binding Analysis).  In that case you would need to put some  
atom in the middle of the inner surface, select it, and then use some  
cutoff from that atom.  You can add a single atom with Build  
Structure (under Tools... Structure Editing), Add Atoms section,  
"atom" (make sure to put atom in a "new model") and then move it  
relative to your first structure by checking/unchecking the boxes  
under the Command Line and using the mouse.  It can be hard to get  
the atom where you want it, and even if that part is successful, it  
may work very well either if a spherical cutoff does not separate the  
inner and outer surfaces.

The "Structure Analysis and Comparison" tutorial includes showing  
just the surface of a binding pocket:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html#surfaces>

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

On Sep 22, 2009, at 2:07 AM, Xarana wrote:

> Hi Elaine,
> Thank you very much for your quick help. That really helped a lot  
> and the
> differences are small. One last question:
>
> Is there a possibility to only show this "inner surface" without  
> the outer
> one for more clarity? I have to compare in 10 different structures  
> (NMR
> solved) the extent of this cavities. And sadly SYBYL is not able to  
> save as
> any other file format.
>
> Best wishes,
> Natalie Bordag
> PhD student



From nataliebordag at gmx.de  Tue Sep 22 11:53:34 2009
From: nataliebordag at gmx.de (Natalie Bordag)
Date: Tue, 22 Sep 2009 20:53:34 +0200
Subject: [Chimera-users] You are the best,
	that helped a lot. Thank you so much.
In-Reply-To: <4731859F-A861-4522-A105-26BFD9E74CB6@cgl.ucsf.edu>
References: <091153DEE5E949EB83F6ED5D17C17A2E@agkellernb4>
	<3AE4EBAE-67B9-4F25-A757-D4938BAF705B@cgl.ucsf.edu>
	<FFA06759B7CD4504B4CFF70C887A29AA@agkellernb4>
	<4731859F-A861-4522-A105-26BFD9E74CB6@cgl.ucsf.edu>
Message-ID: <2081945B0DB64EDFA5F31B13E5383575@agkellernb4>



-----Urspr?ngliche Nachricht-----
Von: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Gesendet: Dienstag, 22. September 2009 20:23
An: Xarana
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] Thanks for the help, Is it possible to only
show the "inner surface"?

Hi Natalie,
If the inner surface is totally disconnected from the outer surface  
(like an inside "bubble"), it is fairly easy:

- Ctrl-click to select the surface
- use command: ac Sc
(this makes the disconnected parts into separate "surface pieces"  
that can be controlled separately; choose "Favorites... Command Line"  
from the menu to get the command line)
- Ctrl-click empty space to clear selection
- Ctrl-click outer surface to select it (now the inner surface will  
not be selected)
- choose "Actions... Inspect" from the menu to open the Selection  
Inspector.  In that dialog, Inspect "Surface Piece" and set  
"displayed" to "false."  That will undisplay the outer surface,  
leaving the inner surface.  If there are other pieces to turn off,  
repeat by selecting them and using the Selection Inspector to  
undisplay them.

If inner and outer surfaces are connected, however, it may be  
difficult to just show the part you want.  You can select sets of  
atoms and use "Actions.... Surface... hide/show" to hide or show  
their surface patches, but the problem is that it can be hard to  
figure out which atoms go with which surface patches, and some atoms  
might even form parts of both the inner and outer surfaces.

A third possibility is to use the Surface Zone tool (under Tools...  
Surface/Binding Analysis).  In that case you would need to put some  
atom in the middle of the inner surface, select it, and then use some  
cutoff from that atom.  You can add a single atom with Build  
Structure (under Tools... Structure Editing), Add Atoms section,  
"atom" (make sure to put atom in a "new model") and then move it  
relative to your first structure by checking/unchecking the boxes  
under the Command Line and using the mouse.  It can be hard to get  
the atom where you want it, and even if that part is successful, it  
may work very well either if a spherical cutoff does not separate the  
inner and outer surfaces.

The "Structure Analysis and Comparison" tutorial includes showing  
just the surface of a binding pocket:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html#surfaces>

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

On Sep 22, 2009, at 2:07 AM, Xarana wrote:

> Hi Elaine,
> Thank you very much for your quick help. That really helped a lot  
> and the
> differences are small. One last question:
>
> Is there a possibility to only show this "inner surface" without  
> the outer
> one for more clarity? I have to compare in 10 different structures  
> (NMR
> solved) the extent of this cavities. And sadly SYBYL is not able to  
> save as
> any other file format.
>
> Best wishes,
> Natalie Bordag
> PhD student
No virus found in this incoming message.
Checked by AVG - www.avg.com 
Version: 8.5.409 / Virus Database: 270.13.112/2387 - Release Date: 09/21/09
17:55:00



From wuxue at nankai.edu.cn  Tue Sep 22 17:18:10 2009
From: wuxue at nankai.edu.cn (=?gb2312?B?zuLRqQ==?=)
Date: Wed, 23 Sep 2009 08:18:10 +0800
Subject: [Chimera-users] question about Chimera
Message-ID: <WAVAMYTUSJEUFVQAMJIZBDCDDVZH.wuxue@nankai.edu.cn>

Dear Elaine:
    Thank you very much for your instruction.
   We'll follow your guide.
    Best wishes
    WU Xue



>From: Elaine Meng <meng at cgl.ucsf.edu>
>Reply-To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
>To: ??<wuxue at nankai.edu.cn>
>Subject: Re: [Chimera-users] question about Chimera
>Date: Tue, 22 Sep 2009 11:00:11 -0700
>
>Dear Wu Xue,
>There are several different distance and angle cutoffs that depend on  
>the donor and acceptor atom types.  For example, the distance and  
>angle cutoffs for finding a H-bond donated from hydroxyl -OH to  
>carbonyl =O will be different than from amine -NH3 to carbonyl =O.   
>The cutoff values are taken from tables in this paper:
>
>     Three-dimensional hydrogen-bond geometry and probability  
>information from a crystal survey. Mills JE, Dean PM. J Comput Aided  
>Mol Des. 1996 Dec;10(6):607-22.
>
>As discussed in the FindHBond documentation,
>
findhbond.html#criteria>
>
>the criteria in this paper were based on very high resolution crystal  
>structures of small molecules.  Typically the structures in the PDB  
>are not so high resolution and so the criteria are relaxed.  For  
>example, if a strict criterion from the paper is 2.8 Angstroms  
>cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms.   
>We set the default relaxation amounts to what we felt gives  
>reasonable results on most PDB structures.  However, we made them  
>user-adjustable so that if you don't like them, you can change the  
>values to whatever you want.
>
>I hope this helps,
>ELaine
>-----
>Elaine C. Meng, Ph.D.
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>
>On Sep 22, 2009, at 4:18 AM, ?? wrote:
>
>> Dear colleague:
>>     I have  a question about the "find hydrongen bond" in Chimera.  
>> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree".
>>    I don't understand the meaning of the parameter. 20 degree may  
>> means the angle bias the line,but I can't figure out what is the  
>> 0.04nm.
>> The cutoff of the hydrogen is 0.4nm, and the angle is about 90  
>> degree or some other parameters depending on the strength of the  
>> hydrogen bond.
>>   If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds  
>> are found. I don't know the criteria. Can you give me some advice  
>> so that I can follow your instruction?
>>    Sincerly Yours
>>    WU Xue
>
> 

From victor1587 at gmail.com  Wed Sep 23 02:29:48 2009
From: victor1587 at gmail.com (=?ISO-8859-1?Q?Victor_Mu=F1oz?=)
Date: Wed, 23 Sep 2009 11:29:48 +0200
Subject: [Chimera-users] [chimera-dev] select opt
In-Reply-To: <1C257263-D84D-4670-B605-07683AA2D08C@cgl.ucsf.edu>
References: <20090921142516.M40592@klingon.uab.es>
	<1C257263-D84D-4670-B605-07683AA2D08C@cgl.ucsf.edu>
Message-ID: <849ba95b0909230229q154ad41fse2b90c78c2ded373@mail.gmail.com>

Dear Mr/Mss:

Thanks a lot for your help, the command work with my script.

Bye!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090923/6c787eca/attachment.html>

From chiendarret at gmail.com  Fri Sep 25 02:50:09 2009
From: chiendarret at gmail.com (Francesco Pietra)
Date: Fri, 25 Sep 2009 11:50:09 +0200
Subject: [Chimera-users] segmentation fault
Message-ID: <b87c422a0909250250m61d14fedweb8af02ddeb22f05@mail.gmail.com>

Hi:

On Debian Linux i386 squeeze I had the X  system broken while
attempting to install the gnome cd burner "brasero". I purged
everything about that bad code, installed and reconfigured the X
system, however something is still broken. Attempts at launching
CHIMERA returned "segmentation fault". That also sitting in the
directory where chimera is installed ( /usr/local/chimera/bin).

As I had an old version, I reinstalled chimera-1.3-linux.exe, while
that did not solve the above problem.

I do not remember where to put the hands in such cases. Thankful for
reminding me about that.

francesco at deb32:~$ gcc --version
gcc (Debian 4.3.4-2) 4.3.4


francesco pietra


From goddard at cgl.ucsf.edu  Fri Sep 25 09:41:56 2009
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 25 Sep 2009 09:41:56 -0700
Subject: [Chimera-users] Zoom factor for model when first opened
In-Reply-To: <Pine.GSO.4.64.0909241831170.2597@home.scripps.edu>
References: <Pine.GSO.4.64.0909241831170.2597@home.scripps.edu>
Message-ID: <4ABCF2D4.9050206@cgl.ucsf.edu>

Hi Kevin,

  The camera settings (position, amount of zoom, angular field of view) 
all contribute to how much of the Chimera window is filled when you open 
a map.  How those are initially set when you start Chimera and open a 
map has changed a few times over the last year or two so if you run 
different Chimera versions (Help / About Chimera... to check version 
number) you may see different initial sizes.

    Tom


-------- Original Message --------
Subject: chimera question
From: Kevin Koehntop
To: goddard
Date: 9/24/09 6:34 PM
> Hi Tom,
>
> I have a quick chimera question.  When I open the same EM map in two 
> different chimera sessions, even though the scale factor, origin, 
> voxel size, and isosurface threshold level are exactly the same, the 
> map appears much smaller in one of the windows and I can't determine 
> why.  Is there another parameter that I need to check?  Thank you
>
> Kevin



From gtzotzos at mac.com  Sun Sep 27 10:40:38 2009
From: gtzotzos at mac.com (George Tzotzos)
Date: Sun, 27 Sep 2009 19:40:38 +0200
Subject: [Chimera-users] Using Chimera to read SMILES string
	into	structure
In-Reply-To: <719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
Message-ID: <03904BCE-36D0-4182-82C2-BFEF7E360F37@mac.com>

Hi Elaine

I'm using the <open smiles> command as per your instructions (see your  
message below).

The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- 
ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO

What I get is nonanol. The program returns

opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues

Obviously, I'm using a different SMILES convention than Chimera.

I'd appreciate you suggestion regarding the SMILES convention, I  
should be using.

All the best

George

George T. Tzotzos, PhD
Dept. of Molecular Genetics
Univ. of Gent, Belgium


On Sep 3, 2009, at 7:46 PM, Elaine Meng wrote:

> Hi Miriam,
> Are you on a Mac?  I'm using a Mac and was able to copy text from
> Terminal and paste it into both those places.  The copy/paste
> procedure depends on your platform.  Using the Mac aqua version, I
> highlighted text in Terminal and pressed command-c to copy, then to
> paste, I clicked into the blank dialog text area and pressed command-
> v.  Using the Mac X11 version, I used the same copying procedure but
> then to paste, clicked into the blank dialog text area and then
> clicked middle mouse button.  On Windows, copy and paste may be Ctrl-c
> and Ctrl-v.
>
> You can also get SMILES->3D from the Chimera command line, e.g.
>
> open smiles:C1CCC(O)CC1
>
> and the copy/paste procedure there is the same, but again platform-
> dependent.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:
>
>> I have downloaded the latest build (Aug 30, 2009) and don't seem to
>> be able to input a SMILES string.  I have tried both the Utilities -
>>> Structure Diagram and the Structure Editing -> Build Structure
>> tool, and in both cases I can see a box to input the SMILES string,
>> but the copy and paste mechanism won't work.  I can enter text in
>> the box, but cannot paste it in, which I need to do.  Thanks for
>> your help.
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090927/21ba00db/attachment.html>

From chiendarret at gmail.com  Sun Sep 27 23:38:44 2009
From: chiendarret at gmail.com (Francesco Pietra)
Date: Mon, 28 Sep 2009 08:38:44 +0200
Subject: [Chimera-users] Fwd: segmentation fault
In-Reply-To: <b87c422a0909250250m61d14fedweb8af02ddeb22f05@mail.gmail.com>
References: <b87c422a0909250250m61d14fedweb8af02ddeb22f05@mail.gmail.com>
Message-ID: <b87c422a0909272338t5866c31cie493f06bc09049d1@mail.gmail.com>

I wonder whether for some reason I am no more on the chimera-users
list. I do not receive message any more and my message below had no
reply.

thanks
francesco pietra


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Fri, Sep 25, 2009 at 11:50 AM
Subject: segmentation fault
To: chimera <chimera-users at cgl.ucsf.edu>


Hi:

On Debian Linux i386 squeeze I had the X ?system broken while
attempting to install the gnome cd burner "brasero". I purged
everything about that bad code, installed and reconfigured the X
system, however something is still broken. Attempts at launching
CHIMERA returned "segmentation fault". That also sitting in the
directory where chimera is installed ( /usr/local/chimera/bin).

As I had an old version, I reinstalled chimera-1.3-linux.exe, while
that did not solve the above problem.

I do not remember where to put the hands in such cases. Thankful for
reminding me about that.

francesco at deb32:~$ gcc --version
gcc (Debian 4.3.4-2) 4.3.4


francesco pietra


From meng at cgl.ucsf.edu  Mon Sep 28 08:55:06 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 28 Sep 2009 08:55:06 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string
	into	structure
In-Reply-To: <03904BCE-36D0-4182-82C2-BFEF7E360F37@mac.com>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
	<03904BCE-36D0-4182-82C2-BFEF7E360F37@mac.com>
Message-ID: <16FB7A9C-CA87-4F04-B783-21BEED00AA26@cgl.ucsf.edu>

Hi George,
The smiles->3D conversion is done by a Web service at Indiana  
University, and as far as I know it uses the standard SMILES notation  
as described by Daylight:
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

However, I did reproduce the problem you reported, which seems to be  
related to the slashes (\ /) in the string.  For example, you do get  
the correct molecule, albeit without control over stereochemistry,  
with smiles:CC=CC=CCCCCCCCCCO

The status line message suggests that Chimera may be processing the  
string incorrectly before sending it to the Web service, but we will  
have to investigate that further and get back to you.  I'll file a bug  
report and put you on the notification list (you will get some  
additional messages about that later).  If it is a limitation of the  
Web server, however, we may not be able to fix it.  In the future, if  
you run into another problem that could be a bug, please use "Help...  
Report a Bug" in the Chimera menu to send us the information -- that  
will automatically include what version of Chimera and type of  
computer you are using, since sometimes those are important.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 27, 2009, at 10:40 AM, George Tzotzos wrote:

> Hi Elaine
>
> I'm using the <open smiles> command as per your instructions (see  
> your message below).
>
> The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- 
> ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO
>
> What I get is nonanol. The program returns
>
> opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues
>
> Obviously, I'm using a different SMILES convention than Chimera.
>
> I'd appreciate you suggestion regarding the SMILES convention, I  
> should be using.
>
> All the best
>
> George
>
> George T. Tzotzos, PhD
> Dept. of Molecular Genetics
> Univ. of Gent, Belgium



From meng at cgl.ucsf.edu  Mon Sep 28 09:13:16 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 28 Sep 2009 09:13:16 -0700
Subject: [Chimera-users] Fwd: segmentation fault
In-Reply-To: <b87c422a0909272338t5866c31cie493f06bc09049d1@mail.gmail.com>
References: <b87c422a0909250250m61d14fedweb8af02ddeb22f05@mail.gmail.com>
	<b87c422a0909272338t5866c31cie493f06bc09049d1@mail.gmail.com>
Message-ID: <12074780-0114-48CB-80ED-A96BD4E7B42A@cgl.ucsf.edu>

Hi Francesco,
I did see both your previous message and this one on the chimera-users  
list.  There has been no answer, probably because nobody knows the  
answer or can figure out what exactly is the question.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 27, 2009, at 11:38 PM, Francesco Pietra wrote:

> I wonder whether for some reason I am no more on the chimera-users
> list. I do not receive message any more and my message below had no
> reply.
>
> thanks
> francesco pietra
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Fri, Sep 25, 2009 at 11:50 AM
> Subject: segmentation fault
> To: chimera <chimera-users at cgl.ucsf.edu>
>
>
> Hi:
>
> On Debian Linux i386 squeeze I had the X  system broken while
> attempting to install the gnome cd burner "brasero". I purged
> everything about that bad code, installed and reconfigured the X
> system, however something is still broken. Attempts at launching
> CHIMERA returned "segmentation fault". That also sitting in the
> directory where chimera is installed ( /usr/local/chimera/bin).
>
> As I had an old version, I reinstalled chimera-1.3-linux.exe, while
> that did not solve the above problem.
>
> I do not remember where to put the hands in such cases. Thankful for
> reminding me about that.
>
> francesco at deb32:~$ gcc --version
> gcc (Debian 4.3.4-2) 4.3.4
>
>
> francesco pietra
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From chiendarret at gmail.com  Mon Sep 28 09:25:02 2009
From: chiendarret at gmail.com (Francesco Pietra)
Date: Mon, 28 Sep 2009 18:25:02 +0200
Subject: [Chimera-users] Fwd: segmentation fault
In-Reply-To: <12074780-0114-48CB-80ED-A96BD4E7B42A@cgl.ucsf.edu>
References: <b87c422a0909250250m61d14fedweb8af02ddeb22f05@mail.gmail.com>
	<b87c422a0909272338t5866c31cie493f06bc09049d1@mail.gmail.com>
	<12074780-0114-48CB-80ED-A96BD4E7B42A@cgl.ucsf.edu>
Message-ID: <b87c422a0909280925j1df42ba0k97040f7af42741d8@mail.gmail.com>

Hi Elaine:
Thanks. Any specific command that could illuminate? What I can say is
that some fonts have gone lost. The screen, before launching X with
startx, has unusual fonts. Otherwise all other programs, including VMD
are operative.
Thanks
francesco

On Mon, Sep 28, 2009 at 6:13 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> I did see both your previous message and this one on the chimera-users list.
> ?There has been no answer, probably because nobody knows the answer or can
> figure out what exactly is the question.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Sep 27, 2009, at 11:38 PM, Francesco Pietra wrote:
>
>> I wonder whether for some reason I am no more on the chimera-users
>> list. I do not receive message any more and my message below had no
>> reply.
>>
>> thanks
>> francesco pietra
>>
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret at gmail.com>
>> Date: Fri, Sep 25, 2009 at 11:50 AM
>> Subject: segmentation fault
>> To: chimera <chimera-users at cgl.ucsf.edu>
>>
>>
>> Hi:
>>
>> On Debian Linux i386 squeeze I had the X ?system broken while
>> attempting to install the gnome cd burner "brasero". I purged
>> everything about that bad code, installed and reconfigured the X
>> system, however something is still broken. Attempts at launching
>> CHIMERA returned "segmentation fault". That also sitting in the
>> directory where chimera is installed ( /usr/local/chimera/bin).
>>
>> As I had an old version, I reinstalled chimera-1.3-linux.exe, while
>> that did not solve the above problem.
>>
>> I do not remember where to put the hands in such cases. Thankful for
>> reminding me about that.
>>
>> francesco at deb32:~$ gcc --version
>> gcc (Debian 4.3.4-2) 4.3.4
>>
>>
>> francesco pietra
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>


From meng at cgl.ucsf.edu  Mon Sep 28 12:14:48 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 28 Sep 2009 12:14:48 -0700
Subject: [Chimera-users] Solvent Accessible Surface Area
In-Reply-To: <483711.31367.qm@web53901.mail.re2.yahoo.com>
References: <483711.31367.qm@web53901.mail.re2.yahoo.com>
Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB@cgl.ucsf.edu>

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
> I am using Chimera for identifying the surface residues.
>
> I select areaSAS > 0.05 square angstroms, is this same as saying  
> areaSAS > 5%, I am getting confused with the numbers  5% and 0.05 sq  
> angstroms have these been switched some how or are they curiously  
> the same in the following statement?
>
> I just need some help in understanding.
> Thank You
> Sincerely
> -Thiru Ramaraj


Hi Thiru,
In Chimera there is no percentage (%) measurement, it is only the area  
value in square angstroms.  Some other programs give % exposed for a  
residue, which is a ratio of the area of that residue in your  
structure to the area of the same type of residue in some theoretical  
unfolded state.  See for example the GetArea server, which gives  
"Ratio(%)":
<http://curie.utmb.edu/area_man.html>

However, what Chimera reports is just the surface area of the atom or  
residue in your structure.  To choose surface residues, I'd probably  
use a bigger cutoff, say

select :/areaSAS>10

but it depends on what you are going to do with the results.  You can  
try different values and see what looks reasonable.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco




From thiruvaranganr at yahoo.com  Mon Sep 28 13:49:00 2009
From: thiruvaranganr at yahoo.com (Thiruvarangan Ramaraj)
Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT)
Subject: [Chimera-users] Solvent Accessible Surface Area
In-Reply-To: <E24233F9-9564-4824-8D82-6D9506261ACB@cgl.ucsf.edu>
Message-ID: <842106.2825.qm@web53905.mail.re2.yahoo.com>

Thanks,? Elaine for the information.

Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault. 

Is there anyway I could resolve this problem.

Thank You

-Thiru Ramaraj

--- On Mon, 9/28/09, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: Solvent Accessible Surface Area
To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Date: Monday, September 28, 2009, 1:14 PM

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
> I am using Chimera for identifying the surface residues.
> 
> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement?
> 
> I just need some help in understanding.
> Thank You
> Sincerely
> -Thiru Ramaraj


Hi Thiru,
In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)":
<http://curie.utmb.edu/area_man.html>

However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say

select :/areaSAS>10

but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco





      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090928/4d53c7ef/attachment.html>

From gregc at cgl.ucsf.edu  Mon Sep 28 16:00:08 2009
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 28 Sep 2009 16:00:08 -0700 (PDT)
Subject: [Chimera-users] Solvent Accessible Surface Area
In-Reply-To: <842106.2825.qm@web53905.mail.re2.yahoo.com>
References: <842106.2825.qm@web53905.mail.re2.yahoo.com>
Message-ID: <Pine.OSF.4.63.0909281534380.1997062@guanine.cgl.ucsf.edu>

On Mon, 28 Sep 2009, Thiruvarangan Ramaraj wrote:

> Also I am having problems with installing Chimera on Linux Fedora 11(32 
> bit version). I am able to download it and install it. When I start 
> chimera it comes up and then crashes immediately, the only message it 
> gives is Segmentation Fault.
>
> Is there anyway I could resolve this problem.
>
> Thank You
>
> -Thiru Ramaraj

The first thing to try is a chimera daily build.  The daily builds make 
fewer assumptions about what Linux provides.  However, there is still a 
good chance that chimera will crash in Fedora 11 -- because Fedora 11's 
OpenGL support is based on the latest and greatest Mesa code and as the 
Mesa website says "Those especially concerned about stability may want to 
wait for the follow-on 7.6.1 bug-fix release.".

Currently, we have found that the default NVidia driver does not work, but 
that the driver from NVidia does.  The opposite is true for ATI drivers, 
the default driver works, but the one from ATI fails.  The default Intel 
driver is mostly okay (e.g,. when doing area selections, the selection box 
can appear in a different application's window!).

 	So good luck, and please tell me how it goes,

 	Greg


From pett at cgl.ucsf.edu  Tue Sep 29 14:08:24 2009
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 29 Sep 2009 14:08:24 -0700
Subject: [Chimera-users] Using Chimera to read SMILES string
	into	structure
In-Reply-To: <16FB7A9C-CA87-4F04-B783-21BEED00AA26@cgl.ucsf.edu>
References: <8F37ABB227136A48A611B3BA213DF7F02C5779B64E@TUMAIL.tuca.touro.edu>
	<719CF208-A7DA-48D2-96AD-8BEEEB895229@cgl.ucsf.edu>
	<03904BCE-36D0-4182-82C2-BFEF7E360F37@mac.com>
	<16FB7A9C-CA87-4F04-B783-21BEED00AA26@cgl.ucsf.edu>
Message-ID: <B2A49F7B-CB47-48A9-80E3-A2B331A844E7@cgl.ucsf.edu>

On Sep 28, 2009, at 8:55 AM, Elaine Meng wrote:

> Hi George,
> The smiles->3D conversion is done by a Web service at Indiana  
> University, and as far as I know it uses the standard SMILES  
> notation as described by Daylight:
> http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

It turns out that the web service at Indiana University wasn't  
handling SMILES with forward slashes correctly, only translating the  
string after the last slash.  They have fixed that bug and Chimera  
will now get the right structure for your SMILES string.

--Eric

>
> However, I did reproduce the problem you reported, which seems to be  
> related to the slashes (\ /) in the string.  For example, you do get  
> the correct molecule, albeit without control over stereochemistry,  
> with smiles:CC=CC=CCCCCCCCCCO
>
> The status line message suggests that Chimera may be processing the  
> string incorrectly before sending it to the Web service, but we will  
> have to investigate that further and get back to you.  I'll file a  
> bug report and put you on the notification list (you will get some  
> additional messages about that later).  If it is a limitation of the  
> Web server, however, we may not be able to fix it.  In the future,  
> if you run into another problem that could be a bug, please use  
> "Help... Report a Bug" in the Chimera menu to send us the  
> information -- that will automatically include what version of  
> Chimera and type of computer you are using, since sometimes those  
> are important.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Sep 27, 2009, at 10:40 AM, George Tzotzos wrote:
>
>> Hi Elaine
>>
>> I'm using the <open smiles> command as per your instructions (see  
>> your message below).
>>
>> The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- 
>> ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO
>>
>> What I get is nonanol. The program returns
>>
>> opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues
>>
>> Obviously, I'm using a different SMILES convention than Chimera.
>>
>> I'd appreciate you suggestion regarding the SMILES convention, I  
>> should be using.
>>
>> All the best
>>
>> George
>>
>> George T. Tzotzos, PhD
>> Dept. of Molecular Genetics
>> Univ. of Gent, Belgium
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From vamsi at nus.edu.sg  Wed Sep 30 03:33:51 2009
From: vamsi at nus.edu.sg (vamsi krishna)
Date: Wed, 30 Sep 2009 18:33:51 +0800
Subject: [Chimera-users] Chimera-users Digest, Vol 77, Issue 26
In-Reply-To: <mailman.1.1254250806.1932754.chimera-users@cgl.ucsf.edu>
References: <mailman.1.1254250806.1932754.chimera-users@cgl.ucsf.edu>
Message-ID: <4AC3340F.20404@nus.edu.sg>

Dear all,
                  I am using chimera to calculate solvent accessibility 
of residues , may i ask you what cutoff is appropriate to identify 
surface residues significant for substrate binding .

Thank you
vamsi

chimera-users-request at cgl.ucsf.edu wrote:
> Send Chimera-users mailing list submissions to
> 	chimera-users at cgl.ucsf.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> or, via email, send a message with subject or body 'help' to
> 	chimera-users-request at cgl.ucsf.edu
>
> You can reach the person managing the list at
> 	chimera-users-owner at cgl.ucsf.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
>
>
> Today's Topics:
>
>    1. Re: Solvent Accessible Surface Area (Elaine Meng)
>    2. Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj)
>    3. Re: Solvent Accessible Surface Area (Greg Couch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 28 Sep 2009 12:14:48 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Thiruvarangan Ramaraj <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:
>
>   
>> Hi Elaine,
>> I am using Chimera for identifying the surface residues.
>>
>> I select areaSAS > 0.05 square angstroms, is this same as saying  
>> areaSAS > 5%, I am getting confused with the numbers  5% and 0.05 sq  
>> angstroms have these been switched some how or are they curiously  
>> the same in the following statement?
>>
>> I just need some help in understanding.
>> Thank You
>> Sincerely
>> -Thiru Ramaraj
>>     
>
>
> Hi Thiru,
> In Chimera there is no percentage (%) measurement, it is only the area  
> value in square angstroms.  Some other programs give % exposed for a  
> residue, which is a ratio of the area of that residue in your  
> structure to the area of the same type of residue in some theoretical  
> unfolded state.  See for example the GetArea server, which gives  
> "Ratio(%)":
> <http://curie.utmb.edu/area_man.html>
>
> However, what Chimera reports is just the surface area of the atom or  
> residue in your structure.  To choose surface residues, I'd probably  
> use a bigger cutoff, say
>
> select :/areaSAS>10
>
> but it depends on what you are going to do with the results.  You can  
> try different values and see what looks reasonable.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT)
> From: Thiruvarangan Ramaraj <thiruvaranganr at yahoo.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> Message-ID: <842106.2825.qm at web53905.mail.re2.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks,? Elaine for the information.
>
> Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault. 
>
> Is there anyway I could resolve this problem.
>
> Thank You
>
> -Thiru Ramaraj
>
> --- On Mon, 9/28/09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: Solvent Accessible Surface Area
> To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Date: Monday, September 28, 2009, 1:14 PM
>
> On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:
>
>   
>> Hi Elaine,
>> I am using Chimera for identifying the surface residues.
>>
>> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement?
>>
>> I just need some help in understanding.
>> Thank You
>> Sincerely
>> -Thiru Ramaraj
>>     
>
>
> Hi Thiru,
> In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)":
> <http://curie.utmb.edu/area_man.html>
>
> However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say
>
> select :/areaSAS>10
>
> but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
>
>       
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090928/4d53c7ef/attachment-0001.html>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 28 Sep 2009 16:00:08 -0700 (PDT)
> From: Greg Couch <gregc at cgl.ucsf.edu>
> To: Thiruvarangan Ramaraj <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> Message-ID: <Pine.OSF.4.63.0909281534380.1997062 at guanine.cgl.ucsf.edu>
> Content-Type: TEXT/Plain; charset=US-ASCII; format=flowed
>
> On Mon, 28 Sep 2009, Thiruvarangan Ramaraj wrote:
>
>   
>> Also I am having problems with installing Chimera on Linux Fedora 11(32 
>> bit version). I am able to download it and install it. When I start 
>> chimera it comes up and then crashes immediately, the only message it 
>> gives is Segmentation Fault.
>>
>> Is there anyway I could resolve this problem.
>>
>> Thank You
>>
>> -Thiru Ramaraj
>>     
>
> The first thing to try is a chimera daily build.  The daily builds make 
> fewer assumptions about what Linux provides.  However, there is still a 
> good chance that chimera will crash in Fedora 11 -- because Fedora 11's 
> OpenGL support is based on the latest and greatest Mesa code and as the 
> Mesa website says "Those especially concerned about stability may want to 
> wait for the follow-on 7.6.1 bug-fix release.".
>
> Currently, we have found that the default NVidia driver does not work, but 
> that the driver from NVidia does.  The opposite is true for ATI drivers, 
> the default driver works, but the one from ATI fails.  The default Intel 
> driver is mostly okay (e.g,. when doing area selections, the selection box 
> can appear in a different application's window!).
>
>  	So good luck, and please tell me how it goes,
>
>  	Greg
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> End of Chimera-users Digest, Vol 77, Issue 26
> *********************************************
>   



From Andrew.Waight at med.nyu.edu  Wed Sep 30 08:33:29 2009
From: Andrew.Waight at med.nyu.edu (Waight, Andrew)
Date: Wed, 30 Sep 2009 11:33:29 -0400
Subject: [Chimera-users] Transparent Spheres
Message-ID: <3760BF13083CBF4F94D34D000ACFB3AB12C5BD5608@MSGWSDCPMB04.nyumc.org>

Hello everyone again. 


                     I apologize for a potentially embarassing question but is it possible to display sidechains as transparent spheres with solid stick representation inside. Seeing as I also can't find an image in the Chimera gallery where it is represented as such, I am wondering if it is possible to individually color (and set opacity) on spheres. I am also aware that vdw will create dots of varying density, but is it alternatively possible to display vdw as solid surface with opacity. Thanks to all for your patience.

                                                                                                                      Drew

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================



From meng at cgl.ucsf.edu  Wed Sep 30 08:53:45 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 30 Sep 2009 08:53:45 -0700
Subject: [Chimera-users] solvent-accessible area cutoff
In-Reply-To: <4AC3340F.20404@nus.edu.sg>
References: <mailman.1.1254250806.1932754.chimera-users@cgl.ucsf.edu>
	<4AC3340F.20404@nus.edu.sg>
Message-ID: <0F6B9A57-47FE-4B3D-9A90-FA65080D16CC@cgl.ucsf.edu>

Dear Vamsi,
I do not think there is a definite answer.  This is a somewhat  
philosophical rather than technical question... it depends what you  
are going to do with the resulting list of residues.  You could try  
different values and see whether the resulting set of residues agrees  
with your intuition.

If I remember correctly, there are some alanine scanning papers that  
indicate even residues that are in contact are not always important  
for binding energy.  These were experiments done on protein-protein  
systems, however. Perhaps there are some published papers that discuss  
these issues for substrates -- if anybody has an opinion on this topic  
or can suggest references, please speak up!

However, if you have a protein-ligand complex structure, why not just  
use the "Find Contacts/Clashes" tool instead of dealing with solvent- 
accessible surface areas?   That is what I would use.

"Find Contacts/Clashes" documentation:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
 >

Also, the "distances, H-bonds, contacts" section of this tutorial  
includes an example of finding residues that interact with a ligand:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>

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

On Sep 30, 2009, at 3:33 AM, vamsi krishna wrote:

> Dear all,
>                 I am using chimera to calculate solvent  
> accessibility of residues , may i ask you what cutoff is appropriate  
> to identify surface residues significant for substrate binding .
>
> Thank you
> vamsi



From meng at cgl.ucsf.edu  Wed Sep 30 09:28:18 2009
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 30 Sep 2009 09:28:18 -0700
Subject: [Chimera-users] Transparent Spheres
In-Reply-To: <3760BF13083CBF4F94D34D000ACFB3AB12C5BD5608@MSGWSDCPMB04.nyumc.org>
References: <3760BF13083CBF4F94D34D000ACFB3AB12C5BD5608@MSGWSDCPMB04.nyumc.org>
Message-ID: <96B9980E-9017-4CF2-9AAF-2CB6FAF6E009@cgl.ucsf.edu>

Hi Drew,
No need to apologize, it is not a simple issue!

The "sphere" representation is the solid VDW surface, so just use that  
unless you actually wanted dots.  Since something can't be both sticks  
and spheres at the same time, you could do it by opening the structure  
twice and showing one as sticks and the other as spheres.  Then make  
the spheres a transparent color.  More details below....

However, I don't think this will look very good because you see all  
the sphere intersections.  Showing a transparent surface would look  
better.  The tricky part in that case would be getting surfaces that  
enclose the sets of atoms you want rather than the entire structure,  
where a given residue might only contribute a tiny scrap to the  
molecule's surface.

First, the transparent spheres example commands:

open 1zik
open 1zik
disp :tyr
rep sphere #1
colordef tyellow 1 1 0 .5
color tyellow #1

(or you could skip the colordef and just use "color 1,1,0,.5 #1" but  
sometimes it is more convenient to define a bunch of transparent  
colors first, or have a command file to do that, and then use them  
later)

If you use the surface approach, it is not necessary to open the  
structure twice, and it is easier to just make the surface transparent  
without changing its color (see Actions... Surface menu and/or  
"surftransparency" command).  There are at least a couple different  
surface approaches.

(A) molecular surface, but then you must use surfcat to make the  
surface enclose just the sets of atoms you want:

open 1zik
disp :tyr
surf :tyr
(see that only the patches for those residues in the context of the  
whole surface are shown)
surfcat mytyrs :tyr
surf mytyrs

... and then color the surface and make it transparent as desired

(B) use "molmap" command to make a density map from specified atoms  
which is shown as an isosurface, but that would not automatically be  
at the VDW surface... you'd have to play with the contour level

open 1zik
molmap :tyr 2

and then play around with contour level and use various other options  
in Volume Viewer to adjust appearance (set color, make transparent,  
see "Features... Surface and Mesh Options" for smoothing etc.).  You  
can also use the "Actions... Surface" menu and command  
"surftransparency" on this kind of surface, at least in recent  
versions of Chimera.

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

On Sep 30, 2009, at 8:33 AM, Waight, Andrew wrote:

> Hello everyone again.
>
>
>                     I apologize for a potentially embarassing  
> question but is it possible to display sidechains as transparent  
> spheres with solid stick representation inside. Seeing as I also  
> can't find an image in the Chimera gallery where it is represented  
> as such, I am wondering if it is possible to individually color (and  
> set opacity) on spheres. I am also aware that vdw will create dots  
> of varying density, but is it alternatively possible to display vdw  
> as solid surface with opacity. Thanks to all for your patience.
>
>                                                                                                                      Drew
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use  
> of the intended recipient(s) and may contain information that is  
> proprietary, confidential, and exempt from disclosure under  
> applicable law. Any unauthorized review, use, disclosure, or  
> distribution is prohibited. If you have received this email in error  
> please notify the sender by return email and delete the original  
> message. Please note, the recipient should check this email and any  
> attachments for the presence of viruses. The organization accepts no  
> liability for any damage caused by any virus transmitted by this  
> email.
> =================================



From bongini at fi.infn.it  Wed Sep 30 15:40:10 2009
From: bongini at fi.infn.it (lorenzo)
Date: Thu, 01 Oct 2009 00:40:10 +0200
Subject: [Chimera-users] mouse selection not working
Message-ID: <1254350410.7012.19.camel@ubuntu.ubuntu-domain>

Hi everybody,
I just installed chimera-1.3-linux.exe on an atom netbook. The OS is
ubuntu 9.04. My problem is that the mouse selection tool does not work.
To complete the scenario I add a few details 
1) I don't have the green outline and setting Fill mode for selection
highlighting in Preferences does not work around the problem (probably
just a screen setting problem).
2) Other forms of selections work. For example by Select -> Chemistry ->
Element -> H and then by Actions -> Atoms/Bonds -> Delete I can delete
hydrogens. 
3) I cannot delete anything that I select by ctrl + mouse left button.
4) libgl1-mesa-glx and libgl1-mesa-dri are installed. 

Thanks for your attention

     Lorenzo Bongini