From dmitry_o at org.chem.msu.su Wed Oct 4 05:30:01 2006
From: dmitry_o at org.chem.msu.su (Dmitry Osolodkin)
Date: Wed, 04 Oct 2006 16:30:01 +0400
Subject: [Chimera-users] OpenGL error in GfxInfo::initialize 'out of memory'
Message-ID: <4523A949.8080105@org.chem.msu.su>
Hello all,
I have a very small but annoying problem.
I had two versions of libGL.so.1, so I have renamed the version in
/usr/X11R6/lib/. Now I can run Chimera, but it works rather slow and
says OpenGL error in GfxInfo::initialize 'out of memory'. I use Mandriva
Linux 2006 and FireGL drivers by ATI.
Could anone help me?
Thanks.
Dmitry Osolodkin
From goddard at cgl.ucsf.edu Wed Oct 4 14:51:51 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 4 Oct 2006 14:51:51 -0700 (PDT)
Subject: [Chimera-users] Slicing a 3d model
Message-ID: <200610042151.k94Lppd62001099@guanine.cgl.ucsf.edu>
Hi Pu Qian,
Use clip planes to cut a model in half in Chimera. There are two
types of clip planes. The front and back clip planes are always
parallel to the screen. The per-model clip planes can be oriented at
any angle. Both can clip away the back as well as the front. The
following web page describes how to use both for EM density maps.
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#slab
Clipping works on all types of data in Chimera including atomic models
of proteins. For EM data it helps to have Chimera cover the holes left
when a contour surface is clipped. This is described here.
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#capping
Also you can color according to density on the sliced surface.
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorcap
All of these URLs come from the Chimera guide to volume display
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html
and you may find other useful features for viewing your EM map there.
The following page shows examples of clipping, capping and coloring
including a movie of a slab moving through an EM map of a virus particle.
http://www.cgl.ucsf.edu/chimera/experimental/viper_em/viper_em.html
Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR,
Purdue image format, ...)
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
I do not know if IMAGIC5 uses any of these formats or has its own. Chimera
does not read any specific IMAGIC5 format.
Tom
> From: P Qian
> Date: October 4, 2006 1:43:50 PM PDT
> Subject: Sheffield Qian, how to make cut 3d model
>
>
>
> To whom it may concern,
>
> I'm a new user of Chimera. It is a very good software!
>
> Here, I would like to ask you a few questions? To show inside of
> protein
> (3d model),I need to cut it into half (sometime, maybe only part,
> for example,
> 1/4 etc.). Just like an apple, if I want to show its core, I need
> to cut the
> apple into two parts from its middle. Does Chimera has such
> function? (I think
> it has.) My 3d data comes from electron microscopy single particle
> analysis
> using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so,
> which type of
> 3d data I should produce for Chimera? It would be a great
> appreciated if you
> could reply me in your convenience. Hope it will not bother you too
> much.
>
> Sincerely yours,
>
>
> Pu Qian
>
> Dr. Pu Qian
> Department of Molecular Biology
> The University of Sheffield
> Firth Court, Western Bank
> Sheffield, S10 2TN
> UK
>
From jayant_jacques at rediffmail.com Wed Oct 4 16:13:20 2006
From: jayant_jacques at rediffmail.com (jayant_jacques)
Date: 4 Oct 2006 23:13:20 -0000
Subject: [Chimera-users] volumetric filling
Message-ID: <20061004231320.11920.qmail@webmail58.rediffmail.com>
hi!
I am striving to perform voluertric filling of a crystal structure into an EM reconstruction. I have down loaded and complited the Linux_64 bit version.
I first load my crystal structure and then the EM reconstruction on the same screen and set the EM reconstruction as DATa. I am not able to figure out where the FIT buttons is located in the pop up menus!!!
I would be very grateful if you could help me sort out this issue!
Thanks
Jayant
NB I am using the online manual to help me in this endeavour
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodels.html
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA.
http://www.chick.com/reading/tracts/0001/0001_01.asp
Phone office:335-5937, Cell:1-509-432-5790
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From goddard at cgl.ucsf.edu Wed Oct 4 16:23:18 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 4 Oct 2006 16:23:18 -0700 (PDT)
Subject: [Chimera-users] volumetric filling
In-Reply-To: <20061004231320.11920.qmail@webmail58.rediffmail.com>
(jayant_jacques@rediffmail.com)
References: <20061004231320.11920.qmail@webmail58.rediffmail.com>
Message-ID: <200610042323.k94NNIFu2025419@guanine.cgl.ucsf.edu>
Hi Jayant,
The Chimera guide to volume data display gives a step by step
description of fitting atomic models in EM maps.
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmodel
Other descriptions on that page may be useful for looking at your EM data.
The Chimera User's Guide is oriented towards giving complete
descriptions of Chimera capabilities and is where you should look to
get the fine details.
Tom
From meng at cgl.ucsf.edu Wed Oct 4 16:23:30 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 4 Oct 2006 16:23:30 -0700
Subject: [Chimera-users] volumetric filling
In-Reply-To: <20061004231320.11920.qmail@webmail58.rediffmail.com>
References: <20061004231320.11920.qmail@webmail58.rediffmail.com>
Message-ID:
Hello!
One way to get this tool is to choose
Tools... Volume Data... Fit Models in Maps
from the Chimera menu.
Near the top of the man page you mention, there is a link "several
ways to start" that talks about all the different ways to start
tools. I hope this helps,
Elaine
On Oct 4, 2006, at 4:13 PM, jayant_jacques wrote:
>
> hi!
> I am striving to perform voluertric filling of a crystal structure
> into an EM reconstruction. I have down loaded and complited the
> Linux_64 bit version.
> I first load my crystal structure and then the EM reconstruction on
> the same screen and set the EM reconstruction as DATa. I am not
> able to figure out where the FIT buttons is located in the pop up
> menus!!!
> I would be very grateful if you could help me sort out this issue!
> Thanks
> Jayant
> NB I am using the online manual to help me in this endeavour
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/
> fitmodels.html
>
> Jayasundar Jayant James
> Postdoc,
> Department of Veterinary and Comparative Anatomy, Pharmacology and
> Physiology(VCAPP), Washington state university, Pullman 99164-6520,
> USA.
> http://www.chick.com/reading/tracts/0001/0001_01.asp
> Phone office:335-5937, Cell:1-509-432-5790
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From gregc at cgl.ucsf.edu Wed Oct 4 16:35:09 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Wed, 4 Oct 2006 16:35:09 -0700 (PDT)
Subject: [Chimera-users] volumetric filling
In-Reply-To: <20061004231320.11920.qmail@webmail58.rediffmail.com>
References: <20061004231320.11920.qmail@webmail58.rediffmail.com>
Message-ID:
On Wed, 4 Oct 2006, jayant_jacques wrote:
> I have down loaded and complited the Linux_64 bit version.
Please use the 32-bit version, the 64-bit version hasn't been updated in a
long time and there have been lots of improvements and bug fixes since
then. If your data won't fit in 32-bits, please let us know.
Greg Couch
UCSF Computer Graphics Lab
From bd92 at mail.gatech.edu Thu Oct 5 08:34:00 2006
From: bd92 at mail.gatech.edu (Batsal Devkota)
Date: Thu, 5 Oct 2006 11:34:00 -0400
Subject: [Chimera-users] Spider to Brix
Message-ID: <2DC6FE10-F236-4551-84BF-0F5B76972ABB@mail.gatech.edu>
Hi,
When I convert spider file to brix and load both of them in Chimera,
they do not superimpose on top of each other. I adjusted the origin
to be 0,0,0 for both the maps and still the maps seem to be rotated
with respect to one another.
any insight??
Thank you,
Batsal.
--------------------------------------------------
Batsal Devkota
Graduate Student, School of Biology
GeorgiaInstitute
ofTechnology
Atlanta, GA 30332-0400
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From goddard at cgl.ucsf.edu Thu Oct 5 10:59:13 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 5 Oct 2006 10:59:13 -0700 (PDT)
Subject: [Chimera-users] Spider to Brix
In-Reply-To: <2DC6FE10-F236-4551-84BF-0F5B76972ABB@mail.gatech.edu> (message
from Batsal Devkota on Thu, 5 Oct 2006 11:34:00 -0400)
References: <2DC6FE10-F236-4551-84BF-0F5B76972ABB@mail.gatech.edu>
Message-ID: <200610051759.k95HxDZt1830635@guanine.cgl.ucsf.edu>
Hi Batsal,
Are the SPIDER and BRIX maps in Chimera related by some permutation of
the x, y, or z axes? If there are a different number of grid points
reported by the Chimera volume viewer dialog along each axis then the
permutation should be apparent. If the axes have the same number of
grid points, you might want to do a test with a map having different
numbers of grid points along each axis.
What conversion program did you use. I think this is most likely a
problem with that program. But it could be a Chimera problem. The SPIDER
format includes phi, theta, and gamma header values that specify a rotation
that the Chimera file reader ignores.
Here is documentation on SPIDER file format
http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html
and here is documentation on BRIX format
http://www.uoxray.uoregon.edu/tnt/manual/node104.html
Let me know what you find out.
Tom
From jkhilmer at gmail.com Thu Oct 5 13:55:12 2006
From: jkhilmer at gmail.com (Jonathan Hilmer)
Date: Thu, 5 Oct 2006 14:55:12 -0600
Subject: [Chimera-users] Chimera-users Digest, Vol 42, Issue 2
In-Reply-To:
References:
Message-ID: <81277ce10610051355v101d4a5aqb265872e65cd13e4@mail.gmail.com>
Pu Qian,
Although resources-intensive, I find it useful to have multiple,
identical, overlapping copies of the same density set. It allows
complex 'removal' of sections in the final image by the combination of
multiple clipping planes. For example, the three planes with
definitions of [1,0,0], [0,1,0], and [0,0,1] all with an origin at the
center of your data will cut away 1/8 of a spherical region, if you
have three copies of the density loaded. This also makes it easy to
animate the cutout. The alternative is to use the volume eraser
(http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html),
which works, but I've found it less useful for movies. When working
with large data sets and this method, use cropped density sets to
minimize unnecessary resource usage.
Jonathan
> > To whom it may concern,
> >
> > I'm a new user of Chimera. It is a very good software!
> >
> > Here, I would like to ask you a few questions? To show inside of
> > protein
> > (3d model),I need to cut it into half (sometime, maybe only part,
> > for example,
> > 1/4 etc.). Just like an apple, if I want to show its core, I need
> > to cut the
> > apple into two parts from its middle. Does Chimera has such
> > function? (I think
> > it has.) My 3d data comes from electron microscopy single particle
> > analysis
> > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so,
> > which type of
> > 3d data I should produce for Chimera? It would be a great
> > appreciated if you
> > could reply me in your convenience. Hope it will not bother you too
> > much.
> >
> > Sincerely yours,
> >
> >
> > Pu Qian
> >
> > Dr. Pu Qian
> > Department of Molecular Biology
> > The University of Sheffield
> > Firth Court, Western Bank
> > Sheffield, S10 2TN
> > UK
From gregc at cgl.ucsf.edu Thu Oct 5 16:17:24 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 5 Oct 2006 16:17:24 -0700 (PDT)
Subject: [Chimera-users] OpenGL error in GfxInfo::initialize 'out of
memory'
In-Reply-To: <4523A949.8080105@org.chem.msu.su>
References: <4523A949.8080105@org.chem.msu.su>
Message-ID:
On Wed, 4 Oct 2006, Dmitry Osolodkin wrote:
> I have a very small but annoying problem.
> I had two versions of libGL.so.1, so I have renamed the version in
> /usr/X11R6/lib/. Now I can run Chimera, but it works rather slow and
> says OpenGL error in GfxInfo::initialize 'out of memory'. I use Mandriva
> Linux 2006 and FireGL drivers by ATI.
> Could anone help me?
If you had to rename one of the versions of libGL.so.1, then you probably
had a problem installing the ATI drivers or you forgot to reinstall the
ATI/NVidia driver when you upgraded your kernel and/or X11. So the first
thing to do is to reinstall the ATI driver.
If the ATI drivers are properly installed (using the latest 8.29.6 drivers),
you will see (with different dates):
% cd /usr/lib; ls -l libGL.so*
lrwxrwxrwx 1 root root 27 Oct 5 15:44 libGL.so -> /usr/X11R6/lib/libGL.so.1.2
lrwxrwxrwx 1 root root 27 Oct 5 15:44 libGL.so.1 -> /usr/X11R6/lib/libGL.so.1.2
% cd /usr/X11R6/lib; ls -l libGL.so*
lrwxrwxrwx 1 root root 27 Oct 5 15:44 libGL.so -> /usr/X11R6/lib/libGL.so.1.2
lrwxrwxrwx 1 root root 27 Oct 5 15:44 libGL.so.1 -> /usr/X11R6/lib/libGL.so.1.2
-rw-r--r-- 1 root root 783353 Oct 5 15:44 libGL.so.1.2
After you reinstall the ATI driver, be sure to reboot. Then run
glxinfo | grep "^OpenGL renderer"
to confirm that the ATI driver instead of the Mesa driver is being used.
If you need further assistance, please use chimera's Help / Report A Bug
dialog and I'll work with you to figure things out.
Greg Couch
UCSF Computer Graphics Lab
From hornak at csb.sunysb.edu Fri Oct 6 05:43:10 2006
From: hornak at csb.sunysb.edu (Viktor Hornak)
Date: Fri, 06 Oct 2006 08:43:10 -0400
Subject: [Chimera-users] window size
Message-ID: <45264F5E.2020607@csb.sunysb.edu>
Dear All,
I was wondering if there's chimera command that sets the size of chimera
window. Basically I just want to have a well defined window size when I
save pictures (or movies)...
Thanks,
-Viktor
--
Viktor Hornak
SUNY at Stony Brook
From meng at cgl.ucsf.edu Fri Oct 6 10:18:14 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 6 Oct 2006 10:18:14 -0700
Subject: [Chimera-users] window size
In-Reply-To: <45264F5E.2020607@csb.sunysb.edu>
References: <45264F5E.2020607@csb.sunysb.edu>
Message-ID: <7c942cc3c4552703b0dec5dd65264360@cgl.ucsf.edu>
Hi Viktor,
From our experimental features page
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
you can download a "set magnification and window size" feature that
includes a "windowsize" command.
A related feature (unfortunately broken in past releases, but will be
available in the next release) is the --geometry startup option. We
plan to make a release this month. The --geometry option is not quite
as straightforward as the windowsize command, because depending on the
system, the specified size might include some of the bars around the
graphics window. However, that just means you need to try it once, use
the "get pixels" button on the image-saving panel (File... Save Image)
to determine the actual graphics window dimensions, and at the next
startup use --geometry with the necessary additions or subtractions to
achieve the target size. That's what I've been doing.
Startup options are described here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html
However, if you are on a Windows system, it is not very convenient to
use startup options (one way is to make a separate Chimera shortcut and
modify its properties). If you are on Windows, getting the "windowsize"
command from the experimental features page may be the way to go.
I hope this helps,
Elaine
On Oct 6, 2006, at 5:43 AM, Viktor Hornak wrote:
> Dear All,
>
> I was wondering if there's chimera command that sets the size of
> chimera
> window. Basically I just want to have a well defined window size when I
> save pictures (or movies)...
>
> Thanks,
> -Viktor
>
> --
> Viktor Hornak
> SUNY at Stony Brook
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
From jayant_jacques at rediffmail.com Fri Oct 6 10:19:38 2006
From: jayant_jacques at rediffmail.com (jayant_jacques)
Date: 6 Oct 2006 17:19:38 -0000
Subject: [Chimera-users] fitting a protein inside an EM reconstruction
Message-ID: <20061006171938.26412.qmail@webmail9.rediffmail.com>
hi!
I am having a small problem in fitting crystal structures into the EM reconstruction.
Problem definition
When I open the protein that I am trying to fit into the EM map along side the EM map, the Em Map shrinks. The EM map which is the super set, which holds 3 proteins appears shrunk with respect to the protein that I am trying to fit inside the EM Map and the crystal structure How am I to overcome this hurdle?
thanks
Jayant
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA.
http://www.chick.com/reading/tracts/0001/0001_01.asp
Phone office:335-5937, Cell:1-509-432-5790
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From goddard at cgl.ucsf.edu Fri Oct 6 10:33:04 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Fri, 6 Oct 2006 10:33:04 -0700 (PDT)
Subject: [Chimera-users] fitting a protein inside an EM reconstruction
In-Reply-To: <20061006171938.26412.qmail@webmail9.rediffmail.com>
(jayant_jacques@rediffmail.com)
References: <20061006171938.26412.qmail@webmail9.rediffmail.com>
Message-ID: <200610061733.k96HX4iA1945291@guanine.cgl.ucsf.edu>
Hi Jayant,
The problem with the EM map being too small for the crystal model is
that the SPIDER map header does not say the grid plane spacing. Chimera
is giving it a default grid plane spacing of 1 angstrom. To fix this
you need to know the grid plane spacing, also called "voxel size" in
Angstroms. Then enter this value in volume dialog, using volume dialog
menu entry Features / Origigin and Scale. Probably the plane spacing is
the same along the x, y and z axes, so you will enter the same number in
the 3 voxel size fields, and press the Return key to then have the map
displayed at the new scale.
Unfortunately the above change does not modify your SPIDER file so it
will still have the wrong scale the next time you open it in Chimera.
Two solutions are to write the SPIDER map out in MRC format using the
volume dialog menu entry File / Save As, or save a Chimera session using
the main Chimera window menu entry File / Save Session As. Chimera is
not able to write out new SPIDER format maps.
Tom
From hornak at csb.sunysb.edu Fri Oct 6 14:00:30 2006
From: hornak at csb.sunysb.edu (Viktor Hornak)
Date: Fri, 06 Oct 2006 17:00:30 -0400
Subject: [Chimera-users] window size
Message-ID: <4526C3EE.7080508@csb.sunysb.edu>
Hi Elaine,
this is exactly what I needed. Also, thanks for a pointer to
experimental features page (it's nice!).
One other vaguely related question I had was whether it's possible to
find out what chimera commands correspond to actions picked from menus
or panels (e.g. Actions->Atoms/Bonds->Hide; Camera -> orthographic from
Viewing/Side View panel, etc.). My objective is to capture everything I
do in a specific session in chimera command scripts, which have an
advantage over saving the session in that 1) I see what I did directly
in the script, 2) these scripts are much smaller than session files.
Thanks for your help!
-Viktor
Elaine Meng wrote:
> Hi Viktor,
> From our experimental features page
>
> http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
>
> you can download a "set magnification and window size" feature that
> includes a "windowsize" command.
>
> A related feature (unfortunately broken in past releases, but will be
> available in the next release) is the --geometry startup option. We
> plan to make a release this month. The --geometry option is not quite
> as straightforward as the windowsize command, because depending on the
> system, the specified size might include some of the bars around the
> graphics window. However, that just means you need to try it once,
> use the "get pixels" button on the image-saving panel (File... Save
> Image) to determine the actual graphics window dimensions, and at the
> next startup use --geometry with the necessary additions or
> subtractions to achieve the target size. That's what I've been doing.
>
> Startup options are described here:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html
>
> However, if you are on a Windows system, it is not very convenient to
> use startup options (one way is to make a separate Chimera shortcut
> and modify its properties). If you are on Windows, getting the
> "windowsize" command from the experimental features page may be the
> way to go.
>
> I hope this helps,
> Elaine
>
> On Oct 6, 2006, at 5:43 AM, Viktor Hornak wrote:
>
>> Dear All,
>>
>> I was wondering if there's chimera command that sets the size of chimera
>> window. Basically I just want to have a well defined window size when I
>> save pictures (or movies)...
>>
>> Thanks,
>> -Viktor
>>
>> --
>> Viktor Hornak
>> SUNY at Stony Brook
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
> -----
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
From meng at cgl.ucsf.edu Fri Oct 6 17:55:33 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 6 Oct 2006 17:55:33 -0700
Subject: [Chimera-users] window size
In-Reply-To: <4526C3EE.7080508@csb.sunysb.edu>
References: <4526C3EE.7080508@csb.sunysb.edu>
Message-ID:
Hi Viktor,
You're welcome!
Unfortunately, although there is a large overlap between menu
operations and commands, there is not a 1-to-1 relationship, and
sometimes the mapping is not obvious. Some things can only be done in
menus or GUIs, some only with commands. A brief historical perspective:
as Chimera was created, many commands from Midas were reimplemented in
the new framework. Midas was almost completely command-driven. As
Chimera has been developed further, the Select and Actions menus and
many new tools with complex GUIs have been added. Some but not all of
these new tools have also been implemented as new commands.
The command
~display
will hide all the atoms and bonds, but there is no command for changing
to the orthographic projection.
If you (and other users out there) need particular operations to be
available as commands, let us know, and that will be factored in as we
set priorities.
Here are some ideas for figuring out correspondences, in order of
decreasing efficiency (in my opinion):
(a) see the Chimera Commands Index
http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/framecommand.html
or the Chimera Quick Reference (PDF file)
http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/quickref.pdf
which give brief explanations of what each command does; then you can
look at the detailed man page for a command if it sounds like what you
want.
(b) There is some degree of cross-referencing in the User's Guide; for
example, the Actions menu listing includes several "see also command"
links:
http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/
menu.html#menuactions
The two beginner tutorials go through mostly the same tasks, one using
the menu, the other using commands. However, it sounds like you are
beyond the beginner stage, and it might not be convenient to put up the
two tutorials in side-by-side browser windows.
(c) you can search for topics of interest with Help... Search
Documentation. The hits will generally include some command man pages.
I hope this helps,
Elaine
On Oct 6, 2006, at 2:00 PM, Viktor Hornak wrote:
> Hi Elaine,
>
> this is exactly what I needed. Also, thanks for a pointer to
> experimental features page (it's nice!).
>
> One other vaguely related question I had was whether it's possible to
> find out what chimera commands correspond to actions picked from menus
> or panels (e.g. Actions->Atoms/Bonds->Hide; Camera -> orthographic from
> Viewing/Side View panel, etc.). My objective is to capture everything I
> do in a specific session in chimera command scripts, which have an
> advantage over saving the session in that 1) I see what I did directly
> in the script, 2) these scripts are much smaller than session files.
>
> Thanks for your help!
> -Viktor
>
> Elaine Meng wrote:
>> Hi Viktor,
>> From our experimental features page
>>
>> http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
>>
>> you can download a "set magnification and window size" feature that
>> includes a "windowsize" command.
>>
>> A related feature (unfortunately broken in past releases, but will be
>> available in the next release) is the --geometry startup option. We
>> plan to make a release this month. The --geometry option is not quite
>> as straightforward as the windowsize command, because depending on the
>> system, the specified size might include some of the bars around the
>> graphics window. However, that just means you need to try it once,
>> use the "get pixels" button on the image-saving panel (File... Save
>> Image) to determine the actual graphics window dimensions, and at the
>> next startup use --geometry with the necessary additions or
>> subtractions to achieve the target size. That's what I've been doing.
>>
>> Startup options are described here:
>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html
>>
>> However, if you are on a Windows system, it is not very convenient to
>> use startup options (one way is to make a separate Chimera shortcut
>> and modify its properties). If you are on Windows, getting the
>> "windowsize" command from the experimental features page may be the
>> way to go.
>>
>> I hope this helps,
>> Elaine
>>
>> On Oct 6, 2006, at 5:43 AM, Viktor Hornak wrote:
>>
>>> Dear All,
>>>
>>> I was wondering if there's chimera command that sets the size of
>>> chimera
>>> window. Basically I just want to have a well defined window size
>>> when I
>>> save pictures (or movies)...
>>>
>>> Thanks,
>>> -Viktor
>>>
>>> --
>>> Viktor Hornak
>>> SUNY at Stony Brook
>>>
>
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
From bshaanan at bgu.ac.il Tue Oct 10 07:48:59 2006
From: bshaanan at bgu.ac.il (Boaz Shaanan)
Date: Tue, 10 Oct 2006 14:48:59 GMT
Subject: [Chimera-users] Request: can model selection be added to the pull
down selection menu?
Message-ID:
Hi,
I wonder if you could consider adding the option of selecting models to the pull-down selection menu. Right now, only chains (and other things) can be selected but quite often, when reading different models with the same chain names, the only way to select specific chains from a model would be by using the command line where models can be specified. This works of course, but having the model-selection option in the pull-down menu might add flexibility. What do you think ?
Regards,
Boaz
Boaz Shaanan, Ph.D.
Associate Professor
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel?
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From meng at cgl.ucsf.edu Tue Oct 10 08:51:03 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 10 Oct 2006 08:51:03 -0700
Subject: [Chimera-users] Request: can model selection be added to the
pull down selection menu?
In-Reply-To:
References:
Message-ID: <396001F4-11C4-4E80-8BDF-9D10E8659AE6@cgl.ucsf.edu>
Hi Boaz,
I thought I'd mention one approach, in case you didn't know about it:
"select" is one of the functions listed in the right side of the
Model Panel. You could use "Configure..." on the Model Panel to make
model selection what happens when you double-click the line for that
model. After that, you need only open the Model Panel (or leave it
up) and double-click different lines to select different models.
Best,
Elaine
On Oct 10, 2006, at 2:48 PM, Boaz Shaanan wrote:
> Hi,
>
> I wonder if you could consider adding the option of selecting
> models to the pull-down selection menu. Right now, only chains (and
> other things) can be selected but quite often, when reading
> different models with the same chain names, the only way to select
> specific chains from a model would be by using the command line
> where models can be specified. This works of course, but having the
> model-selection option in the pull-down menu might add flexibility.
> What do you think ?
>
> Regards,
>
> Boaz
>
>
> Boaz Shaanan, Ph.D.
> Associate Professor
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> ?
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From pett at cgl.ucsf.edu Tue Oct 10 10:21:35 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 10 Oct 2006 10:21:35 -0700
Subject: [Chimera-users] Request: can model selection be added to the
pull down selection menu?
In-Reply-To:
References:
Message-ID: <41763C0F-1A6F-4776-8A68-0D1DEC2DDC97@cgl.ucsf.edu>
Hi Boaz,
I intend to make the chain-selection menu change to using rollovers
when multiple models have that chain, but haven't gotten to it yet.
I'll increase the priority of getting that done. It won't make it
into the upcoming release since the code is now frozen for testing.
Perhaps the release after this next one...
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu
On Oct 10, 2006, at 2:48 PM, Boaz Shaanan wrote:
> Hi,
>
> I wonder if you could consider adding the option of selecting
> models to the pull-down selection menu. Right now, only chains (and
> other things) can be selected but quite often, when reading
> different models with the same chain names, the only way to select
> specific chains from a model would be by using the command line
> where models can be specified. This works of course, but having the
> model-selection option in the pull-down menu might add flexibility.
> What do you think ?
>
> Regards,
>
> Boaz
>
>
> Boaz Shaanan, Ph.D.
> Associate Professor
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> ?
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From okabe at cherry.bio.titech.ac.jp Tue Oct 10 20:13:36 2006
From: okabe at cherry.bio.titech.ac.jp (Atsutoshi Okabe)
Date: Wed, 11 Oct 2006 12:13:36 +0900
Subject: [Chimera-users] Vilualizing solvent distribution
Message-ID: <20061011031503.4D2511D333D@vc-s.net.titech.ac.jp>
Dear all,
I want to visualize solvent(water) distributions around one solute molecule.
I do molecular dynamics calculation with Amber8 program.
So I got the following ouput file using grid command of Ptraj module to
analyze trajectories.
This line is ignored
1
rdparm generated grid density
100 -49 50 100 -49 50 100 -49 50
30.000 30.000 30.000 90.000 90.000 90.000
ZYX
-49
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
I think the output is in the format of a XPLOR formatted contour file and
can visualize this output data
within chimera soft ware. But I don't know how to treat this out put file in
chimera .
Can I use this file directory in chimera or have to do anything else before
I use chimera?
Thanks
Atsutoshi
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From goddard at cgl.ucsf.edu Wed Oct 11 09:43:02 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 11 Oct 2006 09:43:02 -0700 (PDT)
Subject: [Chimera-users] Vilualizing solvent distribution
In-Reply-To: <20061011031503.4D2511D333D@vc-s.net.titech.ac.jp>
(okabe@cherry.bio.titech.ac.jp)
References: <20061011031503.4D2511D333D@vc-s.net.titech.ac.jp>
Message-ID: <200610111643.k9BGh2tQ1932784@guanine.cgl.ucsf.edu>
Hi Atsutoshi,
You should be able to open the XPLOR format file using Chimera menu
entry File / Open.... If the file name ends in ".xplor" it will be
opened in XPLOR format. Or if it has a different file suffix you
can choose "all (ask type)" from the File / Open dialog "File type"
menu, then open the file and you will be asked to identify the file
type from a list. Choose "CNS or XPLOR density map".
Opening the file will display it as a contour surface using the
volume viewer tool. You may want to switch to "solid" display style
in the volume dialog. By moving the square nodes on the data histogram
in the volume dialog you can adjust brightness and control what map
values are displayed.
Chimera can also directly compute occupancy of water or ions from an
MD trajectory. See the "occupancy analysis" section of the Chimera MD Movie
tool documentation:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
Tom
From ThodeL74 at ops.org Thu Oct 12 06:32:17 2006
From: ThodeL74 at ops.org (Lucas J. Thode)
Date: Thu, 12 Oct 2006 08:32:17 -0500
Subject: [Chimera-users] single-sequence FASTA file does not open
Message-ID:
In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot open
a FASTA file that contains a single sequence. (The file in question is
attached and looks to be a valid FASTA file according to the documentation
I have read on the FASTA format.) What should I do about this issue?
Error log:
Opening F:\H Biotech Engineering\cftr.fasta
Error reading F:\H Biotech Engineering\cftr.fasta:
IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
Engineering\cftr.fasta'; check your alignment file for errors
(see reply log for Python traceback info)
Traceback (most recent call last):
File "C:\Program Files\Chimera\share\__main__.py", line 59, in ?
value = chimeraInit.init(sys.argv)
File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init
tkgui.eventLoop()
File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in
eventLoop
app.mainloop()
File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in
mainloop
self.tk.mainloop(n)
File "C:\Program
Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line
1747, in __call__
return apply(self.func, args)
File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 229,
in
self.__buttonFuncName(txt))()
File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 470,
in OK
self.Apply()
File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, in
Apply
openPath(path, ftype)
File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, in
openPath
mols = chimera.openModels.open(path, type=ftype)
File "C:\Program Files\Chimera\share\chimera\__init__.py", line 1086, in
open
models = func(filename, *args, **kw)
File "C:\Program
Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in
lambda fn, e=emo, ft=fileType: e.open(fn, ft),
File "C:\Program
Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in open
self.module('MAViewer').MAViewer(fileName, fileType)
File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line
59, in __init__
seqs, fileAttrs, fileMarkups = self.readFile(
File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line
761, in readFile
seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType)
File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", line
100, in parseFile
raise IOError("Only one sequence found in %s file"
IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
Engineering\cftr.fasta'; check your alignment file for errors
Done opening F:\H Biotech Engineering\cftr.fasta
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From ThodeL74 at ops.org Thu Oct 12 06:34:11 2006
From: ThodeL74 at ops.org (Lucas J. Thode)
Date: Thu, 12 Oct 2006 08:34:11 -0500
Subject: [Chimera-users] Fwd: single-sequence FASTA file does not open
Message-ID:
Oops, sorry about double-posting this, but I forgot to mention that I am
not on the list, so remember to CC me.
----- Original Message -----
In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot open
a FASTA file that contains a single sequence. (The file in question is
attached and looks to be a valid FASTA file according to the documentation
I have read on the FASTA format.) What should I do about this issue?
Error log:
Opening F:\H Biotech Engineering\cftr.fasta
Error reading F:\H Biotech Engineering\cftr.fasta:
IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
Engineering\cftr.fasta'; check your alignment file for errors
(see reply log for Python traceback info)
Traceback (most recent call last):
File "C:\Program Files\Chimera\share\__main__.py", line 59, in ?
value = chimeraInit.init(sys.argv)
File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init
tkgui.eventLoop()
File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in
eventLoop
app.mainloop()
File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in
mainloop
self.tk.mainloop(n)
File "C:\Program
Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line
1747, in __call__
return apply(self.func, args)
File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 229,
in
self.__buttonFuncName(txt))()
File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 470,
in OK
self.Apply()
File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, in
Apply
openPath(path, ftype)
File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, in
openPath
mols = chimera.openModels.open(path, type=ftype)
File "C:\Program Files\Chimera\share\chimera\__init__.py", line 1086, in
open
models = func(filename, *args, **kw)
File "C:\Program
Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in
lambda fn, e=emo, ft=fileType: e.open(fn, ft),
File "C:\Program
Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in open
self.module('MAViewer').MAViewer(fileName, fileType)
File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line
59, in __init__
seqs, fileAttrs, fileMarkups = self.readFile(
File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line
761, in readFile
seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType)
File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", line
100, in parseFile
raise IOError("Only one sequence found in %s file"
IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
Engineering\cftr.fasta'; check your alignment file for errors
Done opening F:\H Biotech Engineering\cftr.fasta
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From meng at cgl.ucsf.edu Thu Oct 12 10:00:16 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 12 Oct 2006 10:00:16 -0700
Subject: [Chimera-users] Fwd: single-sequence FASTA file does not open
In-Reply-To:
References:
Message-ID: <04d8aa3569061b17652208467f8060ee@cgl.ucsf.edu>
Hi Lucas,
Chimera displays alignments of two or more sequences, not a single
sequence by itself. The Multalign Viewer tool performs various
calculations that depend on the presence of more than one sequence, and
the format "aligned FASTA" (as opposed to plain vanilla FASTA) refers
to the presence of more than one sequence.
To show the individual sequence of a structure open in Chimera and have
crosstalk between its sequence and structure, use the Sequence tool
(under Tools... Structure Analysis).
I hope this helps,
Elaine
On Oct 12, 2006, at 6:34 AM, Lucas J. Thode wrote:
> Oops, sorry about double-posting this, but I forgot to mention that I
> am not on the list, so remember to CC me.
> ----- Original Message -----
>
> In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot
> open a FASTA file that contains a single sequence. ?(The file in
> question is attached and looks to be a valid FASTA file according to
> the documentation I have read on the FASTA format.) ?What should I do
> about this issue?
>
> Error log:
> Opening F:\H Biotech Engineering\cftr.fasta
> Error reading F:\H Biotech Engineering\cftr.fasta:
> IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
> Engineering\cftr.fasta'; check your alignment file for errors
> (see reply log for Python traceback info)
> Traceback (most recent call last):
> ??File "C:\Program Files\Chimera\share\__main__.py", line 59, in ?
> ????value = chimeraInit.init(sys.argv)
> ??File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in
> init
> ????tkgui.eventLoop()
> ??File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757,
> in eventLoop
> ????app.mainloop()
> ??File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line
> 965, in mainloop
> ????self.tk.mainloop(n)
> ??File "C:\Program
> Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line
> 1747, in __call__
> ????return apply(self.func, args)
> ??File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line
> 229, in
> ????self.__buttonFuncName(txt))()
> ??File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line
> 470, in OK
> ????self.Apply()
> ??File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160,
> in Apply
> ????openPath(path, ftype)
> ??File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258,
> in openPath
> ????mols = chimera.openModels.open(path, type=ftype)
> ??File "C:\Program Files\Chimera\share\chimera\__init__.py", line
> 1086, in open
> ????models = func(filename, *args, **kw)
> ??File "C:\Program
> Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in
>
> ????lambda fn, e=emo, ft=fileType: e.open(fn, ft),
> ??File "C:\Program
> Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in
> open
> ????self.module('MAViewer').MAViewer(fileName, fileType)
> ??File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py",
> line 59, in __init__
> ????seqs, fileAttrs, fileMarkups = self.readFile(
> ??File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py",
> line 761, in readFile
> ????seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType)
> ??File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py",
> line 100, in parseFile
> ????raise IOError("Only one sequence found in %s file"
> IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
> Engineering\cftr.fasta'; check your alignment file for errors
> Done opening F:\H Biotech Engineering\cftr.fasta
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
From jayant_jacques at rediffmail.com Thu Oct 12 10:15:13 2006
From: jayant_jacques at rediffmail.com (jayant_jacques)
Date: 12 Oct 2006 17:15:13 -0000
Subject: [Chimera-users] fitting a protein inside an EM reconstruction
Message-ID: <20061012171513.15581.qmail@webmail9.rediffmail.com>
Hi!
I have been trying to fit a protein into an EM reconstruction.
methodology
I display my protein of interest and EM map on the same window.
I select the protein and if I click fit.
Problem
1. Nothing happens!! If I move the protein the whole frame moves as a whole.
2. Also is it possible to click drag the protein into the envelope and then give the fit command such that the program will take over the fitting. As I have 3 proteins to fit into this EM Map.
Thanks
Jayant
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA.
http://www.chick.com/reading/tracts/0001/0001_01.asp
Phone office:335-5937, Cell:1-509-432-5790
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From pett at cgl.ucsf.edu Thu Oct 12 10:47:50 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 12 Oct 2006 10:47:50 -0700
Subject: [Chimera-users] Fwd: single-sequence FASTA file does not open
In-Reply-To: <04d8aa3569061b17652208467f8060ee@cgl.ucsf.edu>
References:
<04d8aa3569061b17652208467f8060ee@cgl.ucsf.edu>
Message-ID:
As a supplement to Elaine's answer, Chimera cannot compute a
structure from a sequence, if that is what you are looking for. You
would have to use a homology-modeling tool like MODELLER or MODBASE
to obtain a structure, which Chimera could then display.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu
On Oct 12, 2006, at 10:00 AM, Elaine Meng wrote:
> Hi Lucas,
> Chimera displays alignments of two or more sequences, not a single
> sequence by itself. The Multalign Viewer tool performs various
> calculations that depend on the presence of more than one sequence,
> and
> the format "aligned FASTA" (as opposed to plain vanilla FASTA) refers
> to the presence of more than one sequence.
>
> To show the individual sequence of a structure open in Chimera and
> have
> crosstalk between its sequence and structure, use the Sequence tool
> (under Tools... Structure Analysis).
>
> I hope this helps,
> Elaine
>
> On Oct 12, 2006, at 6:34 AM, Lucas J. Thode wrote:
>
>> Oops, sorry about double-posting this, but I forgot to mention that I
>> am not on the list, so remember to CC me.
>> ----- Original Message -----
>>
>> In Chimera beta 1 build 2199 on Windows XP Professional SP2, I
>> cannot
>> open a FASTA file that contains a single sequence. (The file in
>> question is attached and looks to be a valid FASTA file according to
>> the documentation I have read on the FASTA format.) What should I do
>> about this issue?
>>
>> Error log:
>> Opening F:\H Biotech Engineering\cftr.fasta
>> Error reading F:\H Biotech Engineering\cftr.fasta:
>> IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
>> Engineering\cftr.fasta'; check your alignment file for errors
>> (see reply log for Python traceback info)
>> Traceback (most recent call last):
>> File "C:\Program Files\Chimera\share\__main__.py", line 59, in ?
>> value = chimeraInit.init(sys.argv)
>> File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in
>> init
>> tkgui.eventLoop()
>> File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757,
>> in eventLoop
>> app.mainloop()
>> File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line
>> 965, in mainloop
>> self.tk.mainloop(n)
>> File "C:\Program
>> Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line
>> 1747, in __call__
>> return apply(self.func, args)
>> File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line
>> 229, in
>> self.__buttonFuncName(txt))()
>> File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line
>> 470, in OK
>> self.Apply()
>> File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160,
>> in Apply
>> openPath(path, ftype)
>> File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258,
>> in openPath
>> mols = chimera.openModels.open(path, type=ftype)
>> File "C:\Program Files\Chimera\share\chimera\__init__.py", line
>> 1086, in open
>> models = func(filename, *args, **kw)
>> File "C:\Program
>> Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in
>>
>> lambda fn, e=emo, ft=fileType: e.open(fn, ft),
>> File "C:\Program
>> Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in
>> open
>> self.module('MAViewer').MAViewer(fileName, fileType)
>> File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py",
>> line 59, in __init__
>> seqs, fileAttrs, fileMarkups = self.readFile(
>> File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py",
>> line 761, in readFile
>> seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType)
>> File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py",
>> line 100, in parseFile
>> raise IOError("Only one sequence found in %s file"
>> IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
>> Engineering\cftr.fasta'; check your alignment file for errors
>> Done opening F:\H Biotech Engineering\cftr.fasta
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
> -----
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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From goddard at cgl.ucsf.edu Thu Oct 12 11:07:30 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 12 Oct 2006 11:07:30 -0700 (PDT)
Subject: [Chimera-users] fitting a protein inside an EM reconstruction
In-Reply-To: <20061012171513.15581.qmail@webmail9.rediffmail.com>
(jayant_jacques@rediffmail.com)
References: <20061012171513.15581.qmail@webmail9.rediffmail.com>
Message-ID: <200610121807.k9CI7Uwm1608953@guanine.cgl.ucsf.edu>
Hi Jayant,
The reason that pressing the Fit button on the Fit Models in Maps dialog
is not doing anything is because you have no atoms selected. A warning
about this that says "No atoms selected" appears in the dialog. The fit
only applies to models with selected atoms because that allows you to
fit one PDB model at a time when you have multiple ones opened.
The fit tool only does a local optimization -- relatively small rigid
rotations and shifts -- so you have to first move the PDB model by hand
to approximately where you want it.
How to do this is described in the Guide to Volume Data Display:
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmodel
Tom
From meng at cgl.ucsf.edu Thu Oct 12 14:01:56 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 12 Oct 2006 14:01:56 -0700
Subject: [Chimera-users] fitting a protein inside an EM reconstruction
In-Reply-To: <20061012171434.860.qmail@webmail8.rediffmail.com>
References: <20061012171434.860.qmail@webmail8.rediffmail.com>
Message-ID: <4ce03ecb7d9401243e0a3c82a8ef0706@cgl.ucsf.edu>
Hi Jayant,
Selecting something is not the same as making it movable. Selecting
something makes Actions menu items apply to it. If you want to make
different models movable/unmovable, use the "Active" checkboxes in the
Model Panel (Favorites... Model Panel), or various "activate" functions
in the right side of the Model Panel, or the small checkboxes under the
Command Line (Favorites... Command Line).
These activation methods determine which models can be moved with the
mouse or with movement commands like "move" and "turn."
As Tom said, however, the fitting tool requires atoms to be selected.
Even if only a few atoms are selected, the fitting will move the entire
model containing the atoms, but maximize the density values at the
selected atoms.
I hope this helps,
Elaine
On Oct 12, 2006, at 10:14 AM, jayant_jacques wrote:
> ?
> Hi!
> I have been trying to fit a protein into an EM reconstruction.
>
> methodology
> I display my protein of interest and EM map on the same window.
> I select the protein and if I click fit.
>
> Problem
> 1. Nothing happens!! If I move the protein the whole frame moves as a
> whole.
> 2. Also is it possible to click drag the protein into the envelope
> and then give the fit command such that the program will take over the
> fitting. As I have 3 proteins to fit into this EM Map.
>
> Thanks
> Jayant
> Jayasundar Jayant?James
> Postdoc,
> Department of?Veterinary and?Comparative Anatomy,?Pharmacology
> and?Physiology(VCAPP), Washington?state university,?Pullman
> 99164-6520,?USA.
> http://www.chick.com/reading/tracts/0001/0001_01.asp
> Phone office:335-5937,?Cell:1-509-432-5790
>
> <1963059423 at Middle5.gif>
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
From goddard at cgl.ucsf.edu Tue Oct 17 09:41:39 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 17 Oct 2006 09:41:39 -0700 (PDT)
Subject: [Chimera-users] About Chimera under Linux64
In-Reply-To: <4534C860.7050309@mpi-cbg.de> (message from Quentin on Tue, 17
Oct 2006 14:11:12 +0200)
References: <4534C860.7050309@mpi-cbg.de>
Message-ID: <200610171641.k9HGfdWf2034765@guanine.cgl.ucsf.edu>
Hi Quentin,
I suggest you use the 32-bit Linux Chimera version 1.2255. Or if you
wait a few days a new 32-bit Linux Chimera version 1.2303 will be coming out.
We do not regularly build a 64-bit Linux Chimera because we do not
have a 64-bit Linux system in our lab. (I'll have to check on this --
maybe we have one now.) The only 64-bit version we routinely distribute
is for the very obscure Tru64 operating system running on computers with
Alpha processors.
The current 64-bit Linux build (May 2005) is so old that it lacks
many useful features for looking at EM maps.
The reason we have not moved more quickly to support 64-bit distributions
is because Chimera is strongly oriented towards interactive calculations
-- that is calculations taking at most a few seconds. On gigabyte size
data there is almost nothing that can be done in a few seconds. Still we
understand that you may look at the data subsampled (using the volume
dialog step size) and then want to create an image at full resolution
(for example for a publication or talk) that may take many minutes to
render and will need alot of memory -- not easily accomodated in a 32-bit
address space. It is our plan to regularly distribute 64-bit Linux and
Windows version in the future -- probably within a year. The main hold-up
is that we do not have 64-bit machines setup in our lab yet.
The usual method of working with large EM tomograms in Chimera is to
focus on smaller regions of interest so that segmentation can be done
interactively. Practical size chunks of data are 256^3. You can
select these smaller regions in Chimera. For large pieces the
graphics hardware is not able to render fast enough to allow smooth
interactive rotation used in segmenting interactively. It is possible
to display larger volumes and just display every other data plane
along each axis.
Tom
> Date: Tue, 17 Oct 2006 14:11:12 +0200
> From: Quentin
> User-Agent: Thunderbird 1.5.0.7 (X11/20060922)
> To: goddard at cgl.ucsf.edu
> Subject: About Chimera under Linux64
>
> Dear Mr. Goddard,
>
> I have been setting up the EM tomography in the Max-Planck Institute for
> Molecular Cell Biology and Genetics Dresden (www.mpi-cbg.de Germany )
> since one year. We have a tecnai F30 dedicated for tomogram acquisition
> and it runs after some efforts, with SerialEM/IMOD. I would like to
> improve now the segmentation part of our work which is the bottleneck in
> our fields. So I strive now to get a good set of software to segment and
> visual our huge(600Mb to 6Gb) 3d electron density map (.mrc file format).
>
> Manfred Auer and Sergio Marco oriented me on your work, i.e. the volume
> data display tools in Chimera. The first tests I did the last days, look
> really promising. Your work is really helpful for the 3D Electron
> Microscopy community. Thanks.
>
> I am just wondering why the compiled version for Linux64 of Chimera is
> so old(May 17,2005). Is there some reason? Should I use a newer 32bit
> version ? typically our dataset are 600Mb to 5Gb and we are running a
> dual core Athlon 64 machine with soon 8Gb memory under Ubuntu64bit.
>
> Thanks for your attention,
>
> Best regards,
>
> Quentin de Robillard
>
> Pfottenhauerstr. 108
> 01307 Dresden
> +49 351 210 20 61
>
From jayant_jacques at rediffmail.com Tue Oct 17 12:03:45 2006
From: jayant_jacques at rediffmail.com (jayant_jacques)
Date: 17 Oct 2006 19:03:45 -0000
Subject: [Chimera-users] viewing
Message-ID: <20061017190345.27516.qmail@webmail100.rediffmail.com>
Hi!
I thank chimera users for answering and helping me in fitting my protein into EM Map.
I have a small problem. When I rotate the protein, portions of the map and protein come into view and dissappear. I am not able to figure out how to turn off this feature in chimera! I would be grateful if told how to turn off this feature.
Thanks
Jayant
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA.
http://www.chick.com/reading/tracts/0001/0001_01.asp
Phone office:335-5937, Cell:1-509-432-5790
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From meng at cgl.ucsf.edu Tue Oct 17 12:14:36 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 17 Oct 2006 12:14:36 -0700
Subject: [Chimera-users] viewing
In-Reply-To: <20061017190345.27516.qmail@webmail100.rediffmail.com>
References: <20061017190345.27516.qmail@webmail100.rediffmail.com>
Message-ID: <82D84DEE-15E2-456B-A17D-FC7CE3EDBA4B@cgl.ucsf.edu>
Hi Jayant,
You are probably seeing the effect of the clipping planes. One way
to adjust their positions is to use the Side View (Favorites...Side
View) - drag the vertical lines.
I hope this helps,
Elaine
On Oct 17, 2006, at 12:03 PM, jayant_jacques wrote:
> Hi!
> I thank chimera users for answering and helping me in fitting my
> protein into EM Map.
> I have a small problem. When I rotate the protein, portions of the
> map and protein come into view and dissappear. I am not able to
> figure out how to turn off this feature in chimera! I would be
> grateful if told how to turn off this feature.
> Thanks
> Jayant
>
> Jayasundar Jayant James
> Postdoc,
> Department of Veterinary and Comparative Anatomy, Pharmacology and
> Physiology(VCAPP), Washington state university, Pullman 99164-6520,
> USA.
> http://www.chick.com/reading/tracts/0001/0001_01.asp
> Phone office:335-5937, Cell:1-509-432-5790
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From goddard at cgl.ucsf.edu Tue Oct 17 12:17:55 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 17 Oct 2006 12:17:55 -0700 (PDT)
Subject: [Chimera-users] viewing
In-Reply-To: <20061017190345.27516.qmail@webmail100.rediffmail.com>
(jayant_jacques@rediffmail.com)
References: <20061017190345.27516.qmail@webmail100.rediffmail.com>
Message-ID: <200610171917.k9HJHtxl2083207@guanine.cgl.ucsf.edu>
Hi Jayant,
Elaine was faster at answering this. I'll send my description anyways
since it has a few more step-by-step details.
The molecule and map go out of view because of front and back clip
planes. These are always enabled in Chimera and the normal remedy is to
move the front clip plane forward, and back clip plane back further so
no clipping occurs. To do this use the Side View dialog shown with menu
entry
Favorites / Side View.
The two vertical yellow lines represent the two clip planes in this view
from the side of your data. Drag the yellow lines with the mouse to move
the clip planes. The square at the left represents your eye and the
left vertical line is the front clip plane, the right one is the back clip
plane.
Tom
From dpryan at phy.ucsf.edu Tue Oct 17 12:21:03 2006
From: dpryan at phy.ucsf.edu (Devon Ryan)
Date: Tue, 17 Oct 2006 12:21:03 -0700
Subject: [Chimera-users] Chimera under FreeBSD
Message-ID: <1161112863.45352d1fa09e8@lehrer.ucsf.edu>
Has anyone had success getting chimera to run under FreeBSD? I can get the linux
version to start (under the linuxulator), but it crashes after ~20 seconds when
the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel
architecture. Thanks
--
Devon Ryan | dpryan at sg.uchicago.edu
Neuro Grad Student, Ptacek Lab | dpryan at phy.ucsf.edu
University of Chicago '02 | dpryan at alumni.uchicago.edu
www.dpryan.com | dpryan at dpryan.com
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
From goddard at cgl.ucsf.edu Tue Oct 17 12:29:38 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 17 Oct 2006 12:29:38 -0700 (PDT)
Subject: [Chimera-users] Chimera under FreeBSD
In-Reply-To: <1161112863.45352d1fa09e8@lehrer.ucsf.edu> (message from Devon
Ryan on Tue, 17 Oct 2006 12:21:03 -0700)
References: <1161112863.45352d1fa09e8@lehrer.ucsf.edu>
Message-ID: <200610171929.k9HJTcHM1579608@guanine.cgl.ucsf.edu>
Hi Devon,
We (the Chimera developers) have not built it on FreeBSD. The
trouble is that it requires compiling about 35 third party packages
FFmpeg, HappyDoc, Imaging, MMTK, Mesa, Numeric, Pmw,
PyOpenGL, PyXML, Python, STLport, Scientific, TclTk, Tix, Togl,
al2co, antechamber, autostereo, expat, f2c, freetype, ftgl,
grail, jpeg, mpeg_encode, msms, netcdf, omni, openssl,
pymmlib, qhull, swish-e, tiff, tr, win32, zip, zlib
That's alot of work. We don't have a FreeBSD system, and it does
not seem likely that it would benefit alot of users.
I am not surprised that Chimera will not run under an emulator.
There is alot of low level bit-twiddling code in the packages it uses.
Tom
From pett at cgl.ucsf.edu Tue Oct 17 13:26:56 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 17 Oct 2006 13:26:56 -0700
Subject: [Chimera-users] release candidate
Message-ID: <6D2B0639-3844-4477-9B0A-A45F4C5C177F@cgl.ucsf.edu>
We've made a release candidate (version 1.2303) available for
download. It has many new features relative to the previous
production release (1.2199). The features/improvements are listed here:
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2303.html
Please let us know if you encounter any problems with the release
candidate. If no major problems surface in the next few days, we
will promote the candidate to production release status.
Enjoy!
Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu
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From jayant_jacques at rediffmail.com Tue Oct 17 16:35:16 2006
From: jayant_jacques at rediffmail.com (jayant_jacques)
Date: 17 Oct 2006 23:35:16 -0000
Subject: [Chimera-users] force fitting a protein into select volume in a EM
reconstruction
Message-ID: <20061017233516.9013.qmail@webmail8.rediffmail.com>
hi!
Is it possible in chimera to choose a particular part of a EM envelope and a protein and fit them? AS the protein that I am trying to fit into the map finds a better fit else where in the EM envelope, after I painstakingly align it to the place where its supposed to be!!!
Thanks
Jayant
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA.
http://www.chick.com/reading/tracts/0001/0001_01.asp
Phone office:335-5937, Cell:1-509-432-5790
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From goddard at cgl.ucsf.edu Tue Oct 17 17:45:54 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 17 Oct 2006 17:45:54 -0700 (PDT)
Subject: [Chimera-users] force fitting a protein into select volume in a
EM reconstruction
In-Reply-To: <20061017233516.9013.qmail@webmail8.rediffmail.com>
(jayant_jacques@rediffmail.com)
References: <20061017233516.9013.qmail@webmail8.rediffmail.com>
Message-ID: <200610180045.k9I0js6M1689250@guanine.cgl.ucsf.edu>
Hi Jayant,
The Chimera fit optimization tool
Tools / Volume Data / Fit Models in Maps
rigidly rotates and moves the model to increase the average density
value at the positions of selected atoms. That is not necessarily
what you want. Depending on your map it may push your PDB model
towards some high density region even though another position better
matches the shape of the map contour surface to the shape of the
molecule. We don't have any fitting tool to optimize this shape
matching although maybe we should make one. I could imagine taking a
molecular surface for the PDB model and trying to position it to best
match the contour surface of the EM map.
The one choice you can make is which atoms you select for doing the
fit. If some subdomain of your model fits the map well you could just
select that domain. The fit will move the whole PDB model to optimize
just the density at the selected atom positions.
If that does not work, the current fitting tool may not be helpful,
and a hand placement may be the best that can be done. It is possible
to extract just a portion of the map around your hand placed model.
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#zone
Then you could use the fit optimization tool just on that saved piece of
the map. But that very likely is not helpful. Your PDB model will just
move towards the undesirable position until it hits a boundary where you
cut the map off.
So I think a hand-fit or using other software (e.g. EMFit or Situs)
is the way to go.
If you hand place your PDB and then the fit optimization messes it
up you can bring the PDB exactly back to the hand placed position with
Tools / Movement / Undo Move
In general this undoes your previous model movements (remembering a
history of I think 100 previous positions). This is so useful that I
put it on the Chimera toolbar using Favorites / Preferences, category
Tools, checking the "On toolbar" button for "Undo Move" and the Save
button on the preferences dialog (so it will be on the toolbar in
future sessions).
Tom
From swamidass at gmail.com Thu Oct 19 00:49:41 2006
From: swamidass at gmail.com (S Joshua Swamidass)
Date: Thu, 19 Oct 2006 00:49:41 -0700
Subject: [Chimera-users] Dock?
Message-ID:
Hello,
Are there any plans to develop a gui frontend for DOCK using chimera?
Josh
From agrosdidier_phd at yahoo.fr Thu Oct 19 01:26:31 2006
From: agrosdidier_phd at yahoo.fr (Aurelien Grosdidier)
Date: Thu, 19 Oct 2006 10:26:31 +0200
Subject: [Chimera-users] Dock?
In-Reply-To:
References:
Message-ID: <200610191026.31397.agrosdidier_phd@yahoo.fr>
Seems like it's on its way...
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm
Cheers,
Aur?lien
On Thursday 19 October 2006 09:49, S Joshua Swamidass wrote:
> Hello,
>
> Are there any plans to develop a gui frontend for DOCK using chimera?
>
> Josh
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
From aurelien.grosdidier at gmail.com Thu Oct 19 01:24:15 2006
From: aurelien.grosdidier at gmail.com (Aurelien Grosdidier)
Date: Thu, 19 Oct 2006 10:24:15 +0200
Subject: [Chimera-users] Dock?
In-Reply-To:
References:
Message-ID: <200610191024.15815.aurelien.grosdidier@gmail.com>
Seems like it's on its way...
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm
Cheers,
Aur?lien
On Thursday 19 October 2006 09:49, S Joshua Swamidass wrote:
> Hello,
>
> Are there any plans to develop a gui frontend for DOCK using chimera?
>
> Josh
> _______________________________________________
> 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 Oct 19 11:24:35 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 19 Oct 2006 11:24:35 -0700
Subject: [Chimera-users] Dock?
In-Reply-To:
References:
Message-ID: <3983443A-7B70-4DD6-89B6-A425496F1283@cgl.ucsf.edu>
Hi Josh,
We don't currently have plans to make a comprehensive Chimera
frontend to DOCK, where you never have to leave Chimera to start your
DOCK run. Something like that would require extremely close
coordination between the Chimera and DOCK teams, since every change
or addition to DOCK input parameters or status messages would need to
be reflected in the frontend (and undoubtedly explained in the
frontend documentation as well). What we have done to date and will
continue to do is develop tools to assist in the preparation of DOCK
input and assessment of DOCK output. Right now the Dock Prep tool
cleans up, protonates, and assigns charges to a receptor for use in a
DOCK run, and ViewDock allows you to browse through and analyze your
DOCK results.
Improvements we anticipate making in the nearer term include: using
a rotamer library to fill out missing side chains (they are currently
truncated to glycine/alanine) and optionally minimize them; have
Chimera create the MS surface file (with normals) directly so that
using DMS is no longer necessary; and making a tool to visualize
sphgen output and allow interactive pruning of unwanted spheres and
writing a new sphere file.
Some of these capabilities aren't necessarily DOCK-specific. For
instance, Dock Prep's result is a Mol2 file that could be used in a
variety of programs.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu
On Oct 19, 2006, at 12:49 AM, S Joshua Swamidass wrote:
> Hello,
>
> Are there any plans to develop a gui frontend for DOCK using chimera?
>
> Josh
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From jared.godar at vanderbilt.edu Fri Oct 20 08:57:24 2006
From: jared.godar at vanderbilt.edu (Jared Godar)
Date: Fri, 20 Oct 2006 10:57:24 -0500
Subject: [Chimera-users] Movie - Display Spheres
Message-ID: <5ca4dd6a0610200857q39f1f9b5mdf1360a99d800017@mail.gmail.com>
Hello,
I am trying to use the 'represent spheres' command to draw attention to
specific residues in a model that is displayed as a ribbon.
I would like to first show the ATP binding site of the molecule with magenta
spheres, then show the three residuse which get phosphorolated.
Currently, I am able to display one of these elements or the other as
spheres, but not both at the same time. I've tried to use a single
represent sphere command to specify all of the desired atoms, but can't seem
to get the context right,
represent sphere #0:426,431,432,ATP and represent sphere #0:426,431,432 &
#0::ATP weren't working.
Help on the syntax to simultaneously display the two commands listed below
which are currently mutually exclusive would be appreciated.
#SHOW ATP:
color magenta #0::ATP; color magenta #0::mg;
represent sphere #0::ATP
#SHOW PO4 Residues
show #0:426,431,432; color yellow #0:426; color orange red #0:431; color red
#0:432;
represent sphere #0:426,431,432
Thanks,
Jared
--
Jared A. Godar
Graduate Student: Stewart Lab
Vanderbilt University Medical Center
Department of Molecular Physiology & Biophysics
708 Light Hall
2215 Garland Ave.
Nashville, TN 37232-0615
Work: 615.322.7898
Fax: 615.322.7236
jared.godar at vanderbilt.edu
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From meng at cgl.ucsf.edu Fri Oct 20 09:12:36 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 20 Oct 2006 09:12:36 -0700
Subject: [Chimera-users] Movie - Display Spheres
In-Reply-To: <5ca4dd6a0610200857q39f1f9b5mdf1360a99d800017@mail.gmail.com>
References: <5ca4dd6a0610200857q39f1f9b5mdf1360a99d800017@mail.gmail.com>
Message-ID: <3788F831-800D-45C2-84A5-A11F6FBFA8C4@cgl.ucsf.edu>
Hi Jared,
First question:
It is not necessary to use a single command. You can use
> rep sphere [stuff]
> rep sphere [more stuff]
and then both sets of things will be shown as spheres. Most commands
only affect what you specify. (main exceptions are "show" and
"chain" ... more on this below)
If you did want to use a single command, the proper separator for the
specifications is a vertical bar "|" (logical OR, union) and not the
ampersand "&" (logical AND, intersection). For example:
> rep sphere #0:426,431,432 | :atp
although I'm thinking this would also work (I don't know which PDB
you're using, or I'd verify this myself):
> rep sphere #0:426,431,432:atp
Second question:
As alluded to above, "show" displays what you specify, undisplays the
rest. If you don't want to undisplay the rest, use "display" instead
of "show" - the rest of what you had looks correct, though. If you
want to undisplay all atoms except those residues and ATP, first
"~display" everything and then specify what you want to show with
"display" either in a single command or multiple commands.
I hope this helps,
Elaine
On Oct 20, 2006, at 8:57 AM, Jared Godar wrote:
> Hello,
>
> I am trying to use the 'represent spheres' command to draw
> attention to specific residues in a model that is displayed as a
> ribbon.
>
> I would like to first show the ATP binding site of the molecule
> with magenta spheres, then show the three residuse which get
> phosphorolated.
>
> Currently, I am able to display one of these elements or the other
> as spheres, but not both at the same time. I've tried to use a
> single represent sphere command to specify all of the desired
> atoms, but can't seem to get the context right,
>
> represent sphere #0:426,431,432,ATP and represent sphere
> #0:426,431,432 & #0::ATP weren't working.
>
> Help on the syntax to simultaneously display the two commands
> listed below which are currently mutually exclusive would be
> appreciated.
>
> #SHOW ATP:
>
> color magenta #0::ATP; color magenta #0::mg;
> represent sphere #0::ATP
>
> #SHOW PO4 Residues
>
> show #0:426,431,432; color yellow #0:426; color orange red #0:431;
> color red #0:432;
> represent sphere #0:426,431,432
>
> Thanks,
>
> Jared
>
> --
> Jared A. Godar
> Graduate Student: Stewart Lab
> Vanderbilt University Medical Center
> Department of Molecular Physiology & Biophysics
> 708 Light Hall
> 2215 Garland Ave.
> Nashville, TN 37232-0615
> Work: 615.322.7898
> Fax: 615.322.7236
>
> jared.godar at vanderbilt.edu
> _______________________________________________
> 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 Mon Oct 23 15:41:39 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 23 Oct 2006 15:41:39 -0700
Subject: [Chimera-users] 1.2304 production
Message-ID:
We haven't received any major bug reports for the release candidate,
so we have promoted it to a production release (1.2304) which
includes a few quite minor bug fixes and some documentation
improvements relative to the release candidate.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu
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From okabe at cherry.bio.titech.ac.jp Mon Oct 23 22:28:03 2006
From: okabe at cherry.bio.titech.ac.jp (Atsutoshi Okabe)
Date: Tue, 24 Oct 2006 14:28:03 +0900
Subject: [Chimera-users] To color atoms
Message-ID: <20061024053004.D06951D3337@vc-s.net.titech.ac.jp>
Hi,
I visualized one ligand molecule (a kind of sugar) written by PDB format
within chimera.
But all atoms have non color(attached file ) I want to color these atoms
(i.e. the oxygen has red .)
Could you please teach me how to color atoms?
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From meng at cgl.ucsf.edu Tue Oct 24 09:40:51 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 24 Oct 2006 09:40:51 -0700
Subject: [Chimera-users] To color atoms
In-Reply-To: <20061024053004.D06951D3337@vc-s.net.titech.ac.jp>
References: <20061024053004.D06951D3337@vc-s.net.titech.ac.jp>
Message-ID:
Hi Atsutoshi,
If you want the "element" coloring (oxygen red, nitrogen blue, ... )
one way is to use the menu item:
Actions... Color... by element
Actually there are many different ways to color atoms, ribbons,
surfaces, and other things. The many ways are listed in this manual
page:
http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/coloring.html
In Chimera, you can search for help using the menu item:
Help... Search Documentation
for example, if you search by "coloring" the page I mentioned above
is hit #2. There are also tutorials for new users of Chimera
(Help... Tutorials).
I hope this helps,
Elaine
On Oct 23, 2006, at 10:28 PM, Atsutoshi Okabe wrote:
> Hi,
>
>
>
> I visualized one ligand molecule (a kind of sugar) written by PDB
> format within chimera.
>
> But all atoms have non color(attached file ) I want to color these
> atoms (i.e. the oxygen has red ?)
>
> Could you please teach me how to color atoms?
>
>
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From okabe at cherry.bio.titech.ac.jp Tue Oct 24 23:53:24 2006
From: okabe at cherry.bio.titech.ac.jp (Atsutoshi Okabe)
Date: Wed, 25 Oct 2006 15:53:24 +0900
Subject: [Chimera-users] To except box information in MD movie
Message-ID: <20061025065529.A3E491D32D1@vc-s.net.titech.ac.jp>
Hello,
I viewed Amber format trajectory files ( topology/parameter file and
trajectory file ) by MD movie.
But I got the figure( attached file) I didn't intend. I think the reason is
to read box information in
the Amber trajectory file . How can I except the box information in MD movie
window ?
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From dekonerding at lbl.gov Wed Oct 25 07:40:09 2006
From: dekonerding at lbl.gov (David E. Konerding)
Date: Wed, 25 Oct 2006 09:40:09 -0500
Subject: [Chimera-users] To except box information in MD movie
In-Reply-To: <20061025065529.A3E491D32D1@vc-s.net.titech.ac.jp>
References: <20061025065529.A3E491D32D1@vc-s.net.titech.ac.jp>
Message-ID: <453F7749.5020300@lbl.gov>
Atsutoshi Okabe wrote:
>
> Hello,
>
> I viewed Amber format trajectory files ( topology/parameter file and
> trajectory file ) by MD movie.
>
> But I got the figure( attached file) I didn?t intend. I think the
> reason is to read box information in
>
> the Amber trajectory file . How can I except the box information in MD
> movie window ?
>
Atsutoshi,
When reading an AMBER format trajectory, not only does the existence of
box information at each
frame in the trajectory have to correspond to the box information in the
prmtop (which can have a box
or not), but also the number of atoms in the trajectory has to
correspond to the number of atoms in the prmtop.
From looking at your snapshot, I think you may have a problem with the
prmtop not corresponding to the trajectory-
did you strip out the waters? If you did, then you need a prmtop file
that also has the waters stripped.
There is an answer to your question (how to see the box data) but it is
programatically, not GUI-available.
Dave
From bala at igib.res.in Thu Oct 26 06:33:46 2006
From: bala at igib.res.in (bala)
Date: Thu, 26 Oct 2006 19:03:46 +0530
Subject: [Chimera-users] viewing grid density
Message-ID: <1D011717865DAE46B56AA1455F02CAC54B1132@n1ex>
Hello all,
1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same.
2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc.
3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it.
Bala
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From meng at cgl.ucsf.edu Thu Oct 26 10:06:59 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 26 Oct 2006 10:06:59 -0700
Subject: [Chimera-users] viewing grid density
In-Reply-To: <1D011717865DAE46B56AA1455F02CAC54B1132@n1ex>
References: <1D011717865DAE46B56AA1455F02CAC54B1132@n1ex>
Message-ID:
Hi Bala,
(1) I do not understand your first question. If your PDB is saved
from the same trajectory used to create the solvent density map, I
would expect it to already be in the correct position relative to the
map. I'm not sure what you mean by "fix" (freeze? or change its
position relative to the map?).
(2) the levels shown for the histogram are just the numbers present
in your density map. The meaning of the numbers depends on the
method you used to create the map, including grid spacing, number of
trajectory frames used, and whether any normalization for atomic
weight or number of frames was applied. You would need to look at
the documentation for whatever you used to create the map. If you
used MD Movie in Chimera to create this map, then the numbers are
total counts of atoms in that cube of the grid summed over all the
frames in the trajectory used for the calculation. This "occupancy
analysis" in MD Movie is described here:
http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/
movie.html#occupancy
After you figure out the physical meaning of the numbers, there is
still no rule as to what threshold to use, because it depends on the
system and what degree of solvent localization you are trying to
identify. Certain solute groups may localize water much more
strongly than others.
(3) a link and search interface to the chimera-users archive is
included on this page
http://www.cgl.ucsf.edu/chimera/docs/feedback.html
Also "Help... Contact Us" in the Chimera menu opens a similar page.
I hope this helps,
Elaine
On Oct 26, 2006, at 6:33 AM, bala wrote:
> Hello all,
>
> 1) I hve generated a solvent density map using Amber8 in XPLOR
> format. I am able to open the map in chimera. I hv also generated a
> refernce pdb file. Now i have to fix the reference structure of my
> molecule in the density map. I tried many options but i couldnt do
> that. Someone pls suggest me how i should do the same.
>
> 2) Also i am not clear with the meaning of the threshold levels
> given in the histogram. Although i could see the difference in the
> density map by sliding the vertical bar to various postions, i am
> getting what it can tell us exactly. Which is the most suitable
> threhold level etc.
>
> 3) Someone pls give me the link for the chimera mail list
> archive...i am unable to locate it.
>
> Bala
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From goddard at cgl.ucsf.edu Thu Oct 26 10:11:51 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 26 Oct 2006 10:11:51 -0700 (PDT)
Subject: [Chimera-users] viewing grid density
In-Reply-To: <1D011717865DAE46B56AA1455F02CAC54B1132@n1ex> (bala@igib.res.in)
References: <1D011717865DAE46B56AA1455F02CAC54B1132@n1ex>
Message-ID: <200610261711.k9QHBpuk2020480@guanine.cgl.ucsf.edu>
Hi Bala,
Elaine Meng answered these questions before I finished my email.
I think my answers are the same, but I'll give them to you anyways.
If the solvent map and reference PDB structure produced by Amber8 do
not align when displayed in Chimera that is probably a problem with
Amber or how you are using Amber. If they do not align I do not think
you will be able to align them in Chimera. The one thing you could
try is to use volume dialog menu entry Features / Origin and Scale.
That will show the grid plane spacing (called "voxel size") and the
origin that is being used for the map. You can try changing those
values by hand. Press the Enter key after changing a value to have
the display updated.
Chimera can compute solvent occupancy from a trajectory using its
MD Movie tool. See the "occupancy analysis" section of the Chimera
documentation:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
Perhaps this is an alternative way to do what you want.
The threshold level in the Chimera volume dialog specifies what map
value the contour surface is drawn at. The displayed surface goes
through those points in space where the map has the specified value.
What that means depends on what the values in your map mean. I don't
know what the values in your solvent map computed by Amber8 mean.
Here is the Chimera users list (found under the Contact Us link on
the main Chimera web page):
http://www.cgl.ucsf.edu/pipermail/chimera-users/index.html
Tom
From ajcampbe at csb.sunysb.edu Thu Oct 26 15:07:59 2006
From: ajcampbe at csb.sunysb.edu (AJ Campbell)
Date: Thu, 26 Oct 2006 18:07:59 -0400
Subject: [Chimera-users] question regarding chimera 1.2304-wim32.exe
Message-ID: <454131BF.2040602@csb.sunysb.edu>
I have tried installing Chimera several times on my Windows machine but
keep receiving an error message saying "Outline highlight not supported
by hardware", any advice would be appreciated. ~ Arthur
From gregc at cgl.ucsf.edu Thu Oct 26 15:58:31 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 26 Oct 2006 15:58:31 -0700 (PDT)
Subject: [Chimera-users] question regarding chimera 1.2304-wim32.exe
In-Reply-To: <454131BF.2040602@csb.sunysb.edu>
References: <454131BF.2040602@csb.sunysb.edu>
Message-ID:
On Thu, 26 Oct 2006, AJ Campbell wrote:
> I have tried installing Chimera several times on my Windows machine but
> keep receiving an error message saying "Outline highlight not supported
> by hardware", any advice would be appreciated. ~ Arthur
So the installation succeeded, no need to reinstall chimera. The error is
just a warning and chimera will work mostly work without outline
highlights. So you should fix it:
Chances are that your desktop is configured for 16 bit color -- the
solution is change it to 24 or 32 bit color. Go to Control Panel /
Display / Settings, and change the "Color quality" to highest.
There is also the possibility that you need to install a newer version of
the video driver from your graphics card vendor. Or that you need a
graphics card :-)
Hope this helped,
Greg Couch
UCSF Computer Graphics Lab
From lydka at uoregon.edu Fri Oct 27 04:27:26 2006
From: lydka at uoregon.edu (Lydia Jablonski)
Date: Fri, 27 Oct 2006 04:27:26 -0700
Subject: [Chimera-users] commercial license
In-Reply-To:
References:
Message-ID: <1161948446.609916.alphamail@alphamail.uoregon.edu>
Hello-
Do any of you have an idea of how much a single commercial license for Chimera would cost?
I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max.
Thanks,
Lydia Jablonski
From bala at igib.res.in Fri Oct 27 07:43:45 2006
From: bala at igib.res.in (bala)
Date: Fri, 27 Oct 2006 20:13:45 +0530
Subject: [Chimera-users] generating electrostatic potential map
Message-ID: <1D011717865DAE46B56AA1455F02CAC54B113B@n1ex>
Hello all,
I want to generate the electrostatic potential map using Chimera. I tried through Delphi controler, however i am repeatedly getting an error as follows. I have successfully installed Delphi. Can someone suggest me what is wrong.
__________DelPhi V. 4 Release 1.1 ______________
| |
| A program to solve the PB equation |
| in 3D, using non-linear form, incorporating |
| many dielectric regions, multisalt ionic |
| strength, different probe radii, periodic |
| and focussing boundary conditions, utilizing |
| stripped optimum successive over-relaxation |
| and an improved algorithm for mapping the |
| Mol. Surface to the finite-Difference grid |
| Recompiled on Linux and PC |
| January 2002 -------- Walter Rocchia |
|__________________ ___________________|
DelPhi V. 4
program started on Fri Oct 27 2006
at 14:55:00
opening parameter file /tmp/tmpvpgS8V
At least 30 nonlinear iterations
atom radii read from file
/usr/people/ojha/BALA/chim_amber.siz
unknown header format in radius file:
O5' A 1 1.7210
First it showed the same for H5 atom [which was the first atom in the siz/charge file], then i just tried by deleting the first line in the radius and charge file. Then the same error is coming for the second atom O5' in the file.
Thanks in advance,
Bala
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From menetret at bu.edu Fri Oct 27 08:58:50 2006
From: menetret at bu.edu (jean-francois menetret)
Date: Fri, 27 Oct 2006 11:58:50 -0400 (EDT)
Subject: [Chimera-users] Toolbar and Favorite on PC
Message-ID:
Hello all,
when running chimera on my PC (windows XP), my toolbar stopped
being displayed. If I uninstall and reinstall chimera, my toolbar comes
back until the next reboot.
How can I fix that ?
Is there to restore my preferences after launching chimera?
Regards
Jean-Francois
Jean-Fran?ois M?n?tret, PhD
Boston University School of Medicine
Physiology and Biophysics Department
700 Albany Street W315
Boston, MA 02118
Email: menetret at bu.edu
Mailing address: 715 Albany Street
From jkhilmer at gmail.com Fri Oct 27 13:09:12 2006
From: jkhilmer at gmail.com (Jonathan Hilmer)
Date: Fri, 27 Oct 2006 14:09:12 -0600
Subject: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
In-Reply-To:
References:
Message-ID: <81277ce10610271309q5ebfea1eha1848af0b681bdd5@mail.gmail.com>
Although this does not relate to your question on licensing, is there
any particular reason you're using such a complicated workflow?
Chimera can be used to generate basic geometry (sphere/cylinder) from
PDB files via povray, but so could any import system you have for the
3D modeling software. You would also lose the benefit of
chemistry-centered structure for manipulation or selection: chains,
residues, etc.
I've been using Blender to handle complicated chemical models for a
while now, and it wasn't that difficult to implement the import of
various data types. With BioPython pdb files become trivial, and
volumetric data sets are (very) difficult but possible.
Jonathan
> Hello-
>
> Do any of you have an idea of how much a single commercial license for Chimera would cost?
>
> I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max.
>
> Thanks,
>
> Lydia Jablonski
From meng at cgl.ucsf.edu Fri Oct 27 16:13:40 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 27 Oct 2006 16:13:40 -0700
Subject: [Chimera-users] generating electrostatic potential map
In-Reply-To: <1D011717865DAE46B56AA1455F02CAC54B113B@n1ex>
References: <1D011717865DAE46B56AA1455F02CAC54B113B@n1ex>
Message-ID: <87F1B07D-7146-457E-BDF8-AE48929F3CB4@cgl.ucsf.edu>
Hi Bala,
This error occurs in DelPhi (not in Chimera) and is apparently
because the format of the radius file is wrong. It looks like
DelPhi is expecting a different line at the top of the radius file.
I looked at the "default.siz" file in our local installation of
DelPhi, and it has this line before the radius parameters:
atom__res_radius_color_
You could try putting that line or even a blank line at the top of
your radius file, but probably the best thing to do is check the
description of this file format in the DelPhi manual.
I hope this helps,
Elaine
On Oct 27, 2006, at 7:43 AM, bala wrote:
> Hello all,
>
> I want to generate the electrostatic potential map using Chimera. I
> tried through Delphi controler, however i am repeatedly getting an
> error as follows. I have successfully installed Delphi. Can someone
> suggest me what is wrong.
>
> __________DelPhi V. 4 Release 1.1 ______________
> | |
> | A program to solve the PB equation |
> | in 3D, using non-linear form, incorporating |
> | many dielectric regions, multisalt ionic |
> | strength, different probe radii, periodic |
> | and focussing boundary conditions, utilizing |
> | stripped optimum successive over-relaxation |
> | and an improved algorithm for mapping the |
> | Mol. Surface to the finite-Difference grid |
> | Recompiled on Linux and PC |
> | January 2002 -------- Walter Rocchia |
> |__________________ ___________________|
> DelPhi V. 4
>
> program started on Fri Oct 27 2006
> at 14:55:00
> opening parameter file /tmp/tmpvpgS8V
> At least 30 nonlinear iterations
> atom radii read from file
> /usr/people/ojha/BALA/chim_amber.siz
>
> unknown header format in radius file:
> O5' A 1 1.7210
>
> First it showed the same for H5 atom [which was the first atom in
> the siz/charge file], then i just tried by deleting the first line
> in the radius and charge file. Then the same error is coming for
> the second atom O5' in the file.
>
> Thanks in advance,
> Bala
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From gregc at cgl.ucsf.edu Fri Oct 27 16:39:39 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 27 Oct 2006 16:39:39 -0700 (PDT)
Subject: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
In-Reply-To: <81277ce10610271309q5ebfea1eha1848af0b681bdd5@mail.gmail.com>
References:
<81277ce10610271309q5ebfea1eha1848af0b681bdd5@mail.gmail.com>
Message-ID:
A couple of things:
3DS Max supports importing VRML (.wrl) files, so you'd be better off
using the latest chimera, 1.2304, and exporting VRML for direct import
into 3ds Max.
As for biopython/blender, I believe you'd be better off using chimera to
export to blender using the X3D format. Chimera understands PDB files
better than biopython, generates ribbons and molecular surfaces, deals
with volume data easily (see http://www.cgl.ucsf.edu/chimera/ for
details), and blender can do wonderful animations and other
postprocessing. It's a more powerful combination.
Greg Couch
UCSF Computer Graphics Lab
On Fri, 27 Oct 2006, Jonathan Hilmer wrote:
> Date: Fri, 27 Oct 2006 14:09:12 -0600
> From: Jonathan Hilmer
> To: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
>
> Although this does not relate to your question on licensing, is there
> any particular reason you're using such a complicated workflow?
> Chimera can be used to generate basic geometry (sphere/cylinder) from
> PDB files via povray, but so could any import system you have for the
> 3D modeling software. You would also lose the benefit of
> chemistry-centered structure for manipulation or selection: chains,
> residues, etc.
>
> I've been using Blender to handle complicated chemical models for a
> while now, and it wasn't that difficult to implement the import of
> various data types. With BioPython pdb files become trivial, and
> volumetric data sets are (very) difficult but possible.
>
> Jonathan
>
>
>
>> Hello-
>>
>> Do any of you have an idea of how much a single commercial license for
>> Chimera would cost?
>>
>> I'm a 3D artist/animator/biology student that works at in the art dept.
>> of a biotech company. I'm interested in the exporting .pdb files to
>> .pov, then converting to .3ds to import to 3ds max.
>>
>> Thanks,
>>
>> Lydia Jablonski
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
From wencryo at yahoo.com Mon Oct 30 11:52:42 2006
From: wencryo at yahoo.com (wendy ochoa)
Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST)
Subject: [Chimera-users] rotating molecules for movies
Message-ID: <20061030195242.57847.qmail@web37306.mail.mud.yahoo.com>
Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view?
Thanks
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From goddard at cgl.ucsf.edu Mon Oct 30 12:18:46 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 30 Oct 2006 12:18:46 -0800 (PST)
Subject: [Chimera-users] rotating molecules for movies
In-Reply-To: <20061030195242.57847.qmail@web37306.mail.mud.yahoo.com> (message
from wendy ochoa on Mon, 30 Oct 2006 11:52:42 -0800 (PST))
References: <20061030195242.57847.qmail@web37306.mail.mud.yahoo.com>
Message-ID: <200610302018.k9UKIkDe1679104@guanine.cgl.ucsf.edu>
Hi Wendy,
The "Offset" field in the EMANimator spin settings controls the
center of rotation. I don't see any option to put the rotation center
at the center of the molecule. It looks like the only approach is to
type in the numeric coordinates for the center. (This tool was
written by Steve Ludtke so I do not know all its nuances.) Here's how
you can figure out the right values. Select some or all atoms of the
molecule which will be used to compute the center of rotation. Use
menu entry Actions / Set Pivot. The rotation center coordinates will
be shown in the status line at the bottom of the Chimera main window
(and in the reply log, menu entry Favorites / Reply log). Use the
negative of those coordinates for the offset field in the Spin
settings.
If you only need to spin a molecule around you could make a movie
with the Chimera Movie Recorder instead of EMANimator. Make a Chimera
command script like:
movie record
roll y 3 120
wait 120
movie stop
movie encode mformat mov output /usr/local/src/staff/goddard/test.mov
in a file movie.cmd and open movie.cmd in Chimera.
EMANimator is better for composing more complex movies.
Tom
From goddard at cgl.ucsf.edu Mon Oct 30 12:44:49 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 30 Oct 2006 12:44:49 -0800 (PST)
Subject: [Chimera-users] rotating molecules for movies
In-Reply-To: <20061030203454.6337.qmail@web37309.mail.mud.yahoo.com> (message
from wendy ochoa on Mon, 30 Oct 2006 12:34:54 -0800 (PST))
References: <20061030203454.6337.qmail@web37309.mail.mud.yahoo.com>
Message-ID: <200610302044.k9UKinon1670111@guanine.cgl.ucsf.edu>
Hi Wendy,
Here are some Chimera commands that are useful for making movies with
Movie Recorder:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecommands.html
Here's a fancier Chimera movie script example.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com
Here is the documentation for the Movie Recorder dialog and movie command:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html
Tom
From goddard at cgl.ucsf.edu Mon Oct 30 13:41:41 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 30 Oct 2006 13:41:41 -0800 (PST)
Subject: [Chimera-users] viewing grid density
References: <1D011717865DAE46B56AA1455F02CAC54B1132@n1ex>
<200610261711.k9QHBpuk2020480@guanine.cgl.ucsf.edu>
<1D011717865DAE46B56AA1455F02CAC54B113A@n1ex>
Message-ID: <200610302141.k9ULffxv1675989@guanine.cgl.ucsf.edu>
Bala reports that the problem was in an Amber input file.
> From: "bala"
> To: "Thomas Goddard"
> Subject: RE: [Chimera-users] viewing grid density
> Date: Fri, 27 Oct 2006 19:59:38 +0530
>
> Hello Thomas and Elaine,
>
> Thank you for your information. I rechecked the amber input files and i =
> found a mistake there in rms fitting the coordinates in my trajectory.
>
> regards,
> Bala
From goddard at cgl.ucsf.edu Mon Oct 30 13:47:59 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 30 Oct 2006 13:47:59 -0800 (PST)
Subject: [Chimera-users] Toolbar and Favorite on PC
In-Reply-To: (message from
jean-francois menetret on Fri, 27 Oct 2006 11:58:50 -0400 (EDT))
References:
Message-ID: <200610302147.k9ULlxSS1702137@guanine.cgl.ucsf.edu>
Hi Jean-Francois,
I'm puzzled about your disappearing Chimera toolbar. It seems Chimera
is not finding its preferences file. The location of the preferences file
is set using Chimera menu entry
Favorites / Preferences, category Preferences
The path of the preferences files may be relative to the directory where
Chimera starts. If you start Chimera by clicking an icon in Windows XP
the start-up directory is set for the icon. Right click on the Chimera
icon and choose Properties and look at the "Start in" field. This should
help you find your Chimera preferences file.
Tom
From jkhilmer at gmail.com Mon Oct 30 14:28:09 2006
From: jkhilmer at gmail.com (Jonathan Hilmer)
Date: Mon, 30 Oct 2006 15:28:09 -0700
Subject: [Chimera-users] changing center of rotation
Message-ID: <81277ce10610301428q37379ee2t3a024169dcf3e9ab@mail.gmail.com>
Although I haven't used EMAnimator, you can set the center of rotation
within Chimera using the Set Pivot action:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot
There's also Tools/Movement/Rotation, and lastly, you can edit
structures to insert artificial points at extreme high/low XYZ
locations, which will in effect manually set the center used via the
'center of models' option. I wouldn't recommend the last option
unless you have a good reason to do so, but it does work.
Jonathan
> Message: 1
> Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST)
> From: wendy ochoa
> Subject: [Chimera-users] rotating molecules for movies
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <20061030195242.57847.qmail at web37306.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view?
> Thanks
>
>
>
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>
> ------------------------------
>
> _______________________________________________
> 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 42, Issue 21
> *********************************************
From menetret at bu.edu Mon Oct 30 14:28:36 2006
From: menetret at bu.edu (jean-francois menetret)
Date: Mon, 30 Oct 2006 17:28:36 -0500 (EST)
Subject: [Chimera-users] Toolbar and Favorite on PC
In-Reply-To: <200610302147.k9ULlxSS1702137@guanine.cgl.ucsf.edu>
References:
<200610302147.k9ULlxSS1702137@guanine.cgl.ucsf.edu>
Message-ID:
Hi Tom,
I have set the location of the preferences file as you just described.
That helps, thank you
Now, something else that disapears: in the volume viewer, if I add a few
new features then click "Save Default Dialog Settings", the new features
are forgotten the next time I reopen Chimera ...
Is there a way to fix that?
Jean-Francois
Jean-Fran?ois M?n?tret, PhD
Boston University School of Medicine
Physiology and Biophysics Department
700 Albany Street W315
Boston, MA 02118
Email: menetret at bu.edu
Mailing address: 715 Albany Street
On Mon, 30 Oct 2006, Thomas Goddard wrote:
> Hi Jean-Francois,
>
> I'm puzzled about your disappearing Chimera toolbar. It seems Chimera
> is not finding its preferences file. The location of the preferences file
> is set using Chimera menu entry
>
> Favorites / Preferences, category Preferences
>
> The path of the preferences files may be relative to the directory where
> Chimera starts. If you start Chimera by clicking an icon in Windows XP
> the start-up directory is set for the icon. Right click on the Chimera
> icon and choose Properties and look at the "Start in" field. This should
> help you find your Chimera preferences file.
>
> Tom
>
From goddard at cgl.ucsf.edu Mon Oct 30 14:42:51 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 30 Oct 2006 14:42:51 -0800 (PST)
Subject: [Chimera-users] Saving default volume dialog settings fails
In-Reply-To: (message from
jean-francois menetret on Mon, 30 Oct 2006 17:28:36 -0500 (EST))
References:
<200610302147.k9ULlxSS1702137@guanine.cgl.ucsf.edu>
Message-ID: <200610302242.k9UMgpUo1728311@guanine.cgl.ucsf.edu>
Hi Jean-Francois,
There is a bug in Chimera 1.2304 that prevents saving default volume
dialog settings. It generates an error message. I've fixed the
problem in our code. If you want to fix it in your copy of Chimera
you can edit the text file:
chimera/share/VolumeViewer/defaultsettings.py
changing line 194 from
p['shown_panels'] = d.shown_panel_names()
to
p['shown_panels'] = map(lambda p: p.name, d.shown_panels())
Then restart Chimera.
This fix will be in the next Chimera snapshot.
Tom
From lydka at uoregon.edu Mon Oct 30 14:47:06 2006
From: lydka at uoregon.edu (Lydia Jablonski)
Date: Mon, 30 Oct 2006 14:47:06 -0800
Subject: [Chimera-users] Exporting VRML, Using Blender
In-Reply-To:
References:
Message-ID: <1162248426.665996.alphamail@alphamail.uoregon.edu>
Jonathan and Greg-
Thank you for your suggestions. I wanted to at least try them before I responded.
Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible.
Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up.
Any more pointers would be much appreciated.
-Lydia
On Fri, 27 Oct 2006 16:39:39 -0700 (PDT), Greg Couch wrote:
> A couple of things:
>
> 3DS Max supports importing VRML (.wrl) files, so you'd be better off
> using the latest chimera, 1.2304, and exporting VRML for direct import
> into 3ds Max.
>
> As for biopython/blender, I believe you'd be better off using chimera to
> export to blender using the X3D format. Chimera understands PDB files
> better than biopython, generates ribbons and molecular surfaces, deals
> with volume data easily (see http://www.cgl.ucsf.edu/chimera/ for
> details), and blender can do wonderful animations and other
> postprocessing. It's a more powerful combination.
>
> Greg Couch
> UCSF Computer Graphics Lab
>
> On Fri, 27 Oct 2006, Jonathan Hilmer wrote:
>
> > Date: Fri, 27 Oct 2006 14:09:12 -0600
> > From: Jonathan Hilmer
> > To: chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
> >
> > Although this does not relate to your question on licensing, is there
> > any particular reason you're using such a complicated workflow?
> > Chimera can be used to generate basic geometry (sphere/cylinder) from
> > PDB files via povray, but so could any import system you have for the
> > 3D modeling software. You would also lose the benefit of
> > chemistry-centered structure for manipulation or selection: chains,
> > residues, etc.
> >
> > I've been using Blender to handle complicated chemical models for a
> > while now, and it wasn't that difficult to implement the import of
> > various data types. With BioPython pdb files become trivial, and
> > volumetric data sets are (very) difficult but possible.
> >
> > Jonathan
> >
> >
> >
> >> Hello-
> >>
> >> Do any of you have an idea of how much a single commercial license for
> >> Chimera would cost?
> >>
> >> I'm a 3D artist/animator/biology student that works at in the art dept.
> >> of a biotech company. I'm interested in the exporting .pdb files to
> >> .pov, then converting to .3ds to import to 3ds max.
> >>
> >> Thanks,
> >>
> >> Lydia Jablonski
> > _______________________________________________
> > 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 gregc at cgl.ucsf.edu Mon Oct 30 15:03:41 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 30 Oct 2006 15:03:41 -0800 (PST)
Subject: [Chimera-users] Exporting VRML, Using Blender
In-Reply-To: <1162248426.665996.alphamail@alphamail.uoregon.edu>
References:
<1162248426.665996.alphamail@alphamail.uoregon.edu>
Message-ID:
Blender is free alternative to 3ds Max or Maya available from
. I am not qualified to compare them, so my
recommendation is for you to download blender and try it out to see if you
like it. If you have already bought and are comfortable with 3ds Max,
then there is probably no reason to change.
- Greg
On Mon, 30 Oct 2006, Lydia Jablonski wrote:
>
> Jonathan and Greg-
>
> Thank you for your suggestions. I wanted to at least try them before I
> responded.
>
> Exporting VRML: I did try the export to VRML from version 1.2304 and it
> is good to know that it works for ribbons now. Unfortunately, the
> imported VRML meshes don't seem to respond to the mesh smoothing in 3ds
> max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a
> completely smooth surface on the ribbon. With the imported .wrl (VRML) I
> am able to see the triangulation on the surface, especially with shiny
> materials. Increasing the subdivision quality in Chimera makes these
> triangles smaller, but they are still visible.
>
> Blender: Can you explain more the advantages of Blender for
> rendering/animating molecular models? I've been using 3ds max for quite
> a while (since the DOS days) so I feel very comfortable with it. But the
> need to work with molecular models is new so I'm still bumping around
> trying to figure out what all the possibilities are. If another 3D
> animation program would work better with exported .pdb files I'd be
> willing to pick it up.
>
> Any more pointers would be much appreciated.
>
> -Lydia
From goddard at cgl.ucsf.edu Mon Oct 30 15:04:52 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 30 Oct 2006 15:04:52 -0800 (PST)
Subject: [Chimera-users] Preferences file location
In-Reply-To: (message from
jean-francois menetret on Mon, 30 Oct 2006 17:28:36 -0500 (EST))
References:
<200610302147.k9ULlxSS1702137@guanine.cgl.ucsf.edu>
Message-ID: <200610302304.k9UN4q0T1949819@guanine.cgl.ucsf.edu>
Hi Jean-Francois,
In a previous message I suggested looking at the Chimera Preferences
dialog, category Preferences, to see where the preferences file is
saved. But I don't recommend changing that setting. Changing the
setting only changes where Chimera preferences are saved for the
current session. Next time you start Chimera it will not use that
location unless it is the first preferences file Chimera finds. Why
not? Because Chimera can only remember settings by placing them in
the preferences file so it does not save the location of the
preferences file even if you press the Save button on the dialog
because it would not be useful. I believe Chimera looks in the 3
places listed in that menu in the listed order (preferences,
.chimera/preferences, $HOME/.chimera/preferences) and uses the first
location where the file exists. So if you have a file called
preferences in the directory where Chimera starts and you change the
menu setting to ".chimera/preferences" then any new preference
settings will occur in ".chimera/preferences". But next time you
start you will still get the settings from the preferences file in the
start-up directory and not the newer ones in file ".chimera/preferences".
This is so confusing I am going to report it as a bug.
Tom
From jkhilmer at gmail.com Mon Oct 30 16:07:42 2006
From: jkhilmer at gmail.com (Jonathan Hilmer)
Date: Mon, 30 Oct 2006 17:07:42 -0700
Subject: [Chimera-users] Chimera, 3dsmax, blender
Message-ID: <81277ce10610301607nf27d7cdydb04c24a9d58f165@mail.gmail.com>
Lydia,
It's been years since I've had access to a 3dsmax license, so I can't
really make good comparisons between it and Blender. Fundamentally,
they serve the same role, so I expect you would find using them
similar, especially compared to PyMOL, Chimera, etc.
Before getting into the benefits, you should be aware that compared to
any software truly designed for chemical modeling, Blender has some
serious drawbacks. There is no pre-existing set of structural tools
that is standard for chemistry modeling software: if you want ribbons,
you have to write a procedure that will generate them. I'm assuming
you're already familiar with this, though, since you're using 3dsmax.
As another sizeable negative, CSG in Blender is still somewhat flaky.
I seem to remember having far fewer problems in 3d studio, even back
around ~R5 or 6.
On the benefit side, Blender's plugin/scripting system is extremely
free of restrictions. The scripting system is pure Python, and many
Python "plugins" are available. The true plugins are done in C, but
are currently restricted to some post-processing features. You could
also use the scripting system to access C libraries. These features
really help to make up for the lack of built-in chemistry-centered
tools. The other reason why you might prefer Blender over 3dsmax is
that the scripting and plugin system is very much like Chimera, so if
you're using both it's only one system to learn.
Jonathan
> Message: 8
> Date: Mon, 30 Oct 2006 14:47:06 -0800
> From: "Lydia Jablonski"
> Subject: [Chimera-users] Exporting VRML, Using Blender
>
> Jonathan and Greg-
>
> Thank you for your suggestions. I wanted to at least try them before I responded.
>
> Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible.
>
> Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up.
>
> Any more pointers would be much appreciated.
>
> -Lydia
From goeritz at caltech.edu Mon Oct 30 17:00:08 2006
From: goeritz at caltech.edu (Mareike Goeritz)
Date: Mon, 30 Oct 2006 17:00:08 -0800 (PST)
Subject: [Chimera-users] problems with starting Chimera
Message-ID: <4285737859goeritz@caltech.edu>
Hello,
I'm interested in using Chimera, but after downloading and installing
the software I'm unable to launch the program. I always get the
following error message:
"Microsoft Visual C++ Runtime Library:
Assertion failed!
Program: C:\Program Files\Chimera\bin\pythonw.exe
File: togl.c
Line: 2994
Expression: res==TRUE
For information on how your program can cause an assertion failure, see
the Visual C++ documentation on asserts
(Press Retry to debug the application - JIT must be enabled)"
I'm not familiar with C++, so I don't know what to do. Does anybody know
what might be missing or what's the problem?
Thank you for your help!!
Mareike
--
********************************
Dr. Mareike Goeritz
Department of Chemistry, MC 164-30
California Institute of Technology
1200 E. California Blvd.
Pasadena, CA 91125
(626) 395-6032 Tel
(626) 683-8753 Fax
goeritz at caltech.edu
********************************
From gregc at cgl.ucsf.edu Mon Oct 30 17:12:05 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 30 Oct 2006 17:12:05 -0800 (PST)
Subject: [Chimera-users] problems with starting Chimera
In-Reply-To: <4285737859goeritz@caltech.edu>
References: <4285737859goeritz@caltech.edu>
Message-ID:
This is a graphics driver problem. Please upgrade your graphics driver to
latest version available for your computer. If you have a laptop, get the
graphics driver from your laptop vendor (unless you have a NVidia GeForce
7 Go or an ATI Mobility Radeon 9600 or newer). Otherwise, if you have a
NVidia graphics card, get the latest driver -- likewise for ATI, 3DLabs,
Intel, SiS, etc.
Greg Couch
UCSF Computer Graphics Lab
On Mon, 30 Oct 2006, Mareike Goeritz wrote:
> Date: Mon, 30 Oct 2006 17:00:08 -0800 (PST)
> From: Mareike Goeritz
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] problems with starting Chimera
>
> Hello,
>
> I'm interested in using Chimera, but after downloading and installing
> the software I'm unable to launch the program. I always get the
> following error message:
> "Microsoft Visual C++ Runtime Library:
> Assertion failed!
> Program: C:\Program Files\Chimera\bin\pythonw.exe
> File: togl.c
> Line: 2994
> Expression: res==TRUE
> For information on how your program can cause an assertion failure, see
> the Visual C++ documentation on asserts
> (Press Retry to debug the application - JIT must be enabled)"
>
> I'm not familiar with C++, so I don't know what to do. Does anybody know
> what might be missing or what's the problem?
> Thank you for your help!!
>
> Mareike
> --
>
> ********************************
> Dr. Mareike Goeritz
>
> Department of Chemistry, MC 164-30
> California Institute of Technology
> 1200 E. California Blvd.
> Pasadena, CA 91125
>
> (626) 395-6032 Tel
> (626) 683-8753 Fax
> goeritz at caltech.edu
> ********************************
From gregdp at gmail.com Tue Oct 31 10:07:31 2006
From: gregdp at gmail.com (Greg Pintilie)
Date: Tue, 31 Oct 2006 13:07:31 -0500
Subject: [Chimera-users] atom name balloons
Message-ID:
I was wondering why in the new release of Chimera ballons no longer pop up
when the mouse is placed over an atom and is left there... is this an option
that has to be set somewhere? I found it extremely usefull and now am
missing it...
Greg
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From meng at cgl.ucsf.edu Tue Oct 31 10:53:29 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 31 Oct 2006 10:53:29 -0800
Subject: [Chimera-users] atom name balloons
In-Reply-To:
References:
Message-ID:
Hi Greg,
The atom-name balloons should still show, and that is the default
behavior. They still pop up in at least the Mac OSX/X11 version of
1.2304 I'm using on my desktop. I guess the first thing to do is
make sure they are still set to display in your Preferences:
menu: Favorites... Preferences, General category
"Show atomspec balloon" should be set to "true"
If that was somehow set to "false" just change it to "true" and click
Save to save the preferences. If it was already set to "true," there
must be some other problem. If so, let us know what platform you are
using. Best,
Elaine
On Oct 31, 2006, at 10:07 AM, Greg Pintilie wrote:
>
> I was wondering why in the new release of Chimera ballons no longer
> pop up when the mouse is placed over an atom and is left there...
> is this an option that has to be set somewhere? I found it
> extremely usefull and now am missing it...
>
> Greg
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
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From gregc at cgl.ucsf.edu Tue Oct 31 14:17:35 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 31 Oct 2006 14:17:35 -0800 (PST)
Subject: [Chimera-users] commercial license
In-Reply-To: <1161948446.609916.alphamail@alphamail.uoregon.edu>
References:
<1161948446.609916.alphamail@alphamail.uoregon.edu>
Message-ID:
On Fri, 27 Oct 2006, Lydia Jablonski wrote:
> Do any of you have an idea of how much a single commercial license for
> Chimera would cost?
The official answer is: "Commercial licensing costs are tier-based,
depending on the number of users. Please contact chimera at cgl.ucsf.edu if
you are interested in using Chimera for commercial purposes."
In Lydia's case, we decided that asking the question on the chimera-users
mailing list was equivalent to sending email to chimera at cgl.ucsf.edu. But
we would prefer email.
Greg Couch
UCSF Computer Graphics Lab