Dear All, It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-dev-request@cgl.ucsf.edu Data: Dimecres, Juliol 22, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 7
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Today's Topics:
1. small suggestion regarding savepos (Jean Didier Pie Marechal) 2. Re: small suggestion regarding savepos (Eric Pettersen)
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Message: 1 Date: Wed, 22 Jul 2009 13:20:56 +0200 From: Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> Subject: [chimera-dev] small suggestion regarding savepos To: chimera-dev@cgl.ucsf.edu Message-ID: <3a0ecec54f4c.4a671238@uab.es> Content-Type: text/plain; charset=iso-8859-1
Dear all,
I see that when I close a session, the savepos list continues containing the poses I defined for my anterior session. May be that is something you want to have this way, but I was wondering if the savepos (with an option for example) could list only the poses for the working session.
All the best, 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@uab.es
------------------------------
Message: 2 Date: Wed, 22 Jul 2009 11:43:20 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [chimera-dev] small suggestion regarding savepos To: JeanDidier.Marechal@uab.es Cc: chimera-dev@cgl.ucsf.edu, Chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <D600289F-8E55-4765-96AB-F2F4E264138C@cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1"
Hi JD, I think you're right: closing a session should clear saved positions. In tomorrow's build that's what will happen.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 22, 2009, at 4:20 AM, Jean Didier Pie Marechal wrote:
Dear all,
I see that when I close a session, the savepos list continues containing the poses I defined for my anterior session. May be that is something you want to have this way, but I was wondering if the savepos (with an option for example) could list only the poses for the working session.
All the best, 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@uab.es
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi JD, I believe we no longer provide the programmer's reference guide. It was automatically generated from source code comments using HappyDoc. It's quality was so poor we stopped generating it. Tom -------- Original Message -------- Subject: [chimera-dev] Programmer's reference From: Jean Didier Pie Marechal To: chimera-dev@cgl.ucsf.edu Date: 7/24/09 2:34 AM
Dear All,
It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server?
All the best, JD
Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es
----- Missatge original ----- De: chimera-dev-request@cgl.ucsf.edu Data: Dimecres, Juliol 22, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 7
Send Chimera-dev mailing list submissions to chimera-dev@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-dev-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..."
Today's Topics:
1. small suggestion regarding savepos (Jean Didier Pie Marechal) 2. Re: small suggestion regarding savepos (Eric Pettersen)
-------------------------------------------------------------------- --
Message: 1 Date: Wed, 22 Jul 2009 13:20:56 +0200 From: Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> Subject: [chimera-dev] small suggestion regarding savepos To: chimera-dev@cgl.ucsf.edu Message-ID: <3a0ecec54f4c.4a671238@uab.es> Content-Type: text/plain; charset=iso-8859-1
Dear all,
I see that when I close a session, the savepos list continues containing the poses I defined for my anterior session. May be that is something you want to have this way, but I was wondering if the savepos (with an option for example) could list only the poses for the working session.
All the best, 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@uab.es
------------------------------
Message: 2 Date: Wed, 22 Jul 2009 11:43:20 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [chimera-dev] small suggestion regarding savepos To: JeanDidier.Marechal@uab.es Cc: chimera-dev@cgl.ucsf.edu, Chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <D600289F-8E55-4765-96AB-F2F4E264138C@cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1"
Hi JD, I think you're right: closing a session should clear saved positions. In tomorrow's build that's what will happen.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 22, 2009, at 4:20 AM, Jean Didier Pie Marechal wrote:
Dear all,
I see that when I close a session, the savepos list continues containing the poses I defined for my anterior session. May be
that
is something you want to have this way, but I was wondering if
the
savepos (with an option for example) could list only the poses
for
the working session.
All the best, 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@uab.es
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Tom and All, thanks for the answer. I knew the pdf was removed, but not the full reference. Though it was complicated sometime to get to the right place, I finally got used to it and it was useful to me. Do you think of posting another kind of reference in the future or will you stop to provide any? all the best, JD -------- Original Message -------- Subject: Re: [chimera-dev] Programmer's refere <goddard@cgl.ucsf.edu> To: Jean Didier Marechal Date: 7/24/09 10:10 PM
Hi JD,
I believe we no longer provide the programmer's reference guide. It was automatically generated from source code comments using HappyDoc. It's quality was so poor we stopped generating it.
Tom
-------- Original Message -------- Subject: [chimera-dev] Programmer's reference From: Jean Didier Pie Marechal To: chimera-dev@cgl.ucsf.edu Date: 7/24/09 2:34 AM
Dear All,
It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server?
All the best, JD
Hi JD, The automatically generated programmer's reference was removed from the Chimera distribution because it was large and rarely useful. When it was taken out of the distribution we did not set up a daily automated build for a web site reference guide. I believe that used to come from the automatic Chimera distribution builds. We'll discuss whether we should bring this back at this Thursday's developer meeting. For development here we use dir() and help() in the IDLE shell as described previously http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002354.html Also we look directly at Python code files which are included with all Chimera distributions under the chimera/share directory (Chimera.app/Contents/Resources/share on Mac) and we look at the C++ header files which are included in distributions under chimera/include. Of course we work all the time on Chimera code so these methods may not be ideal for your less frequent programming needs. While we ponder this, you can use the Chimera 1.3 programmer's reference included with the distribution in share/chimera/helpdir/ProgrammersGuide Tom -------- Original Message -------- Subject: Re: [chimera-dev] Programmer's reference From: Thomas Goddard To: chimera-dev@cgl.ucsf.edu Date: 7/27/09 1:34 PM
Hi Tom and All,
thanks for the answer. I knew the pdf was removed, but not the full reference. Though it was complicated sometime to get to the right place, I finally got used to it and it was useful to me.
Do you think of posting another kind of reference in the future or will you stop to provide any?
all the best, JD
-------- Original Message -------- Subject: Re: [chimera-dev] Programmer's refere <goddard@cgl.ucsf.edu> To: Jean Didier Marechal Date: 7/24/09 10:10 PM
Hi JD,
I believe we no longer provide the programmer's reference guide. It was automatically generated from source code comments using HappyDoc. It's quality was so poor we stopped generating it.
Tom
-------- Original Message -------- Subject: [chimera-dev] Programmer's reference From: Jean Didier Pie Marechal To: chimera-dev@cgl.ucsf.edu Date: 7/24/09 2:34 AM
Dear All,
It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server?
All the best, JD
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi JD, We decided at or Chimera developer meeting today that we would revive the programmer's reference on the web. It will still be auto-generated from code comments, probably from a newer version of HappyDoc. Eric Pettersen will look into it. It may be many months away since we have lots of higher priority projects. Tom -------- Original Message -------- Subject: Re: [chimera-dev] Programmer's reference From: Thomas Goddard To: chimera-dev@cgl.ucsf.edu Date: 7/27/09 4:58 PM
Hi JD,
The automatically generated programmer's reference was removed from the Chimera distribution because it was large and rarely useful. When it was taken out of the distribution we did not set up a daily automated build for a web site reference guide. I believe that used to come from the automatic Chimera distribution builds. We'll discuss whether we should bring this back at this Thursday's developer meeting.
For development here we use dir() and help() in the IDLE shell as described previously http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002354.html
Also we look directly at Python code files which are included with all Chimera distributions under the chimera/share directory (Chimera.app/Contents/Resources/share on Mac) and we look at the C++ header files which are included in distributions under chimera/include. Of course we work all the time on Chimera code so these methods may not be ideal for your less frequent programming needs.
While we ponder this, you can use the Chimera 1.3 programmer's reference included with the distribution in
share/chimera/helpdir/ProgrammersGuide
Tom
-------- Original Message -------- Subject: Re: [chimera-dev] Programmer's reference From: Thomas Goddard To: chimera-dev@cgl.ucsf.edu Date: 7/27/09 1:34 PM
Hi Tom and All,
thanks for the answer. I knew the pdf was removed, but not the full reference. Though it was complicated sometime to get to the right place, I finally got used to it and it was useful to me.
Do you think of posting another kind of reference in the future or will you stop to provide any?
all the best, JD
-------- Original Message -------- Subject: Re: [chimera-dev] Programmer's refere <goddard@cgl.ucsf.edu> To: Jean Didier Marechal Date: 7/24/09 10:10 PM
Hi JD,
I believe we no longer provide the programmer's reference guide. It was automatically generated from source code comments using HappyDoc. It's quality was so poor we stopped generating it.
Tom
-------- Original Message -------- Subject: [chimera-dev] Programmer's reference From: Jean Didier Pie Marechal To: chimera-dev@cgl.ucsf.edu Date: 7/24/09 2:34 AM
Dear All,
It seems that we have a problem in getting to the programmer's reference. Is there something wrong with the server?
All the best, JD
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (3)
-
Jean Didier Pie Marechal -
Thomas Goddard -
Tom Goddard