From JeanDidier.Marechal at uab.cat  Thu Feb  1 03:46:10 2007
From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal)
Date: Thu, 01 Feb 2007 12:46:10 +0100
Subject: [Chimera-users] access to pdb parser
Message-ID: <bacc5176c40.45c1e112@uab.es>

Hi Eric,

Well, the truth is that these are two good news. Most likely I didn't explain myself correctly. In reality, for practical reasons, I'd like to use only chimera for the teaching. So, I am planning to only use its internal python shell for python applications. Therefore the tips you gave me are perfect. 

Thanks a lot for the help!  
Cheers


JD

Dr. Jean-Didier Mar?chal
Professor Lector
Unitat de Qu?mica F?sica
Departament de Qu?mica
Universitat Aut?noma de Barcelona
Edifici C.n.
08193 Cerdonyola (Barcelona)
Tel: +34.935814988
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: Eric Pettersen <pett at cgl.ucsf.edu>
Data: Dimecres, Gener 31, 2007 10:31 pm
Assumpte: Re: [Chimera-users] access to pdb parser

> Hi JD,
> 	I have good news and I have bad news.  The good news it that using 
> 
> PDBio to do what you want is pretty easy.  The bad news is that you 
> 
> can't use it in a generic Python shell, only in Chimera's own 
> Python  
> shell.  This is because we use a modified version of Python so that 
> 
> the types we define in the C++ layer (Molecule, etc.) can have  
> attributes added to them in the Python layer -- otherwise they 
> would  
> behave like the built-in Python types (dict, list. etc.) that can't 
> 
> have arbitrary attributes added to them.  We intend to improve our  
> own code to make modifying Python unnecessary, but haven't gotten 
> to  
> it so far.
> 	Nonetheless, you can basically use Chimera in place of a Python  
> interpreter.  "chimera --nogui script.py" will execute the Python  
> script named script.py without bringing up the Chimera interface.   
> Also, you can start Chimera normally and bring up the graphical  
> interface to its interactive Python shell, IDLE (under Tools-
> >General  
> Controls) and type Python commands to that.
> 	Here's a session of me using PDBio in IDLE.  I've added some 
> comments.
> >>> from chimera import PDBio  # import PDBio
> >>> pdbio = PDBio()  # create a PDBio instance
> >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent")  # read a  
> PDB file given its file name
> >>> m = mols[0]  # readPDBfile() returned a list of models (NMR 
> can  
> have many) so get the model itself
> >>> m.pdbHeaders["HEADER"]  # each model will have a pdbHeaders  
> dictionary, keyed by the record type, the values will be a list of  
> strings -- the PDB records
> ['HEADER    HORMONE                                 17-OCT-77    
> 1GCN      1GCN   3']
> >>>
> 
> --Eric
> 
> On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote:
> 
> > Hi Eric,
> >
> > Yes, that would be better to explain more what I'd like to do.
> >
> > I am planning to give a practical on computational (bio)chemistry 
> 
> > in my department next year. I'd stongly like to have the students 
> 
> > using chimera and python as their main tools (though both are 
> tools  
> > I am in process of learning :-)).
> >
> > One of the "simple things" I have in mind, is to obtain pdb infos 
> 
> > directly from the shell e.g list the SEQRES entry or access to 
> the  
> > resolution (REMARK 2), the crystallization conditions  etc. The  
> > students will be chemists and I think that from a didactic point 
> of  
> > view, obtaining infos from the python shell would be better that  
> > reading the pdb files, especially if we want to compare different 
> 
> > structures e.g. Writing a comand that gives you ALL the 
> resolutions  
> > of the 10 structures you loaded would be interesting. I looked at 
> 
> > the PDBio, but I can see how to catch REMARKS infos.
> >
> > I'd really like to have this work going on, but as you can see, I 
> 
> > am a bit lost in where to begin.
> >
> > Any help to tell me where to start would be fantastic!
> >
> > Cheers
> >
> > JD
> >
> >
> >
> >
> > Dr. Jean-Didier Mar?chal
> > Professor Lector
> > Unitat de Qu?mica F?sica
> > Departament de Qu?mica
> > Universitat Aut?noma de Barcelona
> > Edifici C.n.
> > 08193 Cerdonyola (Barcelona)
> > Tel: +34.935814988
> > e-mail: JeanDidier.Marechal at uab.es
> >
> > ----- Missatge original -----
> > De: Eric Pettersen <pett at cgl.ucsf.edu>
> > Data: Dimarts, Gener 30, 2007 1:25 am
> > Assumpte: Re: [Chimera-users] access to pdb parser
> >
> >> Hi JD,
> >> 	Chimera does its PDB parsing in the C++ layer (the PDBio class in
> >>
> >> the Python layer).  There is a file named PDB.py in the mmCIF-
> >> parsing
> >> module, but it's not for parsing PDB files.  Perhaps if you
> >> described
> >> why you need Python PDB parsing I could suggest options -- using
> >> PDBio possibly being one of them.
> >>
> >> --Eric
> >>
> >>                         Eric Pettersen
> >>                         UCSF Computer Graphics Lab
> >>                         pett at cgl.ucsf.edu
> >>                         http://www.cgl.ucsf.edu
> >>
> >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote:
> >>
> >>> Hello everyone,
> >>>
> >>> a short question. What is the right call for importing the
> >>> pdbparser module in the chimera python shell? I found the PDB.py
> >>
> >>> module in the site-package mmlib, but I don't know how to import
> >> it...>
> >>> Thanks a lot,
> >>>
> >>> JD
> >>>
> >>>
> >>> Dr. Jean-Didier Mar?chal
> >>> Professor Lector
> >>> Unitat de Qu?mica F?sica
> >>> Departament de Qu?mica
> >>> Universitat Aut?noma de Barcelona
> >>> Edifici C.n.
> >>> 08193 Cerdonyola (Barcelona)
> >>> Tel: +34.935814988
> >>> e-mail: JeanDidier.Marechal at uab.es
> >>>
> >>>
> >>> _______________________________________________
> >>> Chimera-users mailing list
> >>> Chimera-users at cgl.ucsf.edu
> >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >>
> >>
> >
> >
> 
> 




From heiland at indiana.edu  Thu Feb  1 10:01:00 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Thu, 1 Feb 2007 13:01:00 -0500
Subject: [Chimera-users] cavity cropped view
Message-ID: <000e01c7462a$f187d450$d4977cf0$@edu>

What options exist in Chimera for letting me show only that portion of a
protein that is "near" another smaller molecule?  Specifically, I have a
ligand in a cavity of a large protein and would like to eliminate the
"clutter" of the protein away from the cavity of interest.

Thanks, Randy



From meng at cgl.ucsf.edu  Thu Feb  1 10:22:04 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 1 Feb 2007 10:22:04 -0800
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <000e01c7462a$f187d450$d4977cf0$@edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
Message-ID: <74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>

Hi Randy,
You can use a "zone" specification, either with commands or via the  
menu.  An example of the command approach:

show ligand zr<5
    or
show :glc zr<5

The first example would show all residues [with any atom] within 5  
angstroms of what is considered "ligand" ... in the second example, I  
gave a specific residue name.  GLC is the residue name of glucose in  
the PDB entry 2gbp.  You could also use a residue number or range of  
numbers. "za" instead of "zr" would just the atoms within the cutoff  
rather than their whole residues, and > instead of < gets the  
complementary set.  The "show" command (unlike "display") undisplays  
everything that is not specified, so you don't have to undisplay  
anything beforehand.

See the "Zones" section of
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
frameatom_spec.html

The mostly-menu approach has more steps:
- select the small molecule (for example by Ctrl-clicking one of its  
atoms and then pressing the up arrow key)
- use the command
         ~display
to undisplay everything (if you use the Actions menu, it would just  
undisplay the current selection)
- select a zone defined by the current selection (Select... Zone)  
with specified cutoff and whether you want it to be atom-based or  
residue-based
- display that selection (for example, with Actions... Atoms/Bonds...  
show)

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




On Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:

> What options exist in Chimera for letting me show only that portion  
> of a
> protein that is "near" another smaller molecule?  Specifically, I  
> have a
> ligand in a cavity of a large protein and would like to eliminate the
> "clutter" of the protein away from the cavity of interest.
>
> Thanks, Randy
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From triffo at rice.edu  Thu Feb  1 10:28:42 2007
From: triffo at rice.edu (Jeff)
Date: Thu, 01 Feb 2007 10:28:42 -0800
Subject: [Chimera-users] anyone using chimera on a an IBM T43p
Message-ID: <45C2315A.2090203@rice.edu>

hello,

I have an IBM T43p (June '05 or so release) which has an ATI FireGL 
v3200 (Mobility). In XP, it isn't possible to try out drivers from the 
vendor, I am limited to drivers from IBM.

In Linux, I have been able to install proprietary drivers from ATI, but 
there is no selection for the 'Mobility' version of the v3200 on ATI's 
website; the install has not complained though, and basic stuff appears 
to be fine (GUI is ok, glxgears, etc).

In both XP and Linux, chimera will crash when attempting to use volume 
maps. It appears fine with pdb files, although I typically work with 
volume data so haven't rigorously tested that.

I have been assuming that the FireGL v3200 (Mobility) is the same logic 
as the v3200, at least documentation I have been able to find seems to 
imply that.

Does anyone know (or suggest) a chimera-stable driver version from ATI 
that I might test? I might at least be able to get it to work in Linux, 
as the driver suite downloaded from ATI appears to cover most 
late-generation cards.

thanks for any suggestions,

-Jeff



From gregc at cgl.ucsf.edu  Thu Feb  1 11:22:49 2007
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 1 Feb 2007 11:22:49 -0800 (PST)
Subject: [Chimera-users] anyone using chimera on a an IBM T43p
In-Reply-To: <45C2315A.2090203@rice.edu>
References: <45C2315A.2090203@rice.edu>
Message-ID: <Pine.OSF.4.63.0702011043240.1870114@guanine.cgl.ucsf.edu>

On Thu, 1 Feb 2007, Jeff wrote:

>
> I have an IBM T43p (June '05 or so release) which has an ATI FireGL
> v3200 (Mobility). In XP, it isn't possible to try out drivers from the
> vendor, I am limited to drivers from IBM.
>
> In Linux, I have been able to install proprietary drivers from ATI, but
> there is no selection for the 'Mobility' version of the v3200 on ATI's
> website; the install has not complained though, and basic stuff appears
> to be fine (GUI is ok, glxgears, etc).
>
> In both XP and Linux, chimera will crash when attempting to use volume
> maps. It appears fine with pdb files, although I typically work with
> volume data so haven't rigorously tested that.
>
> I have been assuming that the FireGL v3200 (Mobility) is the same logic
> as the v3200, at least documentation I have been able to find seems to
> imply that.
>
> Does anyone know (or suggest) a chimera-stable driver version from ATI
> that I might test? I might at least be able to get it to work in Linux,
> as the driver suite downloaded from ATI appears to cover most
> late-generation cards.
>
> thanks for any suggestions,
>
> -Jeff

Except for some newer laptops, laptop driver support is practically 
non-existent, as you have found out.  There are unofficial programs that 
modify the current ATI/NVidia graphics drivers to make them work on 
laptops.  A major reason for using the laptop vendor's graphics driver is 
that it supports the external video connector correctly.  So you may need 
to downgrade to the vendor's driver to use your laptop for presentations.

For ATI, check out <http://www.theinquirer.net/default.aspx?article=28636>
and the tool is at <http://www.driverheaven.net/modtool/>.

For NVidia, check out <http://www.laptopvideo2go.com/>.

For Linux, you should check out Xi Graphics, <http://www.xig.com/>, they 
have a laptop version of their X server for Linux that might work.  And 
they let you test a full-featured demo before you buy!  That said, your 
laptop is not listed as supported, nor is your graphics chipset, so 
in this case, there's a good chance it won't work.

 	Good luck,

 	Greg Couch
 	UCSF Computer Graphics Lab


From pett at cgl.ucsf.edu  Thu Feb  1 11:40:40 2007
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 1 Feb 2007 11:40:40 -0800
Subject: [Chimera-users] access to pdb parser
In-Reply-To: <bacc5176c40.45c1e112@uab.es>
References: <bacc5176c40.45c1e112@uab.es>
Message-ID: <70096418-FC94-4092-8BAA-800C532D7E4E@cgl.ucsf.edu>

Hi JD,
	Depending on what you want to do, you may not even have to use PDBio  
directly.  Once you open a molecular model by any means in Chimera,  
it will have that pdbHeaders dictionary attribute.  You can get a  
list of the currently open molecular models in Chimera like this:

	import chimera
	mols = chimera.openModels.list(modelTypes=[chimera.Molecule])

--Eric

On Feb 1, 2007, at 3:46 AM, Jean Didier Pie Marechal wrote:

> Hi Eric,
>
> Well, the truth is that these are two good news. Most likely I  
> didn't explain myself correctly. In reality, for practical reasons,  
> I'd like to use only chimera for the teaching. So, I am planning to  
> only use its internal python shell for python applications.  
> Therefore the tips you gave me are perfect.
>
> Thanks a lot for the help!
> Cheers
>
>
> JD
>
> Dr. Jean-Didier Mar?chal
> Professor Lector
> Unitat de Qu?mica F?sica
> Departament de Qu?mica
> Universitat Aut?noma de Barcelona
> Edifici C.n.
> 08193 Cerdonyola (Barcelona)
> Tel: +34.935814988
> e-mail: JeanDidier.Marechal at uab.es
>
> ----- Missatge original -----
> De: Eric Pettersen <pett at cgl.ucsf.edu>
> Data: Dimecres, Gener 31, 2007 10:31 pm
> Assumpte: Re: [Chimera-users] access to pdb parser
>
>> Hi JD,
>> 	I have good news and I have bad news.  The good news it that using
>>
>> PDBio to do what you want is pretty easy.  The bad news is that you
>>
>> can't use it in a generic Python shell, only in Chimera's own
>> Python
>> shell.  This is because we use a modified version of Python so that
>>
>> the types we define in the C++ layer (Molecule, etc.) can have
>> attributes added to them in the Python layer -- otherwise they
>> would
>> behave like the built-in Python types (dict, list. etc.) that can't
>>
>> have arbitrary attributes added to them.  We intend to improve our
>> own code to make modifying Python unnecessary, but haven't gotten
>> to
>> it so far.
>> 	Nonetheless, you can basically use Chimera in place of a Python
>> interpreter.  "chimera --nogui script.py" will execute the Python
>> script named script.py without bringing up the Chimera interface.
>> Also, you can start Chimera normally and bring up the graphical
>> interface to its interactive Python shell, IDLE (under Tools-
>>> General
>> Controls) and type Python commands to that.
>> 	Here's a session of me using PDBio in IDLE.  I've added some
>> comments.
>>>>> from chimera import PDBio  # import PDBio
>>>>> pdbio = PDBio()  # create a PDBio instance
>>>>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent")  # read a
>> PDB file given its file name
>>>>> m = mols[0]  # readPDBfile() returned a list of models (NMR
>> can
>> have many) so get the model itself
>>>>> m.pdbHeaders["HEADER"]  # each model will have a pdbHeaders
>> dictionary, keyed by the record type, the values will be a list of
>> strings -- the PDB records
>> ['HEADER    HORMONE                                 17-OCT-77
>> 1GCN      1GCN   3']
>>>>>
>>
>> --Eric
>>
>> On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote:
>>
>>> Hi Eric,
>>>
>>> Yes, that would be better to explain more what I'd like to do.
>>>
>>> I am planning to give a practical on computational (bio)chemistry
>>
>>> in my department next year. I'd stongly like to have the students
>>
>>> using chimera and python as their main tools (though both are
>> tools
>>> I am in process of learning :-)).
>>>
>>> One of the "simple things" I have in mind, is to obtain pdb infos
>>
>>> directly from the shell e.g list the SEQRES entry or access to
>> the
>>> resolution (REMARK 2), the crystallization conditions  etc. The
>>> students will be chemists and I think that from a didactic point
>> of
>>> view, obtaining infos from the python shell would be better that
>>> reading the pdb files, especially if we want to compare different
>>
>>> structures e.g. Writing a comand that gives you ALL the
>> resolutions
>>> of the 10 structures you loaded would be interesting. I looked at
>>
>>> the PDBio, but I can see how to catch REMARKS infos.
>>>
>>> I'd really like to have this work going on, but as you can see, I
>>
>>> am a bit lost in where to begin.
>>>
>>> Any help to tell me where to start would be fantastic!
>>>
>>> Cheers
>>>
>>> JD
>>>
>>>
>>>
>>>
>>> Dr. Jean-Didier Mar?chal
>>> Professor Lector
>>> Unitat de Qu?mica F?sica
>>> Departament de Qu?mica
>>> Universitat Aut?noma de Barcelona
>>> Edifici C.n.
>>> 08193 Cerdonyola (Barcelona)
>>> Tel: +34.935814988
>>> e-mail: JeanDidier.Marechal at uab.es
>>>
>>> ----- Missatge original -----
>>> De: Eric Pettersen <pett at cgl.ucsf.edu>
>>> Data: Dimarts, Gener 30, 2007 1:25 am
>>> Assumpte: Re: [Chimera-users] access to pdb parser
>>>
>>>> Hi JD,
>>>> 	Chimera does its PDB parsing in the C++ layer (the PDBio class in
>>>>
>>>> the Python layer).  There is a file named PDB.py in the mmCIF-
>>>> parsing
>>>> module, but it's not for parsing PDB files.  Perhaps if you
>>>> described
>>>> why you need Python PDB parsing I could suggest options -- using
>>>> PDBio possibly being one of them.
>>>>
>>>> --Eric
>>>>
>>>>                         Eric Pettersen
>>>>                         UCSF Computer Graphics Lab
>>>>                         pett at cgl.ucsf.edu
>>>>                         http://www.cgl.ucsf.edu
>>>>
>>>> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote:
>>>>
>>>>> Hello everyone,
>>>>>
>>>>> a short question. What is the right call for importing the
>>>>> pdbparser module in the chimera python shell? I found the PDB.py
>>>>
>>>>> module in the site-package mmlib, but I don't know how to import
>>>> it...>
>>>>> Thanks a lot,
>>>>>
>>>>> JD
>>>>>
>>>>>
>>>>> Dr. Jean-Didier Mar?chal
>>>>> Professor Lector
>>>>> Unitat de Qu?mica F?sica
>>>>> Departament de Qu?mica
>>>>> Universitat Aut?noma de Barcelona
>>>>> Edifici C.n.
>>>>> 08193 Cerdonyola (Barcelona)
>>>>> Tel: +34.935814988
>>>>> e-mail: JeanDidier.Marechal at uab.es
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Chimera-users mailing list
>>>>> Chimera-users at cgl.ucsf.edu
>>>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>
>>>>
>>>
>>>
>>
>>
>
>




From goddard at cgl.ucsf.edu  Thu Feb  1 12:00:38 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 01 Feb 2007 12:00:38 -0800
Subject: [Chimera-users] anyone using chimera on a an IBM T43p
In-Reply-To: <45C2315A.2090203@rice.edu>
References: <45C2315A.2090203@rice.edu>
Message-ID: <45C246E6.7050801@cgl.ucsf.edu>

Hi Jeff,

   The Chimera graphics bug page

	http://www.cgl.ucsf.edu/chimera/graphicsbugs.html

lists a FireGL V3400 (desktop) that also causes system crashes on volume 
display.  I helped Gary with that and the latest ATI driver had the same 
problem.  We did not find a driver that works.

	Tom


Jeff wrote:
> hello,
> 
> I have an IBM T43p (June '05 or so release) which has an ATI FireGL 
> v3200 (Mobility). In XP, it isn't possible to try out drivers from the 
> vendor, I am limited to drivers from IBM.
> 
> In Linux, I have been able to install proprietary drivers from ATI, but 
> there is no selection for the 'Mobility' version of the v3200 on ATI's 
> website; the install has not complained though, and basic stuff appears 
> to be fine (GUI is ok, glxgears, etc).
> 
> In both XP and Linux, chimera will crash when attempting to use volume 
> maps. It appears fine with pdb files, although I typically work with 
> volume data so haven't rigorously tested that.
> 
> I have been assuming that the FireGL v3200 (Mobility) is the same logic 
> as the v3200, at least documentation I have been able to find seems to 
> imply that.
> 
> Does anyone know (or suggest) a chimera-stable driver version from ATI 
> that I might test? I might at least be able to get it to work in Linux, 
> as the driver suite downloaded from ATI appears to cover most 
> late-generation cards.
> 
> thanks for any suggestions,
> 
> -Jeff
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


From kalju at chem.ucsb.edu  Thu Feb  1 11:43:41 2007
From: kalju at chem.ucsb.edu (Kalju Kahn)
Date: Thu, 01 Feb 2007 11:43:41 -0800
Subject: [Chimera-users] Chimera to visualize MOLDEN-generated VRML2.0 files
Message-ID: <20070201194342.4C70674FBFD@ultra.chem.ucsb.edu>

Dear Chimera users, 

I am looking for advice on how to make chimera work with VRML 2.0
files generated by MOLDEN.  MOLDEN seems to generate valid VRML files
(octagaplayer reads these in all right) but chimera crashes with 

Segmentation fault (core dumped)

This happens both on 32-bit Suse 9 system and 64-bit recent Ubuntu
system.
Any ideas are appreciated!

Kalju 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
University of California, Santa Barbara


From gregc at cgl.ucsf.edu  Thu Feb  1 12:31:41 2007
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 1 Feb 2007 12:31:41 -0800 (PST)
Subject: [Chimera-users] Chimera to visualize MOLDEN-generated VRML2.0
 files
In-Reply-To: <20070201194342.4C70674FBFD@ultra.chem.ucsb.edu>
References: <20070201194342.4C70674FBFD@ultra.chem.ucsb.edu>
Message-ID: <Pine.OSF.4.63.0702011223040.1644985@guanine.cgl.ucsf.edu>

On Thu, 1 Feb 2007, Kalju Kahn wrote:

> I am looking for advice on how to make chimera work with VRML 2.0
> files generated by MOLDEN.  MOLDEN seems to generate valid VRML files
> (octagaplayer reads these in all right) but chimera crashes with
>
> Segmentation fault (core dumped)
>
> This happens both on 32-bit Suse 9 system and 64-bit recent Ubuntu
> system.
> Any ideas are appreciated!

First, file a bug using chimera's Help/Report a Bug... dialog and attach 
the VRML 2.0 file that doesn't work.  It shouldn't core dump.

Second, chimera doesn't support all of VRML 2.0, only geometry nodes.  In 
particular, it doesn't support VRML PROTOs.  That is a bug, but I need 
more people to file bug reports about it before it gets fixed.

 	Greg Couch
 	UCSF Computer Graphics Lab


From triffo at rice.edu  Thu Feb  1 22:47:48 2007
From: triffo at rice.edu (Jeff)
Date: Thu, 01 Feb 2007 22:47:48 -0800
Subject: [Chimera-users] volume path tracer / render surface with marker set
Message-ID: <45C2DE94.1030407@rice.edu>

hello,

is there a way to render a surface of arbitrary thickness using a marker 
set? as in, fit some sort of spline to a marker set, with the constraint 
being that the algorithm assumes they all lie on the same surface? this 
would be useful for modeling membranes, perhaps it is already 
implemented and I am not seeing it in the dialogs.

thanks,

-J


From bernard_heymann at nih.gov  Fri Feb  2 08:28:39 2007
From: bernard_heymann at nih.gov (Bernard Heymann)
Date: Fri, 2 Feb 2007 11:28:39 -0500
Subject: [Chimera-users] Saving modified PDB files
Message-ID: <F1F77BAF-39C9-41E4-ADE5-17FA72DE9785@nih.gov>

I have a problem saving PDB files relative to density maps in recent  
versions of Chimera. When I load a  PDB file and move it relative to  
a density map, and then try to save it relative to the density map,  
it does not apply the transformation to the PDB coordinates. This  
used to work in older versions. My workaround is to have another  
molecule open and save the transformed one relative to that. However,  
I would prefer to be able to save a transformed molecule relative to  
a density map. Can this be fixed?

Bernard Heymann, Research Fellow
Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH
Bethesda MD 20892-8025
Tel. 301-451-8241, Fax. 301-480-7629



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From goddard at cgl.ucsf.edu  Fri Feb  2 09:44:32 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Fri, 02 Feb 2007 09:44:32 -0800
Subject: [Chimera-users] Saving modified PDB files
In-Reply-To: <F1F77BAF-39C9-41E4-ADE5-17FA72DE9785@nih.gov>
References: <F1F77BAF-39C9-41E4-ADE5-17FA72DE9785@nih.gov>
Message-ID: <45C37880.9050200@cgl.ucsf.edu>

Hi Bernard,

  Unfortunately Chimera versions 1.2304 (Oct 2006), 1.2309 (Nov 2006), 
and 1.2318 (Dec 2006) were all broken -- not able to save a PDB model 
relative to a density map, which made it hard to save fits of atomic 
models into maps.  This was fixed on Dec 27, 2006 but there has not been 
a Chimera snapshot since then.

  You can replace a file in your Chimera distribution

    chimera/share/ModelPanel/writePDBdialog.py

with the one attached to this email to fix the problem in 1.2304 or 
newer versions.

  The bug report for this problem is

    
http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3390&database=chimera

  We plan on having a new Chimera snapshot this month that will include 
the fix.

    Tom

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From nsomboon at berkeley.edu  Thu Feb  1 20:11:53 2007
From: nsomboon at berkeley.edu (nsomboon at berkeley.edu)
Date: Thu, 1 Feb 2007 20:11:53 -0800 (PST)
Subject: [Chimera-users] Question on how to represent only chain A of Chimera
Message-ID: <33875.209.77.137.57.1170389513.squirrel@calmail.berkeley.edu>

Hi,

  I need help.  I received the modeling structures of my query (black) and
the best representative 1qopB (magenta) through MODWEB, and used Chimera
to visualize them (please see attached file).  However, the magenta
structure also contains 1qopA, in which I only want the 1qopB and don't
want the 1qopA.  I read through tutorials but cannot find a way to get
rid of the chain A of the 1qop.

  Hence, could you please direct me of how to cut out chain A of 1qop in
this attached file?  Thank you very much.

Sincerely yours,
Nara
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From meng at cgl.ucsf.edu  Fri Feb  2 10:50:40 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 2 Feb 2007 10:50:40 -0800
Subject: [Chimera-users] Question on how to represent only chain A of
	Chimera
In-Reply-To: <33875.209.77.137.57.1170389513.squirrel@calmail.berkeley.edu>
References: <33875.209.77.137.57.1170389513.squirrel@calmail.berkeley.edu>
Message-ID: <f175249255bd6915e29e4916de32abdc@cgl.ucsf.edu>

Hi Nara,
In Chimera you can hide (undisplay) the atoms, ribbon, or whatever is  
shown, or you can delete those parts you are sure you don't want.

In your session, it looks like you already selected the part you don't  
want, chain A.  To hide those ribbons, choose from the menu

Actions... Ribbon... hide

or, to delete that part if you never want to see it again, choose

Actions... Atoms/Bonds... delete

The Actions menu applies to your selection, which is chain A.  If you  
hide it, it will still be selected, until you clear the selection or  
select something else.  If nothing is selected, the Actions will apply  
to everything, so be careful not to choose "delete" unless you are sure  
what you want to delete is selected!  After you delete the selection,  
nothing will be selected.

You could also do the same things using the commands "~ribbon sel" and  
"delete sel" - I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Feb 1, 2007, at 8:11 PM, nsomboon at berkeley.edu wrote:

> Hi,
>
>   I need help.  I received the modeling structures of my query (black)  
> and
> the best representative 1qopB (magenta) through MODWEB, and used  
> Chimera
> to visualize them (please see attached file).  However, the magenta
> structure also contains 1qopA, in which I only want the 1qopB and don't
> want the 1qopA.  I read through tutorials but cannot find a way to get
> rid of the chain A of the 1qop.
>
>   Hence, could you please direct me of how to cut out chain A of 1qop  
> in
> this attached file?  Thank you very much.
>
> Sincerely yours,
> Nara<TrpB.1qopB.refDEFGHIaJ.ver2.chimerax.py>__________________________ 
> _____________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From goddard at cgl.ucsf.edu  Fri Feb  2 11:05:31 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Fri, 02 Feb 2007 11:05:31 -0800
Subject: [Chimera-users] Copying volume settings to a second data set
In-Reply-To: <45C25583.9030609@rice.edu>
References: <45C2315A.2090203@rice.edu> <45C246E6.7050801@cgl.ucsf.edu>
	<45C25583.9030609@rice.edu>
Message-ID: <45C38B7B.30105@cgl.ucsf.edu>

Hi Jeff,

  There is no capability to copy settings (thresholds, colors, 
brightness, display style, rendering options) that are specific to each 
volume data set to another data set.  That would be useful and I'll add 
it to the feature request list.

  Here are some hacks to achieve this.  I don't think they are worth the 
trouble to use but you can decide.  If you save a Chimera session with a 
volume having settings you want to reuse you can edit the session file 
changing the line:

       'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\emd_1282.map',

to

       'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\XXX.map',

Then when you reopen that session Chimera will say it cannot find the 
map file and ask you to select a new map file with a file open dialog.  
You can choose some other map.  The settings from the original map will 
then be applied to this newly opened map.  Another hack is to use the 
Volume Series tool available on the experimental features web page:

    http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

You can open your maps that you want to use the same settings for as a 
"volume series".  That tool copies settings when you use it to flip 
between volume in a series.  It can even adjust thresholds so they have 
the same rank position on the histogram (e.g. greater than 94% of voxel 
values).

    Tom


Jeff wrote:
> thanks Tom,
>
> is there a way to save the thresholds (and color settings) in the 
> volume viewer, so that when I close a map and reopen a 
> similar/filtered one, I don't have to re-do all the settings 
> (brightness and transparency too, for instance)
>
> i realize the histrogram changes for each map, but even if it saved 
> how many control points (and their colors) were there, that would 
> work. is there a 'save volume viewer state' button? I could not find one.
>
> -Jeff
>



From goddard at cgl.ucsf.edu  Fri Feb  2 13:27:48 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Fri, 02 Feb 2007 13:27:48 -0800
Subject: [Chimera-users] volume path tracer / render surface with marker
 set
In-Reply-To: <45C2DE94.1030407@rice.edu>
References: <45C2DE94.1030407@rice.edu>
Message-ID: <45C3ACD4.70502@cgl.ucsf.edu>

Hi Jeff,

  There is no Chimera capability to create surfaces using marker 
positions.  Chimera can read three types of externally generated 
surfaces: VRML, GRASP, and IMOD.  The vrml and grasp readers are a 
standard part of Chimera and the imod file reader is on the experimental 
features page.

    http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

Some years ago I wrote Python code to stitch together loops created in a 
program called PRIISM (used for light and electron microscopy) to form a 
tubular surface.  This was used to hand trace the nuclear envelope of 
cells.  It had no provision for giving the surface a thickness.  It 
created strips of triangles joining loops consisting of tens of points 
in two parallel planes.

  Interactive creation of surfaces would be useful for delimiting 
membranes seen in EM tomography.  I was asked about Chimera support for 
this at a cellular tomography workshop in December.  Programs for 
segmenting em tomography all do this (IMOD, Analyze, ...) and I am not 
decided on whether we should duplicate those capabilities in Chimera 
given the many projects we have.

  Karin Gross and Christoph Best at Max Planck Institute for 
Biochemistry have been looking into making Chimera extensions to trace 
EM tomography structures plane by plane.

    Tom



From mfyang at gmail.com  Mon Feb  5 08:08:24 2007
From: mfyang at gmail.com (Mingfeng Yang)
Date: Mon, 5 Feb 2007 11:08:24 -0500
Subject: [Chimera-users] PDB file format for movie
Message-ID: <e991394b0702050808v4e003f5csd3edef19cb1f4ce4@mail.gmail.com>

Dear Chimera users and developers,

I'd like to use chimera to view the motions of a protein. If all the
snapshots are to be saved in a single PDB file, what's the correct format
for them?

I tried  the following, but chimera complained that a single structure is
included only.

Thanks,
Mingfeng
------------------
MODEL 1
ATOM      1  N   ALA     1      -4.564  -7.956  -6.531  1.00  0.00
N
ATOM      2  CA  ALA     1      -5.237  -8.746  -5.532  1.00  0.00
C
ATOM      3  C   ALA     1      -4.360  -9.172  -4.378  1.00  0.00
C
...
ATOM     81  HN  ALA    10       0.195  11.398   3.736  1.00  0.00
H
END
MODEL 2
ATOM      1  N   ALA     1      -5.031  -8.234  -5.174  1.00  0.00
N
....
END
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From meng at cgl.ucsf.edu  Mon Feb  5 09:42:20 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Feb 2007 09:42:20 -0800
Subject: [Chimera-users] PDB file format for movie
In-Reply-To: <e991394b0702050808v4e003f5csd3edef19cb1f4ce4@mail.gmail.com>
References: <e991394b0702050808v4e003f5csd3edef19cb1f4ce4@mail.gmail.com>
Message-ID: <F27C9743-4A72-4000-AB0D-430E6C63F22C@cgl.ucsf.edu>

Hi Mingfeng,
Each "snapshot" should start with a MODEL record and end with an  
ENDMDL (not END), see the description of "PDB, single file":

http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/ 
framemovie.html

MD Movie will use the MODEL numbers as frame numbers, so they should  
start with 1 or 0 and increment by 1.

Most NMR structures in the PDB that include multiple models are done  
this way, so you could look at those as examples.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 5, 2007, at 8:08 AM, Mingfeng Yang wrote:

> Dear Chimera users and developers,
>
> I'd like to use chimera to view the motions of a protein. If all  
> the snapshots are to be saved in a single PDB file, what's the  
> correct format for them?
>
> I tried  the following, but chimera complained that a single  
> structure is included only.
>
> Thanks,
> Mingfeng
> ------------------
> MODEL 1
> ATOM      1  N   ALA     1      -4.564  -7.956  -6.531  1.00   
> 0.00           N
> ATOM      2  CA  ALA     1      -5.237  -8.746  -5.532  1.00   
> 0.00           C
> ATOM      3  C   ALA     1      -4.360  -9.172  -4.378  1.00   
> 0.00           C
> ...
> ATOM     81  HN  ALA    10       0.195  11.398   3.736  1.00   
> 0.00           H
> END
> MODEL 2
> ATOM      1  N   ALA     1      - 5.031  -8.234  -5.174  1.00   
> 0.00           N
> ....
> END
> _______________________________________________
> 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 Feb  5 10:36:05 2007
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 5 Feb 2007 10:36:05 -0800
Subject: [Chimera-users] PDB file format for movie
In-Reply-To: <e991394b0702050808v4e003f5csd3edef19cb1f4ce4@mail.gmail.com>
References: <e991394b0702050808v4e003f5csd3edef19cb1f4ce4@mail.gmail.com>
Message-ID: <83F84696-3C53-4087-892C-F6E62F5ADE0C@cgl.ucsf.edu>

Hi Mingfeng,
	Chimera's original PDB-parsing code was quite strict for exact  
format adherence.  Over time, I have made it more forgiving in many  
ways, but right now you're getting caught by one of it's remaining  
strictures:  according to the PDB format spec, the model number of a  
MODEL record has to be in columns 11-14.  In your example the model  
numbers start in column 7.  This problem will be fixed in the next  
snapshot, which we will be working on putting out next week.
	Also, as Elaine pointed out, you need to use ENDMDL records instead  
of END records.

--Eric

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


On Feb 5, 2007, at 8:08 AM, Mingfeng Yang wrote:

> Dear Chimera users and developers,
>
> I'd like to use chimera to view the motions of a protein. If all  
> the snapshots are to be saved in a single PDB file, what's the  
> correct format for them?
>
> I tried  the following, but chimera complained that a single  
> structure is included only.
>
> Thanks,
> Mingfeng
> ------------------
> MODEL 1
> ATOM      1  N   ALA     1      -4.564  -7.956  -6.531  1.00   
> 0.00           N
> ATOM      2  CA  ALA     1      -5.237  -8.746  -5.532  1.00   
> 0.00           C
> ATOM      3  C   ALA     1      -4.360  -9.172  -4.378  1.00   
> 0.00           C
> ...
> ATOM     81  HN  ALA    10       0.195  11.398   3.736  1.00   
> 0.00           H
> END
> MODEL 2
> ATOM      1  N   ALA     1      - 5.031  -8.234  -5.174  1.00   
> 0.00           N
> ....
> END
> _______________________________________________
> 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  Mon Feb  5 10:42:13 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 05 Feb 2007 10:42:13 -0800
Subject: [Chimera-users] question about mac laptops / workstations and
	chimera stability
In-Reply-To: <45C51022.8030508@rice.edu>
References: <45C51022.8030508@rice.edu>
Message-ID: <45C77A85.2000000@cgl.ucsf.edu>

Hi Jeff,

   I have not seen any graphics driver bug reports with the MacBook Pro 
with X1600 graphics.  I just ordered this machine to replace my four 
year old Dell with Quadro 4 graphics -- I am confident it will work well 
using volume data in Chimera.

   Here is our graphics driver bug page of problems observed with Chimera

	http://www.cgl.ucsf.edu/chimera/graphicsbugs.html

It only has about 1/3 of the driver bugs and I will be adding more from 
our Chimera bug tracking system when I have time.

	Tom


From mfyang at gmail.com  Mon Feb  5 10:43:01 2007
From: mfyang at gmail.com (Mingfeng Yang)
Date: Mon, 5 Feb 2007 13:43:01 -0500
Subject: [Chimera-users] PDB file format for movie
In-Reply-To: <83F84696-3C53-4087-892C-F6E62F5ADE0C@cgl.ucsf.edu>
References: <e991394b0702050808v4e003f5csd3edef19cb1f4ce4@mail.gmail.com>
	<83F84696-3C53-4087-892C-F6E62F5ADE0C@cgl.ucsf.edu>
Message-ID: <e991394b0702051043n17bc3750yba98d9426f1e4763@mail.gmail.com>

Thanks, Elaine and Eric. That works.

Mingfeng

On 2/5/07, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> Hi Mingfeng, Chimera's original PDB-parsing code was quite strict for
> exact format adherence.  Over time, I have made it more forgiving in many
> ways, but right now you're getting caught by one of it's remaining
> strictures:  according to the PDB format spec, the model number of a MODEL
> record has to be in columns 11-14.  In your example the model numbers start
> in column 7.  This problem will be fixed in the next snapshot, which we will
> be working on putting out next week.
> Also, as Elaine pointed out, you need to use ENDMDL records instead of END
> records.
>
> --Eric
>
>                         Eric Pettersen
>
>                         UCSF Computer Graphics Lab
>
>                         pett at cgl.ucsf.edu
>
>                         http://www.cgl.ucsf.edu
>
>
> On Feb 5, 2007, at 8:08 AM, Mingfeng Yang wrote:
>
> Dear Chimera users and developers,
>
> I'd like to use chimera to view the motions of a protein. If all the
> snapshots are to be saved in a single PDB file, what's the correct format
> for them?
>
> I tried  the following, but chimera complained that a single structure is
> included only.
>
> Thanks,
> Mingfeng
> ------------------
> MODEL 1
> ATOM      1  N   ALA     1      -4.564  -7.956  -6.531  1.00  0.00
> N
> ATOM      2  CA  ALA     1      -5.237  -8.746  -5.532  1.00  0.00
> C
> ATOM      3  C   ALA     1      -4.360  -9.172  -4.378  1.00  0.00
> C
> ...
> ATOM     81  HN  ALA    10       0.195  11.398   3.736  1.00  0.00
> H
> END
> MODEL 2
> ATOM      1  N   ALA     1      - 5.031  -8.234  -5.174  1.00  0.00
> N
> ....
> END
> _______________________________________________
> 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  Mon Feb  5 11:51:19 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 05 Feb 2007 11:51:19 -0800
Subject: [Chimera-users] not able to 'transfer markers'
In-Reply-To: <45C7767B.10104@rice.edu>
References: <45C7767B.10104@rice.edu>
Message-ID: <45C78AB7.6020205@cgl.ucsf.edu>

Hi Jeff,

   Menu entry "Actions / Transfer selected markers to current set" in 
the path tracer dialog moves the markers to the marker set chosen on the 
first line of the path tracer dialog.  That should be the same as the 
one chosen in the marker set scrolling list (Features / Marker set list) 
unless that list has multiple sets selected.

   The error message "Markers in one set cannot link to markers in a 
different set" means you tried to transfer some markers to the current 
set but they were connected by at least one link to markers in another 
set.  That is not supported.

   There is a command, keyboard shortcut "sc" that extends the current 
selection to all markers connected to currently selected ones.  You'll 
need to turn on keyboard shortcuts with main window menu entry Tools / 
General Controls / Accelerators On.  You can have them turned on by 
default every time you start Chimera using the Preferences dialog (menu 
Favorites / Preferences) category Tools and clicking the check button in 
the autostart column next to "Accelerators On".

   One possible confusion about hiding/showing markers is that if you 
have any markers selected then the Actions / Show & Hide menu entries 
act on those selected ones no matter what marker set they belong to.  If 
there are no markers selected then those same menu entries act on all 
markers in the current marker set, that is the one chosen at the top of 
the path tracer dialog.

   The marker set scrolled list is used for closing multiple marker sets 
and for saving multiple marker sets.  This may have been the problem 
when you could not close a marker set.  It closed the one selected in 
the scrolled list which was different from the "current marker set" 
shown at the top of the path tracer dialog.  When you change the current 
marker set menu it unfortunately does not clear the selected marker sets 
in the scrolled list.  That is a bug.

   Let me know if you can reproduce the problem hiding/showing markers.

	Tom

Jeff wrote:
> hi Tom,
> 
> using build 2318, if I select a series of markers, and then click 
> 'actions -> transfer selected markers to current set', it gives the 
> error 'Markers not transfered. Markers in one set cannot link to markers 
> in a different set.' when I did this, I assumed that the 'current set' 
> meant the one selected in the 'marker sets' dialog box in the volume 
> path tracer.
> 
> is there a way for me to get around this? I had traced out a series of 
> actin filaments in one set, and for practical reasons want to be able to 
> show/hide each marker path that corresponds to a filament; the only way 
> I could think of doing this was to have each filament be a separate 
> marker file, unless there is a command that allows me to select a single 
> marker and then just 'display markers connected to selected marker' 
> (preferred, actually), as opposed to using the up-arrow, which selects 
> the entire set.
> 
> after performing the 'transfer markers' request, I was no longer able to 
> show/unshow the marker sets. Also, when I closed a marker set, it was 
> still displayed. I shut down the session and recreated it from scratch. 
> I'll let you know if this show/unshow/close marker file issue occurs 
> again and under what circumstances; it would be hard for me to claim 
> that it was correlated to the 'transfer markers' command, I just know 
> that after that point in the session I could no longer show/unshow/close 
> the markers.
> 
> thanks,
> 
> -Jeff
> 



From eva.vanamee at mssm.edu  Mon Feb  5 13:55:25 2007
From: eva.vanamee at mssm.edu (Eva Vanamee)
Date: Mon, 05 Feb 2007 16:55:25 -0500
Subject: [Chimera-users] rotation by a set angle
Message-ID: <45C7A7CD.7080103@mssm.edu>

Hi,

I am trying to make a figure of my EM fit at different orientations.
Is it possible to rotate the molecule/map by a certain angle
so I know exactly the rotation between views?
Thanks in advance,

- Eva



From meng at cgl.ucsf.edu  Mon Feb  5 14:01:59 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Feb 2007 14:01:59 -0800
Subject: [Chimera-users] rotation by a set angle
In-Reply-To: <45C7A7CD.7080103@mssm.edu>
References: <45C7A7CD.7080103@mssm.edu>
Message-ID: <F2F4D1E2-F1CD-4461-9756-E879C7A02175@cgl.ucsf.edu>

Hi Eva,
You can perform a rotation of a specified number of degrees about the  
X, Y, or Z axes using the command "turn" - however, these are the  
"laboratory" axes (X horizontal in plane of screen, Y vertical in  
plane of screen, Z normal to screen) and not necessarily the data  
axes, unless you align them by clicking the Orient button on Volume  
Viewer before issuing the command.

Man page for "turn"
http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/turn.html

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




On Feb 5, 2007, at 1:55 PM, Eva Vanamee wrote:

> Hi,
>
> I am trying to make a figure of my EM fit at different orientations.
> Is it possible to rotate the molecule/map by a certain angle
> so I know exactly the rotation between views?
> Thanks in advance,
>
> - Eva
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From goddard at cgl.ucsf.edu  Mon Feb  5 14:02:04 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 05 Feb 2007 14:02:04 -0800
Subject: [Chimera-users] rotation by a set angle
In-Reply-To: <45C7A7CD.7080103@mssm.edu>
References: <45C7A7CD.7080103@mssm.edu>
Message-ID: <45C7A95C.4020006@cgl.ucsf.edu>

Hi Eva,

   You can use the Chimera turn command to rotate models by a fixed 
angle.  For example,

	turn y 30

Rotates all active models about the screen vertical axis by 30 degrees.
To type a command you first need to display the Chimera command line 
using menu entry Favorites / Command Line.  Then you type the command in 
the entry field at the bottom of the main Chimera window.

Here is more info about "turn":

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

	Tom


From baucom at msg.ucsf.edu  Mon Feb  5 16:43:54 2007
From: baucom at msg.ucsf.edu (Albion Baucom)
Date: Mon, 5 Feb 2007 16:43:54 -0800
Subject: [Chimera-users] Map Orientation for Symmetry Plug-in
Message-ID: <1DB7252A-FB96-4BDF-BC7A-EF39B3468A83@msg.ucsf.edu>

I am using the Symmetric Molecule Copies plug-in with Chimera.

I am wondering if there is a preferred way to orient an EM volume so  
that it is centered around the z-axis at the origin. From my  
experience with this plug-in, symmetry related molecules are  
generated around z-axis at the origin of the viewing area. I am  
finding that my maps tend to be close, but not exactly oriented  
around the z-axis for a helical volume. Molecules fit into a portion  
of the map then tend to have slightly askew symmetry mates relative  
to the volume (presumably because the z-axis of the map is not  
exactly oriented along the origin of the symmetry z-axis).

After playing around with various map tools (MAPMAN, Priism), I am  
still not satisfied with my orientation protocol and wonder if anyone  
can suggest a tried and true method for this.

Thanks

Albion


From goddard at cgl.ucsf.edu  Mon Feb  5 16:55:44 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 05 Feb 2007 16:55:44 -0800
Subject: [Chimera-users] volume/3586 problem zoning out volume
In-Reply-To: <45C7C7E7.4080601@rice.edu>
References: <45C7C334.1080901@rice.edu> <45C7C6D7.3000300@cgl.ucsf.edu>
	<45C7C7E7.4080601@rice.edu>
Message-ID: <45C7D210.6040702@cgl.ucsf.edu>

Hi Jeff,

   To check the memory limits set by a bash shell use shell command 
"ulimit -a".  For a csh use "limit".  Here's an example on my Mac (no 
memory limit).

	Tom


$ ulimit -a
core file size        (blocks, -c) 0
data seg size         (kbytes, -d) 6144
file size             (blocks, -f) unlimited
max locked memory     (kbytes, -l) unlimited
max memory size       (kbytes, -m) unlimited
open files                    (-n) 256
pipe size          (512 bytes, -p) 1
stack size            (kbytes, -s) 8192
cpu time             (seconds, -t) unlimited
max user processes            (-u) 100
virtual memory        (kbytes, -v) unlimited

Jeff wrote:
> I had forgotten about 4-byte floats versus 2-byte integers,
> 
> you are right in that this is most likely a machine limitation, I was 
> surprised to get a fault and error about an allocation call. is there a 
> specific environment variable I should check to see if the shell is 
> limiting chimera's memory requests, I will change that if possible (?).
> 
> -Jeff
> 


From goddard at cgl.ucsf.edu  Mon Feb  5 19:54:33 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 05 Feb 2007 19:54:33 -0800
Subject: [Chimera-users] Map Orientation for Symmetry Plug-in
In-Reply-To: <1DB7252A-FB96-4BDF-BC7A-EF39B3468A83@msg.ucsf.edu>
References: <1DB7252A-FB96-4BDF-BC7A-EF39B3468A83@msg.ucsf.edu>
Message-ID: <45C7FBF9.90903@cgl.ucsf.edu>

Hi Albion,

   Chimera doesn't currently have a method for locating the symmetry 
axis of a map.  But I have an idea of how to do it that is very simple. 
  There is in Chimera version 1.2318 a new tool to fit one density map 
in another.  If you open your map with symmetry, then open a second copy 
of the map (the volume dialog File / Duplicate is an easy way to do 
that), then rotate and shift the second copy by approximately one 
periodic unit by hand, then use the "fit map in map" tool to optimize 
the fit, you get the transformation matrix that generates the symmetry. 
  The "fit map in map" tool prints that transformation matrix to the 
Chimera Reply Log (Favorites / Reply log) as a 3 by 4 matrix.  But I 
could easily also have it print the transformation as a rotation axis 
vector, a point on the rotation axis, an angle of rotation, and a shift 
distance along the axis.  The axis point would lie on the symmetry axis. 
  You could then shift the origin of the map so this point was at 
(0,0,0) using the volume dialog Features / Origin and Scale.  And you 
could save it as a new MRC map if you wanted that origin in the header.

   Usually the map was created with symmetry imposed in the 
reconstruction and it is of course better to simply know the exact 
symmetry axis that was used to create the map.  But the above technique 
will help when that information is hard to figure out.

   I already have code that determines the axis, angle and shift so it 
should be easy to have that printed out by the "fit map in map" tool. 
I'll look into it tomorrow and perhaps be able to send you some new 
Python code if you would like to try it.

	Tom


From goddard at cgl.ucsf.edu  Tue Feb  6 15:05:39 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 06 Feb 2007 15:05:39 -0800
Subject: [Chimera-users] question about mac laptops / workstations and
	chimera stability
In-Reply-To: <45C905FF.1020309@rice.edu>
References: <45C51022.8030508@rice.edu> <45C77A85.2000000@cgl.ucsf.edu>
	<45C905FF.1020309@rice.edu>
Message-ID: <45C909C3.1030105@cgl.ucsf.edu>

Hi Jeff,

  I just got my MacBook Pro with 2 Gb memory and 160 Gb hard-drive 
yesterday.  It's been working well with Chimera volume display, surface 
and solid.  Performance is roughly a factor of two better than my 4 year 
old Dell Precision M50 with Quadro 4 GoGL 500 graphics (a very heavy 
machine, ~10lb).  I just took a look at a 2k by 2k by 76  tomogram and 
performance was as expected.

  2 Gb memory is adequate for my uses.  I went for the 160 Gb harddrive 
instead of the 120 Gb since volume data and video can take some space.  
The 200 Gb option was a 4200 rpm drive which I suspect would be slower 
than the smaller 5200 rpm models so I avoided it.

  If you'd like to try my laptop before you order you are welcome to 
come over to my house in SF.

    Tom


Jeff wrote:
> Tom,
>
> is the base 2 GB memory sufficient, and do you have any reservations 
> regarding transfer speed from the harddrive?
>
> I am going to place an order, wanted to check with you first about 
> those 2 things before going ahead.
>
> (I figure, if you are developing on it, this is not a bad idea.)
>
> -Jeff



From goddard at cgl.ucsf.edu  Tue Feb  6 16:02:58 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 06 Feb 2007 16:02:58 -0800
Subject: [Chimera-users] Map Orientation for Symmetry Plug-in
In-Reply-To: <72A105A0-BD00-4E98-8E73-E71868DEDD90@msg.ucsf.edu>
References: <1DB7252A-FB96-4BDF-BC7A-EF39B3468A83@msg.ucsf.edu>
	<45C7FBF9.90903@cgl.ucsf.edu>
	<72A105A0-BD00-4E98-8E73-E71868DEDD90@msg.ucsf.edu>
Message-ID: <45C91732.8020507@cgl.ucsf.edu>

Hi Albion,

  Ok, I made the "fit map in map" tool print out a point on the rotation 
axis.  The new code for use with Chimera 1.2318 is here:

    
https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmap2318.zip

The zip file contains a directory FitMap that you put in your Chimera 
distribution under

    chimera/share

or on Mac

    Chimera.app/Contents/Resources/share

For more installation details see

    http://www.cgl.ucsf.edu/chimera/experimental/install.html

This FitMap directory replaces your existing one.

  After restarting Chimera you can fit a helically symmetric map in a 
rotated copy of itself then get the axis point (shown in Favorites / 
Reply Log) and adjust the map origin (volume dialog Features / Origin 
and Scale) to put the axis point at (0,0,0).  I described this in more 
detail in my previous message:

    
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001313.html

The output of the axis point will be included in the next Chimera 
snapshot due out in one to three weeks.

  The matrix you sent me had no rotation, just a translation by 52 along 
z.  You will need to rotate the map copy before fitting to get a 
meaningful rotation axis point.  In fact I suspect the accuracy will be 
increased for rotations near 180 degrees rather than small rotations 
(e.g. 30 degrees).

    Tom

Albion Baucom wrote:
> Thanks Tom.
>
> OK, here is my rotation matrix after following your instructions
>
>     0.99944468  -0.03326699   0.00190528  -0.09024247
>     0.03326443   0.99944566   0.00136109   0.10539160
>    -0.00194951  -0.00129696   0.99999726  52.82194789
>
> Sorry, I forgot how to compute the rotation axis vector from this 
> matrix ... its been awhile since I had to do that manually ... its 
> pretty simple if I remember right.
>
> Any code to automate this would be greatly appreciated.
>
> Thanks again!
>
> Albion



From goddard at cgl.ucsf.edu  Tue Feb  6 16:56:19 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 06 Feb 2007 16:56:19 -0800
Subject: [Chimera-users] NumPy in Chimera
In-Reply-To: <000901c73674$0e622dd0$2b268970$@edu>
References: <000001c735c5$e5dc7bd0$b1957370$@edu>
	<200701120013.l0C0DCS51726134@guanine.cgl.ucsf.edu>
	<000301c7364b$508ca470$f1a5ed50$@edu>
	<200701121759.l0CHxWdo2000747@guanine.cgl.ucsf.edu>
	<000901c73674$0e622dd0$2b268970$@edu>
Message-ID: <45C923B3.2090009@cgl.ucsf.edu>

Hi Chimera Extension Writers,

  If you have written Chimera extensions that use Numeric Python you 
will need to convert them to instead use NumPy to work with future 
versions of Chimera.  NumPy provides almost all the same routines as 
Numeric but some function and module names have changed.

  We are switching Chimera over from Numeric Python to NumPy and will 
have a Chimera snapshot out in one to three weeks that uses NumPy.  We 
envision having a Chimera production release that uses NumPy in perhaps 
3 months.  The change was necessary because Numeric is no longer maintained.

  Numeric will no longer be included with Chimera because dynamic 
library name space collisions with NumPy occur on the Mac because of 
certain Chimera compilation options.

  The conversion of Chimera code was not much trouble, but we had to 
also convert third party packages that are included with Chimera 
(PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular 
surfaces) and that took some work.

  Thanks for your patience.

    Tom


 


From triffo at rice.edu  Tue Feb  6 20:10:35 2007
From: triffo at rice.edu (Jeff)
Date: Tue, 06 Feb 2007 20:10:35 -0800
Subject: [Chimera-users] colorzone tool
Message-ID: <45C9513B.5040900@rice.edu>

would it be possible to allow 'color zone' to go past 30 A radius?

-Jeff



From goddard at cgl.ucsf.edu  Tue Feb  6 20:45:24 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 06 Feb 2007 20:45:24 -0800
Subject: [Chimera-users] Mac laptop benchmark
In-Reply-To: <45C92851.30309@rice.edu>
References: <45C51022.8030508@rice.edu> <45C77A85.2000000@cgl.ucsf.edu>
	<45C905FF.1020309@rice.edu> <45C909C3.1030105@cgl.ucsf.edu>
	<45C91F79.7010406@rice.edu> <45C926CC.9040802@cgl.ucsf.edu>
	<45C92851.30309@rice.edu>
Message-ID: <45C95964.5050302@cgl.ucsf.edu>

Hi Jeff,

  I ran the Chimera benchmark tool on my new MacBook Pro and got scores:

    surface 543   mesh 545   contour 183   solid 256   recolor 132

But running hand tests I see the real surface/mesh scores should be 
380.  It appears the benchmark no longer is reporting correct scores 
either because a graphics driver optimization is speeding things up 
because the test image is not actually displayed, or Chimera code has 
changed (perhaps no longer guaranteeing the OpenGL buffers are 
swapped).  Probably other scores on the Chimera benchmark web page are 
likewise inaccurate.  This will have to be investigated.  At any rate, 
actual surface rendering is about 65% faster than my Dell Precision 
M50.  A test on a GeForce Go 7400 (aka Quadro NVS 120M) in a new Dell 
Lattitude D820 also gave erroneous scores, but hand testing gave surface 
rendering score 420 and horrible mesh (110) and solid (<20) numbers.

    Tom


Jeff wrote:
> could you run the benchmark on your mac? (I have run it on my 
> workstation, but forgot the scores; will do again and compare)
>
> -jeff



From goddard at cgl.ucsf.edu  Tue Feb  6 20:50:02 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 06 Feb 2007 20:50:02 -0800
Subject: [Chimera-users] Hiding part of a marker set
In-Reply-To: <45C94E95.5040505@rice.edu>
References: <45C51022.8030508@rice.edu> <45C77A85.2000000@cgl.ucsf.edu>
	<45C905FF.1020309@rice.edu> <45C909C3.1030105@cgl.ucsf.edu>
	<45C91F79.7010406@rice.edu> <45C926CC.9040802@cgl.ucsf.edu>
	<45C94E95.5040505@rice.edu>
Message-ID: <45C95A7A.4070302@cgl.ucsf.edu>

Hi Jeff,

  You can hide part of a marker set by selecting the markers you want to 
show (maybe using the select connected shortcut "sc" as described 
earlier) then use invert selection (main window menu Select / Invert, or 
shortcut "is"), then use path tracer menu entry Actions / Hide markers 
(or shortcut "ha" for hide atoms).

    Tom


Jeff wrote:
> I don't suppose there's a way to hide only a portion of a marker set 
> (just keep one filament visible out of 10, for instance)
>
> -Jeff



From goddard at cgl.ucsf.edu  Tue Feb  6 20:52:20 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 06 Feb 2007 20:52:20 -0800
Subject: [Chimera-users] colorzone tool
In-Reply-To: <45C9513B.5040900@rice.edu>
References: <45C9513B.5040900@rice.edu>
Message-ID: <45C95B04.8060104@cgl.ucsf.edu>

Hi Jeff,

  You can make the color zone tool use a radius larger than 30 (the 
maximum value for the slider) by typing a larger number into the entry 
field next to the slider.  It would be nice if this tool was smarter in 
setting the maximum slider value -- perhaps to the diameter of the 
displayed surface.

    Tom



From papai at titus.u-strasbg.fr  Wed Feb  7 01:25:38 2007
From: papai at titus.u-strasbg.fr (Gabor Papai)
Date: Wed, 07 Feb 2007 10:25:38 +0100
Subject: [Chimera-users] Map Orientation for Symmetry Plug-in
In-Reply-To: <45C91732.8020507@cgl.ucsf.edu>
References: <1DB7252A-FB96-4BDF-BC7A-EF39B3468A83@msg.ucsf.edu>	<45C7FBF9.90903@cgl.ucsf.edu>	<72A105A0-BD00-4E98-8E73-E71868DEDD90@msg.ucsf.edu>
	<45C91732.8020507@cgl.ucsf.edu>
Message-ID: <45C99B12.7020208@igbmc.u-strasbg.fr>

Hi Albion,

If you are interested in how to compute the Euler angles from the 
rotation matrix I can send you a very simple python code to do that or 
to figure out from it.
Bye,
Gabor

-- 
Gabor Papai
IGBMC
Department of Structural Biology and Genomics
1, rue Laurent Fries, BP 10142
67404 Illkirch, France
phone  +33-3-90244796
Fax +33-3-88653201
E-mail: papai at igbmc.u-strasbg.fr



From goddard at cgl.ucsf.edu  Wed Feb  7 21:05:21 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Wed, 07 Feb 2007 21:05:21 -0800
Subject: [Chimera-users] Morph Map
Message-ID: <45CAAF91.40105@cgl.ucsf.edu>

I've added a Chimera extension called Morph Map

    http://www.cgl.ucsf.edu/chimera/experimental/morph_map/morphmap.html

to the experimental features web page:

    http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

It interpolates between two volume data sets and makes animations.  The 
original version of this tool was written by Wei Zhang in Pawel 
Penczek's lab.

    Tom



From baucom at msg.ucsf.edu  Thu Feb  8 12:10:35 2007
From: baucom at msg.ucsf.edu (Albion Baucom)
Date: Thu, 8 Feb 2007 12:10:35 -0800
Subject: [Chimera-users] Drawing Artifacts
Message-ID: <6B5739E7-7647-481E-83CA-F6E4BAD08CAA@msg.ucsf.edu>

Using the latest stable current production release of Chimera,  
1.2304, I have begun to experience some drawing problems that I never  
had in previous versions.

Specifically I frequently get a thin wireframe rendering of my  
protein structure when I draw the structure as a ribbon with a volume  
open at the same time. This wire frame persists even when I turn the  
display of the molecule off in the model panel, and it also does not  
rotate or translate if the protein is selected as the only active  
object. In effect it leaves behind a ghost image. Curiously this  
representation alternates from a light gray/white color to black when  
I open dialog boxes. The artifact toggles on and off with the volume  
in some instances.

My processing and graphics hardware have not changed recently, nor  
has operating system (Linux). I do not experience this behavior with  
my last version of Chimera, 1.2199; it never renders this artifact.

I have a nVidia Geforce 6800GT graphics card with the nVidia Linux  
drivers 1.0-9746. My X11 server is version 6.8.2.

Here is a screen image of this phenomenon

http://msg.ucsf.edu:8100/~baucom/images/chimera_image.jpg

I have rotate the model slightly to show that the thin wireframe  
stays behind. It is not a separate object in the model panel.

Thanks

Albion


From gregc at cgl.ucsf.edu  Thu Feb  8 12:25:55 2007
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 8 Feb 2007 12:25:55 -0800 (PST)
Subject: [Chimera-users] Drawing Artifacts
In-Reply-To: <6B5739E7-7647-481E-83CA-F6E4BAD08CAA@msg.ucsf.edu>
References: <6B5739E7-7647-481E-83CA-F6E4BAD08CAA@msg.ucsf.edu>
Message-ID: <Pine.OSF.4.63.0702081222450.1699021@guanine.cgl.ucsf.edu>

Please file a bug report using the Chimera's Help/Report a Bug dialog and 
attach the data files needed to recreate the bug.  That way I can figure 
out more about what's going on.  I'd also recommend updating your graphics 
driver, as that often fixes weird graphics bugs.

 	- Greg

On Thu, 8 Feb 2007, Albion Baucom wrote:

> Date: Thu, 8 Feb 2007 12:10:35 -0800
> From: Albion Baucom <baucom at msg.ucsf.edu>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Drawing Artifacts
> 
> Using the latest stable current production release of Chimera,
> 1.2304, I have begun to experience some drawing problems that I never
> had in previous versions.
>
> Specifically I frequently get a thin wireframe rendering of my
> protein structure when I draw the structure as a ribbon with a volume
> open at the same time. This wire frame persists even when I turn the
> display of the molecule off in the model panel, and it also does not
> rotate or translate if the protein is selected as the only active
> object. In effect it leaves behind a ghost image. Curiously this
> representation alternates from a light gray/white color to black when
> I open dialog boxes. The artifact toggles on and off with the volume
> in some instances.
>
> My processing and graphics hardware have not changed recently, nor
> has operating system (Linux). I do not experience this behavior with
> my last version of Chimera, 1.2199; it never renders this artifact.
>
> I have a nVidia Geforce 6800GT graphics card with the nVidia Linux
> drivers 1.0-9746. My X11 server is version 6.8.2.
>
> Here is a screen image of this phenomenon
>
> http://msg.ucsf.edu:8100/~baucom/images/chimera_image.jpg
>
> I have rotate the model slightly to show that the thin wireframe
> stays behind. It is not a separate object in the model panel.
>
> Thanks
>
> Albion
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


From heiland at indiana.edu  Thu Feb  8 12:52:28 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Thu, 8 Feb 2007 15:52:28 -0500
Subject: [Chimera-users] xforms, cpk scale
Message-ID: <011901c74bc3$0c0e2cf0$242a86d0$@edu>

Is there a command to scale sphere of a CPK rep?

Is there a command to save the current viewing transformation to a file and
then read it back/apply it at a later time?

Thanks, Randy



From meng at cgl.ucsf.edu  Thu Feb  8 13:06:44 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 8 Feb 2007 13:06:44 -0800
Subject: [Chimera-users] xforms, cpk scale
In-Reply-To: <011901c74bc3$0c0e2cf0$242a86d0$@edu>
References: <011901c74bc3$0c0e2cf0$242a86d0$@edu>
Message-ID: <933C8012-5D48-4CE5-B7A0-9F3BE01E1BB4@cgl.ucsf.edu>

Hi Randy,
(1) The CPK representation uses the VDW radii.  Several ways to  
change the VDW radii are listed here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html

and of these, the command way is to use "vdwdefine":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html

(2) If you remain within the same session ("later" means you haven't  
quit Chimera in between, or if you have, you saved and then restarted  
a session), "savepos" and "reset" can be used to save collectively  
the model transformations (and scale, and clipping plane positions),  
and restore them:

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

If you want to quit Chimera in between and not save a session, see  
"matrixget" and "matrixset":

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

The matrices would just specify model rotation/translation and not  
the clipping plane positions or scale.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 8, 2007, at 12:52 PM, Randy Heiland wrote:

> Is there a command to scale sphere of a CPK rep?
>
> Is there a command to save the current viewing transformation to a  
> file and
> then read it back/apply it at a later time?
>
> Thanks, Randy
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From heiland at indiana.edu  Fri Feb  9 07:46:52 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Fri, 09 Feb 2007 10:46:52 -0500
Subject: [Chimera-users] copy cmd in nogui script
Message-ID: <1171036012.1052.4.camel@localhost.localdomain>

What cmd should I invoke in a --nogui script to copy the rendered image
to a file?

>From the interactive viewer cmd line, I can successfully execute 'copy
file foo.png png'; however, when trying to execute the following:

% chimera --nogui cmd:dostuff
where 'dostuff' is:
open 1yc4
color byelement #0
copy file foo.png png

I get:
Fetching 1yc4 from web site www.rcsb.org
Done fetching 1yc4; verifying...
Opening 1yc4...
1 model opened
Opened 1yc4 containing 1 model, 1890 atoms, and 427 residues
Rendering high resolution image...Error while processing cmd:dostuff:
AttributeError: '_chimera.NoGuiViewer' object has no attribute
'pilImages'
(see reply log for Python traceback info)
Traceback (most recent call last):
  File "/home/heiland/chimera/build/share/__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "CHIMERA/share/chimeraInit.py", line 298, in init
    prefixableType=1)
  File "CHIMERA/share/chimera/__init__.py", line 1217, in open
  File "CHIMERA/share/Midas/ChimeraExtension.py", line 28, in func
    #        lswdir = os.path.split(thisdir)[0]
  File "CHIMERA/share/Midas/midas_text.py", line 91, in
processCommandFile
  File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand
  File "CHIMERA/share/Midas/midas_text.py", line 542, in doCopy
  File "<string>", line 1, in ?
  File "CHIMERA/share/Midas/__init__.py", line 795, in copy
  File "CHIMERA/share/chimera/printer.py", line 705, in saveImage
AttributeError: '_chimera.NoGuiViewer' object has no attribute
'pilImages'


thanks, Randy



From meng at cgl.ucsf.edu  Fri Feb  9 08:03:08 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 Feb 2007 08:03:08 -0800
Subject: [Chimera-users] copy cmd in nogui script
In-Reply-To: <1171036012.1052.4.camel@localhost.localdomain>
References: <1171036012.1052.4.camel@localhost.localdomain>
Message-ID: <b687f09e2d314467db3eaeb33d25dccc@cgl.ucsf.edu>

Hi Randy,
It is my understanding that the GUI is used to render the image, thus 
it is not possible to save images when in nogui mode.  (Others, please 
correct me if I've gotten this wrong!)
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Feb 9, 2007, at 7:46 AM, Randy Heiland wrote:

> What cmd should I invoke in a --nogui script to copy the rendered image
> to a file?
>
>> From the interactive viewer cmd line, I can successfully execute 'copy
> file foo.png png'; however, when trying to execute the following:
>
> % chimera --nogui cmd:dostuff
> where 'dostuff' is:
> open 1yc4
> color byelement #0
> copy file foo.png png
>
> I get:
> Fetching 1yc4 from web site www.rcsb.org
> Done fetching 1yc4; verifying...
> Opening 1yc4...
> 1 model opened
> Opened 1yc4 containing 1 model, 1890 atoms, and 427 residues
> Rendering high resolution image...Error while processing cmd:dostuff:
> AttributeError: '_chimera.NoGuiViewer' object has no attribute
> 'pilImages'
> (see reply log for Python traceback info)
> Traceback (most recent call last):
>   File "/home/heiland/chimera/build/share/__main__.py", line 59, in ?
>     value = chimeraInit.init(sys.argv)
>   File "CHIMERA/share/chimeraInit.py", line 298, in init
>     prefixableType=1)
>   File "CHIMERA/share/chimera/__init__.py", line 1217, in open
>   File "CHIMERA/share/Midas/ChimeraExtension.py", line 28, in func
>     #        lswdir = os.path.split(thisdir)[0]
>   File "CHIMERA/share/Midas/midas_text.py", line 91, in
> processCommandFile
>   File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand
>   File "CHIMERA/share/Midas/midas_text.py", line 542, in doCopy
>   File "<string>", line 1, in ?
>   File "CHIMERA/share/Midas/__init__.py", line 795, in copy
>   File "CHIMERA/share/chimera/printer.py", line 705, in saveImage
> AttributeError: '_chimera.NoGuiViewer' object has no attribute
> 'pilImages'
>
>
> thanks, Randy
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From meng at cgl.ucsf.edu  Mon Feb 12 09:47:30 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Feb 2007 09:47:30 -0800
Subject: [Chimera-users] opacity for stick representation in chimera
Message-ID: <D1EE7DB7-0966-4CB5-950E-DA2A933F7418@cgl.ucsf.edu>

Hi Jerome,
First make a transparent color and then use it on the atoms/bonds -  
there are a handful of routes.

You can make the transparent color using the Color Editor (under  
Tools... Utilities; click the Opacity to get a slider for that, then  
adjust the red/green/blue/opacity sliders as desired).  This color  
can be used on atoms/bonds, ribbons, whatever (depending on the  
current target setting under Actions.. Color) by choosing "Actions...  
Color... from editor" or it can be used in coloring commands using  
the color name "fromeditor"

Color Editor description:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html

Alternatively, you can make the transparent color with the command  
"colordef" and give it whatever name you want.  The new color name  
can then be used in coloring commands.  Color definitions are saved  
in sessions.  Or, if you don't want to save sessions, just make a  
command file with all of your favorite color definitions and read it  
in whenever you want those colors defined.

"colordef" man page:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html

I hope this makes sense - feel free to write back if it doesn't!
Best,
E
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 11, 2007, at 5:14 PM, Jerome Nilmeier wrote:

> Hi Elaine:
>
> I was wondering:  can you adjust the opacity of the stick  
> representation in chimera?
>
> best, J



From heiland at indiana.edu  Mon Feb 12 12:28:22 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Mon, 12 Feb 2007 15:28:22 -0500
Subject: [Chimera-users] programmatic representation
Message-ID: <1171312102.18057.5.camel@localhost.localdomain>

I'd like to be able to set the representation (wire, stick, bs, cpk) of
a model programmatically, in this case, from a plugin.  I was trying the
following, but the newly displayed model would always be displayed in
wire:

      self.model = ReadSDF.readSDF(tmpfile.name)
      chimera.openModels.add(self.model)

      #Midas.represent('stick', self.model)
      Midas.represent('cpk', self.model)

Suggestions?
thanks, Randy



From pett at cgl.ucsf.edu  Mon Feb 12 13:39:09 2007
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 12 Feb 2007 13:39:09 -0800
Subject: [Chimera-users] programmatic representation
In-Reply-To: <1171312102.18057.5.camel@localhost.localdomain>
References: <1171312102.18057.5.camel@localhost.localdomain>
Message-ID: <577E316F-50CF-4F39-B93B-51A189D59831@cgl.ucsf.edu>

Hi Randy,
	The second argument to Midas.represent() is polymorphic, and if it  
is a list then is is expected to be a list of atoms.  You're giving  
it a list of models, which results in the 'drawMode' attribute of  
those models being set (to no effect).  Perhaps the polymorphism of  
the second argument could be improved to handle lists of models (or  
residues), but right now it doesn't. My suggestion is to use a  
Selection object based on your list of models, which Midas.represent 
() can handle, perhaps like so:

       self.model = ReadSDF.readSDF(tmpfile.name)
       chimera.openModels.add(self.model)

       from chimera.selection import ItemizedSelection
       sel = ItemizedSelection()
       sel.add(self.model)
       Midas.represent('cpk', sel)

--Eric

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


On Feb 12, 2007, at 12:28 PM, Randy Heiland wrote:

> I'd like to be able to set the representation (wire, stick, bs,  
> cpk) of
> a model programmatically, in this case, from a plugin.  I was  
> trying the
> following, but the newly displayed model would always be displayed in
> wire:
>
>       self.model = ReadSDF.readSDF(tmpfile.name)
>       chimera.openModels.add(self.model)
>
>       #Midas.represent('stick', self.model)
>       Midas.represent('cpk', self.model)
>
> Suggestions?
> thanks, Randy
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From msamso at zeus.bwh.harvard.edu  Tue Feb 13 09:10:15 2007
From: msamso at zeus.bwh.harvard.edu (Montserrat Samso)
Date: Tue, 13 Feb 2007 12:10:15 -0500
Subject: [Chimera-users] display two volumes alternatively
Message-ID: <web-1617678@anesthesia.bwh.harvard.edu>

Hi,

I am trying to compare two cryoEM density maps of the same
protein, the only difference between them is a
conformational change. Is there a way to switch directly
from one volume to the other without having to display both
of them together in between?

Thanks,

Montserrat
-------------------------------------------------------
Montserrat Samso, Ph.D.
Assistant Professor
Department of Anesthesia Research
Brigham and Women's Hospital
Harvard Medical School
75 Francis St. 
Boston, MA 02115
Tel: 617 7328107
Fax: 617 7326927
E-mail: msamso at zeus.bwh.harvard.edu
--------------------------------------------------------


CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s). The information contained in this message may be private and confidential, and may also be subject to the work product doctrine. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.  



From goddard at cgl.ucsf.edu  Tue Feb 13 09:30:57 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 13 Feb 2007 09:30:57 -0800
Subject: [Chimera-users] display two volumes alternatively
In-Reply-To: <web-1617678@anesthesia.bwh.harvard.edu>
References: <web-1617678@anesthesia.bwh.harvard.edu>
Message-ID: <45D1F5D1.1090409@cgl.ucsf.edu>

Hi Montserrat,

  The new morph map tool can switch between two maps without displaying 
both.  You might be interested in showing interpolated maps as well 
which that tool does.  You can obtain it from the Chimera experimental 
features page.

    http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

There are instructions on how to install it with your current Chimera 
(1.2304 or newer).
It is presently not included in the Chimera distribution.  Here's 
documentation for it.

    http://www.cgl.ucsf.edu/chimera/experimental/morph_map/morphmap.html

  If you just want to switch between the two maps without interpolation 
use morph map step of 1.

  If this is an inconvenient way to do the simple switching you want I 
could add a keyboard shortcut that hides the current map and displays 
the next one.

  Tom



From goddard at cgl.ucsf.edu  Tue Feb 13 09:55:12 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 13 Feb 2007 09:55:12 -0800
Subject: [Chimera-users] display two volumes alternatively
In-Reply-To: <web-1617678@anesthesia.bwh.harvard.edu>
References: <web-1617678@anesthesia.bwh.harvard.edu>
Message-ID: <45D1FB80.8040602@cgl.ucsf.edu>

Hi Montserrat,

  I forgot to mention that there is a new Chimera tutorial with a 
section on using the morph map tool.

    http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html

  Tom


From goddard at cgl.ucsf.edu  Tue Feb 13 11:02:51 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 13 Feb 2007 11:02:51 -0800
Subject: [Chimera-users] Request for Chimera on CD
In-Reply-To: <442443.74872.qm@web35308.mail.mud.yahoo.com>
References: <442443.74872.qm@web35308.mail.mud.yahoo.com>
Message-ID: <45D20B5B.20002@cgl.ucsf.edu>

Hi Zia,

  Our Chimera software can be downloaded from the web

    http://www.cgl.ucsf.edu/chimera/download.html

We have never distributed it by CD.  Perhaps we can do it.  Our program 
needs about 512 Mbytes of computer memory.  What operating system do you 
need it for? Windows? Linux? Mac OS X?

  Because almost all molecular structure and sequence data used in 
research is obtained from the web I suspect our software will be of 
limited use to you without internet access.

    Tom

zia muhammad wrote:
> Respected Dear Dr.
>  
> I am teaching Bioinformatics at International Islamic University 
> Islamabad, Pakistan. I am teaching molecula Docking and Protein 
> Structure prediction, CHIMERA or HMMs methodology. I hvae done all 
> theoratical work but could not perform any practical due to lack of 
> softwares. I will thankful to you if you kindly provide me some basic 
> softwares in this respect. After basic knowledge and establishing 
> proper labs we will purchase relatd softwares but on initial basis we 
> need your help. I also could not download different softwares so can 
> you kindly send me on CD.
> Your kind attention will be highly acknowledged.
>  
> Please reply.
>  
> Regards
>  
> Zia
>
>
> ********************************
> *Muhammad Zia*
> *Room # 7, Hostel # 2*
> *Quaid-i-Azam University,*
> *Islamabad. Pakistan*
> *45320*
> *********************************ue




From heiland at indiana.edu  Tue Feb 13 18:12:12 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Tue, 13 Feb 2007 21:12:12 -0500
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
Message-ID: <000c01c74fdd$8a7fb360$9f7f1a20$@edu>

Is it possible that doing this "zone" specification would only crop out the
'surf' repr if I had a decent graphics card?  I *thought* I was able to do
this on my work linux box w/ an nividia card, but am unable to do it on my
wimpy Windows laptop or my wimpy Mac mini.

-Randy

> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Thursday, February 01, 2007 1:22 PM
> To: Randy Heiland
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] cavity cropped view
> 
> Hi Randy,
> You can use a "zone" specification, either with commands or via the
> menu.  An example of the command approach:
> 
> show ligand zr<5
>     or
> show :glc zr<5
> 
> The first example would show all residues [with any atom] within 5
> angstroms of what is considered "ligand" ... in the second example, I
> gave a specific residue name.  GLC is the residue name of glucose in
> the PDB entry 2gbp.  You could also use a residue number or range of
> numbers. "za" instead of "zr" would just the atoms within the cutoff
> rather than their whole residues, and > instead of < gets the
> complementary set.  The "show" command (unlike "display") undisplays
> everything that is not specified, so you don't have to undisplay
> anything beforehand.
> 
> See the "Zones" section of
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
> frameatom_spec.html
> 
> The mostly-menu approach has more steps:
> - select the small molecule (for example by Ctrl-clicking one of its
> atoms and then pressing the up arrow key)
> - use the command
>          ~display
> to undisplay everything (if you use the Actions menu, it would just
> undisplay the current selection)
> - select a zone defined by the current selection (Select... Zone)
> with specified cutoff and whether you want it to be atom-based or
> residue-based
> - display that selection (for example, with Actions... Atoms/Bonds...
> show)
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> 
> 
> On Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
> 
> > What options exist in Chimera for letting me show only that portion
> > of a
> > protein that is "near" another smaller molecule?  Specifically, I
> > have a
> > ligand in a cavity of a large protein and would like to eliminate the
> > "clutter" of the protein away from the cavity of interest.
> >
> > Thanks, Randy
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users




From gatsogia at uni-mainz.de  Wed Feb 14 05:14:42 2007
From: gatsogia at uni-mainz.de (Gatsogiannis, Christos)
Date: Wed, 14 Feb 2007 14:14:42 +0100
Subject: [Chimera-users] making movies with MorphMap, exporting povray scenes,
	FitMapInMap
Message-ID: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAB@EXCHANGE02.zdv.Uni-Mainz.DE>

Dear Chimera users and developers,

recently I used the new morph map tool and  it worked very nice in my case. 
I encountered a problem while exporting the animation in any movie-format within Morphmap, I just get empty or very small files, which cannot be displayed in any media-player. I  decided then to use  the chimera-movie recorder utility to record the morphing animation and this worked fine (I?ve tested this with mpeg-2 format). At the moment I?m using the chimera-version 1.2309 in a SUSE LINUX 9.2 environment. Is this a version problem or a bug?

Furthermore, I?ve exported some scenes in the povray format and I?ve noticed that the final images are of lower quality in comparison with images made some months ago with older chimera versions. I haven?t changed the  povray-version, the rendering settings and  the settings for the visualisation of my data in chimera (brightness etc...). The colors are too pale, I could send you  some example-images if needed.

I?ve tried also the Fit Map in Map tool recently and it worked perfectly (you sent this tool to a group-colleague  some months ago). I?m wondering why you didn?t put this tool on the experimental site yet....and one more last question...after using Fit Map in Map, is there any possibility to save the "fitted" map with it?s new orientation?

Thanks,

Christos

Christos Gatsogiannis
Institute of Zoology
Johannes Gutenberg University
55099 Mainz, Germany

Tel: +49(0)6131-39-23091
email: gatsogia at uni-mainz.de






From goddard at cgl.ucsf.edu  Wed Feb 14 09:42:52 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Wed, 14 Feb 2007 09:42:52 -0800
Subject: [Chimera-users] making movies with MorphMap,
 exporting povray scenes, FitMapInMap
In-Reply-To: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAB@EXCHANGE02.zdv.Uni-Mainz.DE>
References: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAB@EXCHANGE02.zdv.Uni-Mainz.DE>
Message-ID: <45D34A1C.7040707@cgl.ucsf.edu>

Hi Christos,

  The problem using the Record button on the Morph Map tool was that it 
was always writing the movie in Quicktime format no matter what format 
you actually chose.  Thanks for identifying the problem.  I've fixed it 
and the updated version is on the experimental features web page:

    http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

  Greg Couch works on the Chimera povray code and will answer that part 
of your email.

  I didn't put the fit map in map tool on the experimental features page 
because it is part of the standard Chimera distribution available in 
version 1.2318 (snapshots for linux and ppc mac only).  We will soon 
(within a week?) have a new Chimera snapshot on all platforms that 
includes fit map in map.

  It is not yet possible to save a map fit into another map in a new map 
file.  The trouble is that none of the map file formats can include a 
rotation so it would be necessary to resample the data on a new grid.  
That can reduce the resolution.  Still we plan on offering that in the 
future.  You can currently save a Chimera session and the rotated map 
position is recorded.  But of course that is not useful for importing 
the rotated map into other software.

    Tom



From meng at cgl.ucsf.edu  Wed Feb 14 10:32:38 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Feb 2007 10:32:38 -0800
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <000c01c74fdd$8a7fb360$9f7f1a20$@edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
	<000c01c74fdd$8a7fb360$9f7f1a20$@edu>
Message-ID: <FA115A4C-115A-4D8F-8B98-D4269958031E@cgl.ucsf.edu>

Hi Randy,
This does not sound like a graphics hardware issue.  All I can say is  
make sure you start with the surface hidden, and then just show  
surface for the zone.  Displaying surface for a zone does not in  
itself hide the surface outside the zone.  If you used a command,  
check that the command is typed correctly and that the atom  
specification really specifies what you wanted.  You could  
alternatively accomplish the same task with the menu: hide all  
surface first, select the atoms used to define the zone, Select...  
Zone... and enter the desired cutoff, then show the surface for that  
zone.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:

> Is it possible that doing this "zone" specification would only crop  
> out the
> 'surf' repr if I had a decent graphics card?  I *thought* I was  
> able to do
> this on my work linux box w/ an nividia card, but am unable to do  
> it on my
> wimpy Windows laptop or my wimpy Mac mini.
>
> -Randy
>
>> -----Original Message-----
>> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
>> Sent: Thursday, February 01, 2007 1:22 PM
>> To: Randy Heiland
>> Cc: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] cavity cropped view
>>
>> Hi Randy,
>> You can use a "zone" specification, either with commands or via the
>> menu.  An example of the command approach:
>>
>> show ligand zr<5
>>     or
>> show :glc zr<5
>>
>> The first example would show all residues [with any atom] within 5
>> angstroms of what is considered "ligand" ... in the second example, I
>> gave a specific residue name.  GLC is the residue name of glucose in
>> the PDB entry 2gbp.  You could also use a residue number or range of
>> numbers. "za" instead of "zr" would just the atoms within the cutoff
>> rather than their whole residues, and > instead of < gets the
>> complementary set.  The "show" command (unlike "display") undisplays
>> everything that is not specified, so you don't have to undisplay
>> anything beforehand.
>>
>> See the "Zones" section of
>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
>> frameatom_spec.html
>>
>> The mostly-menu approach has more steps:
>> - select the small molecule (for example by Ctrl-clicking one of its
>> atoms and then pressing the up arrow key)
>> - use the command
>>          ~display
>> to undisplay everything (if you use the Actions menu, it would just
>> undisplay the current selection)
>> - select a zone defined by the current selection (Select... Zone)
>> with specified cutoff and whether you want it to be atom-based or
>> residue-based
>> - display that selection (for example, with Actions... Atoms/Bonds...
>> show)
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>                       http://www.cgl.ucsf.edu/home/meng/index.html
>>
>>
>>
>>
>> On Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
>>
>>> What options exist in Chimera for letting me show only that portion
>>> of a
>>> protein that is "near" another smaller molecule?  Specifically, I
>>> have a
>>> ligand in a cavity of a large protein and would like to eliminate  
>>> the
>>> "clutter" of the protein away from the cavity of interest.
>>>
>>> Thanks, Randy
>>>
>>> _______________________________________________
>>> 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  Wed Feb 14 13:19:34 2007
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 14 Feb 2007 13:19:34 -0800
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <000c01c74fdd$8a7fb360$9f7f1a20$@edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
	<000c01c74fdd$8a7fb360$9f7f1a20$@edu>
Message-ID: <A77933F7-EB73-4320-AA4B-A71696EF482B@cgl.ucsf.edu>

So does "unable to do it" mean that the command never finishes, or  
that it does finish but somehow doesn't produce the right result?

--Eric

On Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:

> Is it possible that doing this "zone" specification would only crop  
> out the
> 'surf' repr if I had a decent graphics card?  I *thought* I was  
> able to do
> this on my work linux box w/ an nividia card, but am unable to do  
> it on my
> wimpy Windows laptop or my wimpy Mac mini.
>
> -Randy
>
>> -----Original Message-----
>> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
>> Sent: Thursday, February 01, 2007 1:22 PM
>> To: Randy Heiland
>> Cc: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] cavity cropped view
>>
>> Hi Randy,
>> You can use a "zone" specification, either with commands or via the
>> menu.  An example of the command approach:
>>
>> show ligand zr<5
>>     or
>> show :glc zr<5
>>
>> The first example would show all residues [with any atom] within 5
>> angstroms of what is considered "ligand" ... in the second example, I
>> gave a specific residue name.  GLC is the residue name of glucose in
>> the PDB entry 2gbp.  You could also use a residue number or range of
>> numbers. "za" instead of "zr" would just the atoms within the cutoff
>> rather than their whole residues, and > instead of < gets the
>> complementary set.  The "show" command (unlike "display") undisplays
>> everything that is not specified, so you don't have to undisplay
>> anything beforehand.
>>
>> See the "Zones" section of
>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
>> frameatom_spec.html
>>
>> The mostly-menu approach has more steps:
>> - select the small molecule (for example by Ctrl-clicking one of its
>> atoms and then pressing the up arrow key)
>> - use the command
>>          ~display
>> to undisplay everything (if you use the Actions menu, it would just
>> undisplay the current selection)
>> - select a zone defined by the current selection (Select... Zone)
>> with specified cutoff and whether you want it to be atom-based or
>> residue-based
>> - display that selection (for example, with Actions... Atoms/Bonds...
>> show)
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>                       http://www.cgl.ucsf.edu/home/meng/index.html
>>
>>
>>
>>
>> On Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
>>
>>> What options exist in Chimera for letting me show only that portion
>>> of a
>>> protein that is "near" another smaller molecule?  Specifically, I
>>> have a
>>> ligand in a cavity of a large protein and would like to eliminate  
>>> the
>>> "clutter" of the protein away from the cavity of interest.
>>>
>>> Thanks, Randy
>>>
>>> _______________________________________________
>>> 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  Wed Feb 14 14:00:43 2007
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Wed, 14 Feb 2007 14:00:43 -0800 (PST)
Subject: [Chimera-users] making movies with MorphMap,
 exporting povray scenes, FitMapInMap
In-Reply-To: <45D34A1C.7040707@cgl.ucsf.edu>
References: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAB@EXCHANGE02.zdv.Uni-Mainz.DE>
	<45D34A1C.7040707@cgl.ucsf.edu>
Message-ID: <Pine.OSF.4.63.0702141348580.2026574@guanine.cgl.ucsf.edu>

On Wed, 14 Feb 2007, Tom Goddard wrote:

>  Greg Couch works on the Chimera povray code and will answer that part
> of your email.

The POV-Ray output changed to get the colors closer to what you see in the 
chimera window.  There is one additional line at the top of the povray 
file:

 	global_settings { assumed_gamma 1 }

Remove that line and you'll see the previous darker colors.  If that 
doesn't fix the problem you're seeing, please let me know.

I have also in the last month fixed some bugs in the POV-Ray and VRML 
output.  The revised converters will be in the next snapshot release 
(we're hoping it will be out by next week), and you'll be able to use the 
Image Save dialog to call povray directly.  So I am very interested in 
whether or not the assumed_gamma change was the problem.

 	- Greg


From gatsogia at uni-mainz.de  Thu Feb 15 06:07:41 2007
From: gatsogia at uni-mainz.de (Gatsogiannis, Christos)
Date: Thu, 15 Feb 2007 15:07:41 +0100
Subject: [Chimera-users] making movies with MorphMap,
	exporting povray scenes, FitMapInMap
References: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAB@EXCHANGE02.zdv.Uni-Mainz.DE>
	<45D34A1C.7040707@cgl.ucsf.edu>
	<Pine.OSF.4.63.0702141348580.2026574@guanine.cgl.ucsf.edu>
	<FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAD@EXCHANGE02.zdv.Uni-Mainz.DE>
Message-ID: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAE@EXCHANGE02.zdv.Uni-Mainz.DE>

Hello Greg and Tom,

povray: the assumed gamma-change was indeed the problem. Thank you very much! I?m waitin for the next snapshot release 
MorphMap:  the updated version works correctly! Thanks!

Do you  maybe plan in the future on offering the possibility to save a density map also in different formats than mrc (situs, imagic .. etc) ? That would be very useful...

Thanks again,

Christos   






From heiland at indiana.edu  Thu Feb 15 07:12:17 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Thu, 15 Feb 2007 10:12:17 -0500
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <A77933F7-EB73-4320-AA4B-A71696EF482B@cgl.ucsf.edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
	<000c01c74fdd$8a7fb360$9f7f1a20$@edu>
	<A77933F7-EB73-4320-AA4B-A71696EF482B@cgl.ucsf.edu>
Message-ID: <000001c75113$ae9be7f0$0bd3b7d0$@edu>

The latter.  I'm sure I'm simply doing something incorrect.  BTW, I'm back
on my Linux box and still can't get it work.  I've tried to document what
I'm attempting at:
http://poincare.uits.iupui.edu/~heiland/chimera  and hope someone can tell
me what I'm doing wrong.

Thanks, Randy


> -----Original Message-----
> From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
> Sent: Wednesday, February 14, 2007 4:20 PM
> To: Randy Heiland
> Cc: 'Elaine Meng'; chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] cavity cropped view
> 
> So does "unable to do it" mean that the command never finishes, or
> that it does finish but somehow doesn't produce the right result?
> 
> --Eric
> 
> On Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:
> 
> > Is it possible that doing this "zone" specification would only crop
> > out the
> > 'surf' repr if I had a decent graphics card?  I *thought* I was
> > able to do
> > this on my work linux box w/ an nividia card, but am unable to do
> > it on my
> > wimpy Windows laptop or my wimpy Mac mini.
> >
> > -Randy
> >
> >> -----Original Message-----
> >> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> >> Sent: Thursday, February 01, 2007 1:22 PM
> >> To: Randy Heiland
> >> Cc: chimera-users at cgl.ucsf.edu
> >> Subject: Re: [Chimera-users] cavity cropped view
> >>
> >> Hi Randy,
> >> You can use a "zone" specification, either with commands or via the
> >> menu.  An example of the command approach:
> >>
> >> show ligand zr<5
> >>     or
> >> show :glc zr<5
> >>
> >> The first example would show all residues [with any atom] within 5
> >> angstroms of what is considered "ligand" ... in the second example,
> I
> >> gave a specific residue name.  GLC is the residue name of glucose in
> >> the PDB entry 2gbp.  You could also use a residue number or range of
> >> numbers. "za" instead of "zr" would just the atoms within the cutoff
> >> rather than their whole residues, and > instead of < gets the
> >> complementary set.  The "show" command (unlike "display") undisplays
> >> everything that is not specified, so you don't have to undisplay
> >> anything beforehand.
> >>
> >> See the "Zones" section of
> >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
> >> frameatom_spec.html
> >>
> >> The mostly-menu approach has more steps:
> >> - select the small molecule (for example by Ctrl-clicking one of its
> >> atoms and then pressing the up arrow key)
> >> - use the command
> >>          ~display
> >> to undisplay everything (if you use the Actions menu, it would just
> >> undisplay the current selection)
> >> - select a zone defined by the current selection (Select... Zone)
> >> with specified cutoff and whether you want it to be atom-based or
> >> residue-based
> >> - display that selection (for example, with Actions...
> Atoms/Bonds...
> >> show)
> >>
> >> I hope this helps,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> >> UCSF Computer Graphics Lab and Babbitt Lab
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>                       http://www.cgl.ucsf.edu/home/meng/index.html
> >>
> >>
> >>
> >>
> >> On Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
> >>
> >>> What options exist in Chimera for letting me show only that portion
> >>> of a
> >>> protein that is "near" another smaller molecule?  Specifically, I
> >>> have a
> >>> ligand in a cavity of a large protein and would like to eliminate
> >>> the
> >>> "clutter" of the protein away from the cavity of interest.
> >>>
> >>> Thanks, Randy
> >>>
> >>> _______________________________________________
> >>> 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 meng at cgl.ucsf.edu  Thu Feb 15 08:58:06 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 15 Feb 2007 08:58:06 -0800
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <000001c75113$ae9be7f0$0bd3b7d0$@edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
	<000c01c74fdd$8a7fb360$9f7f1a20$@edu>
	<A77933F7-EB73-4320-AA4B-A71696EF482B@cgl.ucsf.edu>
	<000001c75113$ae9be7f0$0bd3b7d0$@edu>
Message-ID: <931D27C7-B189-4491-B25C-1C6E6E061F77@cgl.ucsf.edu>

Hi Randy,
Here is the process you tried:
# Here is what I attempted: display a protein (1yc1)
# display a ligand (in purple)
# 'surf' on the protein
# select the ligand
# '~display' --> removes the selected ligand
# 'show sel zr<5' --> shows ligand + cropped stick repr of protein,  
but doesn't crop the surf

The "show" command only acts on atoms/bonds (not ribbon, not  
surface ...).  You have to use surf/~surf (or the menu) to show and  
hide surface.

Here are two different approaches that will work.  The first displays  
only the surface that you want.  The second displays the whole  
surface and then undisplays the part outside the zone.

command: open 1yc1
command: sel ligand zr<5
command: surf sel & main

(the "& main" part says not to surface the ligand itself)
-- OR --

command: open 1yc1
command: surf
command: ~surf ligand zr>5

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




On Feb 15, 2007, at 7:12 AM, Randy Heiland wrote:

> The latter.  I'm sure I'm simply doing something incorrect.  BTW,  
> I'm back
> on my Linux box and still can't get it work.  I've tried to  
> document what
> I'm attempting at:
> http://poincare.uits.iupui.edu/~heiland/chimera  and hope someone  
> can tell
> me what I'm doing wrong.
>
> Thanks, Randy



From heiland at indiana.edu  Thu Feb 15 09:25:52 2007
From: heiland at indiana.edu (Randy Heiland)
Date: Thu, 15 Feb 2007 12:25:52 -0500
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <931D27C7-B189-4491-B25C-1C6E6E061F77@cgl.ucsf.edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
	<000c01c74fdd$8a7fb360$9f7f1a20$@edu>
	<A77933F7-EB73-4320-AA4B-A71696EF482B@cgl.ucsf.edu>
	<000001c75113$ae9be7f0$0bd3b7d0$@edu>
	<931D27C7-B189-4491-B25C-1C6E6E061F77@cgl.ucsf.edu>
Message-ID: <001301c75126$57cf9ee0$076edca0$@edu>

Thanks very much, Elaine.  Your 2nd approach did indeed produce the desired
result for my case.  (I should have mentioned that I was not using the 1yc1
protein from the PDB, which has a bound ligand, but rather was displaying 2
separate molecules from a local DB.  Therefore I just substituted 'ligand'
with 'sel' after I selected the ligand molecule).

Aside:  why doesn't the 'delete' cmd also delete the MSMS surface?  It
remains displayed, remains in the Model Panel, however I cannot graphically
select it (in order to try to delete it).
 

> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Thursday, February 15, 2007 11:58 AM
> To: Randy Heiland
> Cc: Chimera BB
> Subject: Re: [Chimera-users] cavity cropped view
> 
> Hi Randy,
> Here is the process you tried:
> # Here is what I attempted: display a protein (1yc1)
> # display a ligand (in purple)
> # 'surf' on the protein
> # select the ligand
> # '~display' --> removes the selected ligand
> # 'show sel zr<5' --> shows ligand + cropped stick repr of protein,
> but doesn't crop the surf
> 
> The "show" command only acts on atoms/bonds (not ribbon, not
> surface ...).  You have to use surf/~surf (or the menu) to show and
> hide surface.
> 
> Here are two different approaches that will work.  The first displays
> only the surface that you want.  The second displays the whole
> surface and then undisplays the part outside the zone.
> 
> command: open 1yc1
> command: sel ligand zr<5
> command: surf sel & main
> 
> (the "& main" part says not to surface the ligand itself)
> -- OR --
> 
> command: open 1yc1
> command: surf
> command: ~surf ligand zr>5
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> 
> 
> On Feb 15, 2007, at 7:12 AM, Randy Heiland wrote:
> 
> > The latter.  I'm sure I'm simply doing something incorrect.  BTW,
> > I'm back
> > on my Linux box and still can't get it work.  I've tried to
> > document what
> > I'm attempting at:
> > http://poincare.uits.iupui.edu/~heiland/chimera  and hope someone
> > can tell
> > me what I'm doing wrong.
> >
> > Thanks, Randy




From meng at cgl.ucsf.edu  Thu Feb 15 09:37:15 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 15 Feb 2007 09:37:15 -0800
Subject: [Chimera-users] cavity cropped view
In-Reply-To: <001301c75126$57cf9ee0$076edca0$@edu>
References: <000e01c7462a$f187d450$d4977cf0$@edu>
	<74562949-4836-4600-9E20-B325040F8C52@cgl.ucsf.edu>
	<000c01c74fdd$8a7fb360$9f7f1a20$@edu>
	<A77933F7-EB73-4320-AA4B-A71696EF482B@cgl.ucsf.edu>
	<000001c75113$ae9be7f0$0bd3b7d0$@edu>
	<931D27C7-B189-4491-B25C-1C6E6E061F77@cgl.ucsf.edu>
	<001301c75126$57cf9ee0$076edca0$@edu>
Message-ID: <1BD98AB0-381B-40B6-88A5-45A7CD681118@cgl.ucsf.edu>

Hi Randy,
As defined, "delete" (like "show") is an operation on atoms/bonds,  
not the surface, which is a separate model.  "~surf" can hide part or  
all of surfaces.  You can get rid of a surface as a whole by choosing  
it in the left side of the Model Panel and clicking the "close"  
button on the right (not the Close button for the Model Panel!).

I've described the current process rather than providing an answer to  
your question, which is more about design and data structures.  We  
are planning changes to how surfaces are handled, including (I  
believe) allowing them to be selected, but I must leave it to the  
others who are/will be doing this work to provide any further details  
or the estimated time frame.  I doubt there will be piecewise  
deletion as opposed to our current pattern of allowing partial hiding/ 
showing and deleting a surface as a whole.
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 15, 2007, at 9:25 AM, Randy Heiland wrote:

> Aside:  why doesn't the 'delete' cmd also delete the MSMS surface?  It
> remains displayed, remains in the Model Panel, however I cannot  
> graphically
> select it (in order to try to delete it).



From goddard at cgl.ucsf.edu  Thu Feb 15 10:51:11 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Thu, 15 Feb 2007 10:51:11 -0800
Subject: [Chimera-users] making movies with MorphMap,
 exporting povray scenes, FitMapInMap
In-Reply-To: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAE@EXCHANGE02.zdv.Uni-Mainz.DE>
References: <FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAB@EXCHANGE02.zdv.Uni-Mainz.DE>	<45D34A1C.7040707@cgl.ucsf.edu>	<Pine.OSF.4.63.0702141348580.2026574@guanine.cgl.ucsf.edu>	<FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAD@EXCHANGE02.zdv.Uni-Mainz.DE>
	<FAC7C69DB38F62448B7CFB78B5A4DE2B01A62DAE@EXCHANGE02.zdv.Uni-Mainz.DE>
Message-ID: <45D4AB9F.5090601@cgl.ucsf.edu>

Hi Christos,

  We don't currently plan on adding the ability to write more volume 
file formats except perhaps hdf5.  (The hdf5 would be for handling em 
tomography data sets that are larger than the computer memory.)  The 
main issue is that writing files correctly is much harder than reading 
them, and it is especially difficult with the often poor or non-existent 
documentation for the density map formats.  Still I agree it would be 
useful and I'll put it on our feature request list.

    Tom



From papai at titus.u-strasbg.fr  Fri Feb 16 06:23:34 2007
From: papai at titus.u-strasbg.fr (Gabor Papai)
Date: Fri, 16 Feb 2007 15:23:34 +0100
Subject: [Chimera-users] saving map in different position
Message-ID: <45D5BE66.2050203@igbmc.u-strasbg.fr>

Hi Tom,
Is there a way to save a map with only transformation, or obtain the 
transformation matrix if I do a freehand transformation of an object?
We would like to create a composite volume of several spheres. It would 
be the best to write a single map of several differently positioned 
spheres but I could also apply the transformation in IMAGIC if I would 
know the matrix.
Thanks for helping!
Regards,
Gabor

-- 
Gabor Papai
IGBMC
Department of Structural Biology and Genomics
1, rue Laurent Fries, BP 10142
67404 Illkirch, France
phone  +33-3-90244796
Fax +33-3-88653201
E-mail: papai at igbmc.u-strasbg.fr



From meng at cgl.ucsf.edu  Fri Feb 16 07:44:42 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 16 Feb 2007 07:44:42 -0800
Subject: [Chimera-users] saving map in different position
In-Reply-To: <45D5BE66.2050203@igbmc.u-strasbg.fr>
References: <45D5BE66.2050203@igbmc.u-strasbg.fr>
Message-ID: <3540291f555c39b2cf0d8c4299a9902b@cgl.ucsf.edu>

Hi Gabor,
The "matrixget" command writes the current transformation matrix for 
each model to a file:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html

The matrices for all open models are written to a single file, and they 
describe the absolute transformations (there is no option to write the 
transformation of one model relative to another).
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Feb 16, 2007, at 6:23 AM, Gabor Papai wrote:

> Hi Tom,
> Is there a way to save a map with only transformation, or obtain the
> transformation matrix if I do a freehand transformation of an object?
> We would like to create a composite volume of several spheres. It would
> be the best to write a single map of several differently positioned
> spheres but I could also apply the transformation in IMAGIC if I would
> know the matrix.
> Thanks for helping!
> Regards,
> Gabor
>
> -- 
> Gabor Papai
> IGBMC
> Department of Structural Biology and Genomics
> 1, rue Laurent Fries, BP 10142
> 67404 Illkirch, France
> phone  +33-3-90244796
> Fax +33-3-88653201
> E-mail: papai at igbmc.u-strasbg.fr
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From goddard at cgl.ucsf.edu  Fri Feb 16 10:08:39 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 16 Feb 2007 10:08:39 -0800
Subject: [Chimera-users] saving map in different position
In-Reply-To: <45D5BE66.2050203@igbmc.u-strasbg.fr>
References: <45D5BE66.2050203@igbmc.u-strasbg.fr>
Message-ID: <45D5F327.1090505@cgl.ucsf.edu>

Hi Gabor,

  If you open more than one volume data set in Chimera, there is no way 
to write them out in a single volume file.  Elaine mentioned the 
matrixget command to get the rotation matrix and translation for each 
volume.  If you use the volume dialog Features / Origin and Scale and 
you change the origin and then save the map, the saved map will record 
the new origin.

  When I add the ability to resample a map to save a rotated orientation 
I will try to also allow saving multiple maps into a single new map file.

    Tom



From kay_jay at earthlink.net  Fri Feb 16 14:15:55 2007
From: kay_jay at earthlink.net (Kenward Vaughan)
Date: Fri, 16 Feb 2007 14:15:55 -0800
Subject: [Chimera-users] demo made under Linux has bland atoms in Windows
Message-ID: <1171664155.25160.12.camel@hpotter.vaughan.home>

...in a fashion, that is.

A demo I plan on using at school (a Windows fortress, it is) displays
all atoms as grey--no color (by element).  The demo was created on a
Linux machine (at my home).

:(

Any thoughts?


Kenward
ps. both versions of Chimera are the latest production version (2304).
-- 
In a completely rational society, the best of us would aspire to be 
_teachers_ and the rest of us would have to settle for something less, 
because passing civilization along from one generation to the next 
ought to be the highest honor and the highest responsibility anyone 
could have.     - Lee Iacocca



From meng at cgl.ucsf.edu  Fri Feb 16 15:55:34 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 16 Feb 2007 15:55:34 -0800
Subject: [Chimera-users] demo made under Linux has bland atoms in Windows
In-Reply-To: <1171664155.25160.12.camel@hpotter.vaughan.home>
References: <1171664155.25160.12.camel@hpotter.vaughan.home>
Message-ID: <45d35a7e6fd347fa10877d9cbf46458e@cgl.ucsf.edu>

Hi Kenward,
That is certainly unexpected.  To try to figure this out, a few 
questions:

on those Windows machines,
- does manually entering the command "color byelement"  work on the 
structure(s) in the demo, or on any structures for that matter?
- do other coloring operations work, within or separate from the demo?

I don't think we know of any Chimera bug (yet) that would make 
everything gray. I had a problem once on some oldish Windows computers 
where everything except "wire" representation was really dark - it was 
a problem with the graphics hardware and/or driver.

I could take a look if you want to mail it to me.  I'm not on Windows, 
however.  We could try it on Windows next week.  Sorry about the 
travails,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Feb 16, 2007, at 2:15 PM, Kenward Vaughan wrote:

> ...in a fashion, that is.
>
> A demo I plan on using at school (a Windows fortress, it is) displays
> all atoms as grey--no color (by element).  The demo was created on a
> Linux machine (at my home).
>
> :(
>
> Any thoughts?
>
>
> Kenward
> ps. both versions of Chimera are the latest production version (2304).
> -- 
> In a completely rational society, the best of us would aspire to be
> _teachers_ and the rest of us would have to settle for something less,
> because passing civilization along from one generation to the next
> ought to be the highest honor and the highest responsibility anyone
> could have.     - Lee Iacocca
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From kvaughan at bc.cc.ca.us  Fri Feb 16 16:39:53 2007
From: kvaughan at bc.cc.ca.us (Kenward Vaughan)
Date: Fri, 16 Feb 2007 16:39:53 -0800
Subject: [Chimera-users] demo made under Linux has bland atoms in	Windows
In-Reply-To: <45d35a7e6fd347fa10877d9cbf46458e@cgl.ucsf.edu>
References: <1171664155.25160.12.camel@hpotter.vaughan.home>
	<45d35a7e6fd347fa10877d9cbf46458e@cgl.ucsf.edu>
Message-ID: <1171672793.25160.37.camel@hpotter.vaughan.home>

On Fri, 2007-02-16 at 15:55 -0800, Elaine Meng wrote:
> Hi Kenward,
> That is certainly unexpected.  To try to figure this out, a few 
> questions:
> 
> on those Windows machines,
> - does manually entering the command "color byelement"  work on the 
> structure(s) in the demo, or on any structures for that matter?
> - do other coloring operations work, within or separate from the demo?
> 

AFAIK things behave normally on the machines (I'm not there right now,
so can't test this, but I've had no trouble in the past).

Using "color byelement" (at the command line) in the middle of the demo
straightened things out at least for the frame being looked at.  I'm
_not_ sure but seem to recall that things got messed up again at a later
point.  

I figure I can deal with it by simply adding the command at places where
it is needed, but I'm really curious why it arises at all.

The demo is the "latest" version of the one I sent to you earlier.  I'll
send it under separate cover to you so as to not clutter up the list.
It depends on 2ace.pdb and ach.pdb being in the same directory as the
demo script.


Kenward


> I don't think we know of any Chimera bug (yet) that would make 
> everything gray. I had a problem once on some oldish Windows computers 
> where everything except "wire" representation was really dark - it was 
> a problem with the graphics hardware and/or driver.
> 
> I could take a look if you want to mail it to me.  I'm not on Windows, 
> however.  We could try it on Windows next week.  Sorry about the 
> travails,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> On Feb 16, 2007, at 2:15 PM, Kenward Vaughan wrote:
> 
> > ...in a fashion, that is.
> >
> > A demo I plan on using at school (a Windows fortress, it is) displays
> > all atoms as grey--no color (by element).  The demo was created on a
> > Linux machine (at my home).
> >
> > :(
> >
> > Any thoughts?
> >
> >
> > Kenward
> > ps. both versions of Chimera are the latest production version (2304).

-- 
                                       .'^~;,_
Dr. Kenward Vaughan                    `:,'~~~~~
Professor of Chemistry                 \;:/
Bakersfield College                    |,;|
1801 Panorama Drive                   / ', \
Bakersfield, CA  93305               / o  O \
http://www2.bc.cc.ca.us/kvaughan    (oOoOOoOo)
                                  ---========---
                                   ???$$MM$$???



From meng at cgl.ucsf.edu  Sat Feb 17 10:35:14 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 17 Feb 2007 10:35:14 -0800
Subject: [Chimera-users] demo made under Linux has bland atoms in Windows
In-Reply-To: <1171684550.25160.43.camel@hpotter.vaughan.home>
References: <1171664155.25160.12.camel@hpotter.vaughan.home>
	<45d35a7e6fd347fa10877d9cbf46458e@cgl.ucsf.edu>
	<1171672228.25160.28.camel@hpotter.vaughan.home>
	<5fad4664f3e3c8c292b479a97916fa11@cgl.ucsf.edu>
	<1171684550.25160.43.camel@hpotter.vaughan.home>
Message-ID: <f68e99946274909dec3216ca218e12ef@cgl.ucsf.edu>

On Feb 16, 2007, at 7:55 PM, Kenward Vaughan wrote:

> For me, the byatom coloration is there to begin with under Linux.  The
> ach shows up colored properly, as does the acetylcholinesterase.
>
Aha!!  Problem solved!!  I am 99.99% sure the difference is your 
preferences file.  The demo itself does not say to color by element 
when the structure is opened.  However, there is a New Molecules 
section of the Preferences in which you can say structures should be 
colored that way when they are opened.  Most likely you have this set 
on your home Linux machine, but not in the Chimera preferences used on 
the Windows machines.

Months ago we discussed the need for some way to indicate that 
preferences should be bypassed at startup and/or when opening 
structures.  This option would be appropriate for use with demos or 
scripts to be shared among multiple users each having some arbitrary 
set of preferences settings.  However, this option hasn't been added 
(nor are we sure how best to implement it)... thanks for the additional 
motivation to revisit that issue!

The demos included with Chimera were made in a directory with a default 
preferences file. It is likely, however, that some users with 
nondefault New Molecules preferences have played them back and gotten a 
result different than intended.
>
> I've noticed rotation is slow under Windows, but v. nice with Linux
> (about 7 seconds total).
>
It depends on the graphics capabilities of the system.  It is slow on 
our home desktop computer (>5 years old - you can almost hear gears 
grinding) but fast on my laptop (1-2 years old).

Happy demoing and please do contact us with any problems or suggestions,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



From goddard at cgl.ucsf.edu  Tue Feb 20 09:42:49 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 20 Feb 2007 09:42:49 -0800
Subject: [Chimera-users] Saving full map when zoning
In-Reply-To: <Pine.A41.4.63.0702191442000.226110@acsrs3.bu.edu>
References: <Pine.A41.4.63.0702191442000.226110@acsrs3.bu.edu>
Message-ID: <45DB3319.3020101@cgl.ucsf.edu>

Hi Jean-Francois,

  You can save a map with the original map size while using volume zone 
by first pressing the the
"Full" button in the Features / Subregion Selection panel of the volume 
dialog.  Then use the File / Save Map As button.  You can see what 
region will be saved by looking at the Features / Region Bounds panel 
(and you could type in new bounds there and press the Enter key instead 
of pressing the Full button).

  The volume zone capability (Features / Zone) normally uses a smaller 
box of data so that it is faster.  Even when part of the surface is 
hidden by the zoning the whole surface within the box being used is 
computed and that is sometimes slow.

    Tom


jean-francois menetret wrote:
>
> Hi Thomas,
>
> when using the zone option in Chimera, is it possible to have the size 
> of the saved mrc file (after zoning) be the same as the original file ?
>
> Best wishes
>
> Jean-Francois


From goddard at cgl.ucsf.edu  Tue Feb 20 10:08:08 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 20 Feb 2007 10:08:08 -0800
Subject: [Chimera-users] Create surface from markers
In-Reply-To: <45DA1A61.5050703@rice.edu>
References: <45C9513B.5040900@rice.edu> <45C95B04.8060104@cgl.ucsf.edu>
	<45DA1A61.5050703@rice.edu>
Message-ID: <45DB3908.9000104@cgl.ucsf.edu>

Hi Jeff,

  Chimera cannot currently create a surface from markers placed with the 
volume path tracer tool.  It would not be so hard to write some Python 
code to do this.  Here is an example of Python code that creates a 
surface in Chimera:

    
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/surface.html

  Tom


Jeff wrote:
> hi Tom,
>
> is there a way to use a marker file just to render a surface (a 
> series/group of dots, just needing to be connected by a mesh)? for 
> instance, to represent a membrane.
>
> -Jeff



From ssham44 at uab.edu  Tue Feb 20 09:11:42 2007
From: ssham44 at uab.edu (S W Simon Sham)
Date: Tue, 20 Feb 2007 11:11:42 -0600
Subject: [Chimera-users] An NMR Average Structure
Message-ID: <825387859C59F844BE3C54BC61C6B0D1791D52@UABEXMB4.ad.uab.edu>

Hi,
I need to calculate an average structure from an emsembled structures in
Chimera. Can we do it it Chimera? If yes, how?
Thanks for any helps.

Simon

------------------------------------------------------------------------
-----
Simon Sham, Ph.D.
NMR Core Facility
Comprehensive Cancer Center
Univerisity of Alabama
933 South 19th Street
CH19 B31
Birmingham, AL 35294
Office: (205) 934-5696
Fax   : (205) 934-6475
Email : ssham44 at uab.edu



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From meng at cgl.ucsf.edu  Wed Feb 21 10:03:31 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 21 Feb 2007 10:03:31 -0800
Subject: [Chimera-users] An NMR Average Structure
In-Reply-To: <825387859C59F844BE3C54BC61C6B0D1791D52@UABEXMB4.ad.uab.edu>
References: <825387859C59F844BE3C54BC61C6B0D1791D52@UABEXMB4.ad.uab.edu>
Message-ID: <6D63614A-3E9F-4512-B3BB-DA7F862CC210@cgl.ucsf.edu>

Hi Simon,
Currently Chimera does not calculate an average structure from an  
ensemble, sorry.

This ability might be added in the future, but there are some issues:
If you simply average cartesian coordinates, the result is a somewhat  
distorted structure.  I'm told by my NMR colleagues that usually  
either this "average structure" is energy-minimized, or it is just  
compared to the existing ensemble members in order to select the most  
representative member.  The representative member rather than the  
"average structure" would then be used in further calculations.

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




On Feb 20, 2007, at 9:11 AM, S W Simon Sham wrote:

> Hi,
> I need to calculate an average structure from an emsembled  
> structures in Chimera. Can we do it it Chimera? If yes, how?
> Thanks for any helps.
>
> Simon
>
> ---------------------------------------------------------------------- 
> -------
> Simon Sham, Ph.D.
> NMR Core Facility
> Comprehensive Cancer Center
> Univerisity of Alabama
> 933 South 19th Street
> CH19 B31
> Birmingham, AL 35294
> Office: (205) 934-5696
> Fax   : (205) 934-6475
> Email : ssham44 at uab.edu
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From goddard at cgl.ucsf.edu  Wed Feb 21 10:17:11 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Wed, 21 Feb 2007 10:17:11 -0800
Subject: [Chimera-users] Memory requirements for Chimera
In-Reply-To: <45DC7F6A.8070406@bu.edu>
References: <200702201923.l1KJNjPT1606233@guanine.cgl.ucsf.edu>
	<45DBA1DD.7000609@cgl.ucsf.edu> <45DC6067.9060609@bu.edu>
	<45DC796B.4090507@cgl.ucsf.edu> <45DC7F6A.8070406@bu.edu>
Message-ID: <45DC8CA7.50609@cgl.ucsf.edu>

Hi Christopher,

  I think it starts making sense to use a 64-bit machine if you are 
loading data that requires >= 1 Gbyte.  In general, 32-bit linux 
binaries will run on a 64-bit machine.  Currently we only provide a 
32-bit linux Chimera distribution though we plan on adding 64-bit Linux 
as a standard Chimera platform in the next 6 months.  The 32-bit Chimera 
runs fine on 64-bit linux.  The advantage of a 64-bit version is that it 
uses memory pointers that are 64 bits so they can address more than 4 
Gbytes.   On a 32-bit system the operating system and the many libraries 
that Chimera uses (~50) may occupy a significant portion of the 4 Gbyte 
address space.  Even if you have less than 4 Gbytes of physical memory 
the operating system can and does use the full 32-bit 4 Gbyte address 
space and swap data to disk when there is not enough physical memory.  
But if a program asks for a 512 Mbyte block of memory and there is no 
available segment of that size in the address space then it will fail.

  Graphics drivers use the computer's main memory for data that will not 
fit on the card.  Either 256 or 512 Mbytes on the graphics card should 
give good performance even for large systems.  Unless you are using the 
volume "solid" rendering mode the rendering speed will slow to much less 
than 1 frame per second before you use up 256 Mbytes.

  For reference, the machines I currently use for developing Chimera and 
looking at large volume data sets are: 1) Mac dual G5 desktop with 1.5 
Gbyte memory and 128 Mb ATI Radeon 9800 Pro graphics, and 2) MacBook 
Pro, Intel Core 2 duo, 2 Gbyte memory, 256 Mb ATI X1600 graphics.

  Thanks for the apoptosome papers -- interesting work.

    Tom

Christopher Akey wrote:
> Tom-
> ok, I will keep notes on what is not working and send them to you, as 
> we go through making figures this week.
>
> Will chimera run fine on a 64 bit Linux box? The other option is 32 
> bits, but if I buy a high end workstation it should probably be 64 bit 
> yes?
>
> Also, about making Chimera able to handle big sessions: is the rate 
> limiting factor the RAM or the memory on the Graphics Card. We have a 
> 512 Mb cache on our current graphics card and still have problems, so 
> I presume we are RAM limited.
>
> When buying a new machine, should I invest in a 512 Mb Nvidia card or 
> is 256 fine, as long as there is enough RAM?
>
> By the way, I am attaching two pdfs of papers published using Chimera 
> graphics.
>
> thanks.
>
> CWA
>
>
> Tom Goddard wrote:
>> Hi Christopher,
>>
>>  I'm not sure what causes crashes in Chimera when you are working 
>> close to the available memory limit.  If a memory allocation fails in 
>> C++ it should produce an error message in Chimera indicating that 
>> memory could not be allocated because we catch those exceptions.  
>> Memory allocations in C (not C++) libraries that Chimera uses are 
>> likely to cause a crash though.
>>
>>  It would help us to know what Chimera is doing when the crashes 
>> occur.  We may be able to put some safety checks in our C++ where C 
>> library allocations are known to fail.  Do I understand correctly 
>> that crashes happen while you are saving an image (individual tiles 
>> being displayed on screen)?  Chimera by default makes an image 3 
>> times larger then requested to make a smoother image.  That can take 
>> a good bit of memory.  Are there other actions that cause crashes?
>>
>>    Tom
>
>




From goddard at cgl.ucsf.edu  Wed Feb 21 12:49:15 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Wed, 21 Feb 2007 12:49:15 -0800
Subject: [Chimera-users] Chimera on 64-bit Windows
In-Reply-To: <45DCA890.1040005@bu.edu>
References: <45DCA890.1040005@bu.edu>
Message-ID: <45DCB04B.5020501@cgl.ucsf.edu>

Hi Christopher,

  I believe the 32-bit Windows Chimera distribution will run on 64-bit 
versions of Windows, such as Windows XP Pro x64 Edition.  But I do not 
have a machine to try it on.  It will certainly run on 32-bit Windows 
running on a 64-bit processor -- I've tried that with an AMD64 processor.

    Tom


Christopher Akey wrote:
> Steve and Tom-
>
> Will EMAN and Chimera run ok on a 64 bit machine running windows XP, 
> initially we plan to use it this way, then change over to Linux when 
> we have time. Or do we just install Linux right away?
>
> cheers  C Akey



From mazdak at mazdak.de  Thu Feb 22 20:35:04 2007
From: mazdak at mazdak.de (Mazdak Radjainia)
Date: Fri, 23 Feb 2007 17:35:04 +1300
Subject: [Chimera-users] Combining 2 electron density maps in 1
Message-ID: <002401c75703$fd456390$96b9d882@sbs.auckland.ac.nz>

Hi,

 

I would like to open two electron density maps in chimera and save/merge
them together in one map. Both maps are activated in the "model panel" but I
cannot select/save both at a time using the volume viewer. 

I appreciate your help!

 

 

Kind regards

Mazdak 

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From meng at cgl.ucsf.edu  Fri Feb 23 11:10:12 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 23 Feb 2007 11:10:12 -0800
Subject: [Chimera-users] Combining 2 electron density maps in 1
In-Reply-To: <002401c75703$fd456390$96b9d882@sbs.auckland.ac.nz>
References: <002401c75703$fd456390$96b9d882@sbs.auckland.ac.nz>
Message-ID: <3b9e9d5cdc3295d0b3f20f9f6f79f5f6@cgl.ucsf.edu>

Hi Mazdak,
As mentioned recently by Tom Goddard, currently there is no way to save  
two maps in one file:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/ 
001350.html

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


On Feb 22, 2007, at 8:35 PM, Mazdak Radjainia wrote:

> Hi,
> ?
> I would like to open two electron density maps in chimera and  
> save/merge them together in one map. Both maps are activated in the  
> ?model panel? but I cannot select/save both at a time using the volume  
> viewer.
> I appreciate your help!
> ?
> ?
> Kind regards
> Mazdak
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users




From goddard at cgl.ucsf.edu  Fri Feb 23 11:10:53 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 23 Feb 2007 11:10:53 -0800
Subject: [Chimera-users] Combining 2 electron density maps in 1
In-Reply-To: <002401c75703$fd456390$96b9d882@sbs.auckland.ac.nz>
References: <002401c75703$fd456390$96b9d882@sbs.auckland.ac.nz>
Message-ID: <45DF3C3D.2050008@cgl.ucsf.edu>

Hi Mazdak,

  Chimera cannot currently merge two maps into a single map.  It can 
only save a single map and allows writing just a zone or a subregion or 
a hand-erased modifications, and allows a new origin, grid spacing, and 
file format.

  We would like to add the ability to merge maps.  Could you explain 
your case?  Do the two maps overlap each other?  How would they be 
combined if they overlap (added)?  Are the grids of the two maps aligned 
so that all grid points of both data sets are part of the same bigger 
grid?  Or would the data need to be interpolated at new grid points to 
make a merged map?

  I have written a script that stacks two copies of a map on top of each 
other and writes a single new map for making filaments twice as long 
where the original map contains a single periodic repeat.

    Tom



From JeanDidier.Marechal at uab.cat  Mon Feb 26 11:03:52 2007
From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal)
Date: Mon, 26 Feb 2007 20:03:52 +0100
Subject: [Chimera-users] many days after...another question Re: Select atom
 by serial number.
Message-ID: <b910ac797135.45e33d28@uab.es>

Hi everybody,

I'd like to select a series of atoms by their serial number (again!!!) (e.g. from atom number 1 to atom number 10).

the sel @/serialNumber=1-10 doesn't seem to be the right syntax.

Is it possible to do this kind of selection? If yes, what is the right syntax please.

Cheers,
JD

Dr. Jean-Didier Mar?chal
Professor Lector
Unitat de Qu?mica F?sica
Departament de Qu?mica
Universitat Aut?noma de Barcelona
Edifici C.n.
08193 Cerdonyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: Elaine Meng <meng at cgl.ucsf.edu>
Data: Dijous, Gener 11, 2007 8:59 pm
Assumpte: Re: [Chimera-users] Select atom by serial number.

> 
> Hi JD,
> We also tested Chimera 1.2309 on Windows, and these specifications 
> 
> work correctly.  Example:
>   Command: sel @/serialNumber=232
> will select NZ of Lys 27 in chain A of the PDB entry 1zik. The 
> only  
> other thing I can think of (besides what was in the previous 
> message)  
> is to check if your PDB file is correctly formatted.  The 
> ATOM/HETATM  
> serial number is supposed to be in columns 7-11 and right-justified.
> Best,
> Elaine
> 
> On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote:
> 
> > Hi JD,
> > You are using the correct specifications - both of your examples 
> 
> > should work.  I tested both approaches in Chimera 1.2304 on Mac 
> OSX  
> > and they worked correctly.  We'll have to look into your 
> specific  
> > version/platform and get back to you.  If you want, you could 
> send  
> > me the PDB file you are using so I could test if there is some  
> > issue specific to that structure.  To be clear: the serial 
> number  
> > is the number shown in the column after ATOM (or HETATM) in the 
> PDB  
> > file, regardless of what order the atoms are really in.  That 
> is,  
> > if the first ATOM has 2 in that column, its serial number is 2 
> and  
> > not 1.
> > Best,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> > UCSF Computer Graphics Lab and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >                      http://www.cgl.ucsf.edu/home/meng/index.html
> >
> >
> >
> >
> > On Jan 11, 2007, at 10:47 AM, Jean-Didier Mar?chal wrote:
> >
> >> Hi Everyone,
> >>
> >>
> >>
> >>
> >>
> >> I am desperately trying to select an atom of my pdb by its 
> serial  
> >> number.
> >>
> >> Looking at the archives, it seems that I should put something 
> like  
> >> @/serialNumber=525
> >>
> >> I tried ?sel #0@/serialNumber=525? in the commandl ine and ?@/ 
> >> serialNumber=525? in the Atom Specifier. None of these 
> selections  
> >> worked. Can someone tell me the right way to do this, please ?
> >>
> >>
> >>
> >> Cheers
> >>
> >> JD
> >>
> >>
> >>
> >> Current running chimera: version 1 build 2309
> >>
> >> OS: windows
> >>
> >>
> >>
> >> _______________________________________________
> >> Chimera-users mailing list
> >> Chimera-users at cgl.ucsf.edu
> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> 
> 




From meng at cgl.ucsf.edu  Mon Feb 26 13:27:30 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 26 Feb 2007 13:27:30 -0800
Subject: [Chimera-users] many days after...another question Re: Select
	atom by serial number.
In-Reply-To: <b910ac797135.45e33d28@uab.es>
References: <b910ac797135.45e33d28@uab.es>
Message-ID: <8F91E696-AF0A-432C-A825-B9EE49122937@cgl.ucsf.edu>

Hi JD,
Ranges aren't directly implemented, but you can do it with > >= < <=  
combinations.  For example,  you could select atoms with serial  
numbers 1-10 with:

sel @/serialNumber<=10
or
sel @/serialNumber<11

For a nonterminal range, for example, you could select atoms with  
serial numbers 11-20 with:

sel @/serialNumber>=11 and serialNumber<=20

I tested these on PDB entry 1zik.
Cheers,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 26, 2007, at 11:03 AM, Jean Didier Pie Marechal wrote:

> Hi everybody,
>
> I'd like to select a series of atoms by their serial number  
> (again!!!) (e.g. from atom number 1 to atom number 10).
>
> the sel @/serialNumber=1-10 doesn't seem to be the right syntax.
>
> Is it possible to do this kind of selection? If yes, what is the  
> right syntax please.
>
> Cheers,
> JD
>
> Dr. Jean-Didier Mar?chal
> Professor Lector
> Unitat de Qu?mica F?sica
> Departament de Qu?mica
> Universitat Aut?noma de Barcelona
> Edifici C.n.
> 08193 Cerdonyola (Barcelona)
> Tel: +34.935814936
> e-mail: JeanDidier.Marechal at uab.es
>
> ----- Missatge original -----
> De: Elaine Meng <meng at cgl.ucsf.edu>
> Data: Dijous, Gener 11, 2007 8:59 pm
> Assumpte: Re: [Chimera-users] Select atom by serial number.
>
>>
>> Hi JD,
>> We also tested Chimera 1.2309 on Windows, and these specifications
>>
>> work correctly.  Example:
>>   Command: sel @/serialNumber=232
>> will select NZ of Lys 27 in chain A of the PDB entry 1zik. The
>> only
>> other thing I can think of (besides what was in the previous
>> message)
>> is to check if your PDB file is correctly formatted.  The
>> ATOM/HETATM
>> serial number is supposed to be in columns 7-11 and right-justified.
>> Best,
>> Elaine
>>
>> On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote:
>>
>>> Hi JD,
>>> You are using the correct specifications - both of your examples
>>
>>> should work.  I tested both approaches in Chimera 1.2304 on Mac
>> OSX
>>> and they worked correctly.  We'll have to look into your
>> specific
>>> version/platform and get back to you.  If you want, you could
>> send
>>> me the PDB file you are using so I could test if there is some
>>> issue specific to that structure.  To be clear: the serial
>> number
>>> is the number shown in the column after ATOM (or HETATM) in the
>> PDB
>>> file, regardless of what order the atoms are really in.  That
>> is,
>>> if the first ATOM has 2 in that column, its serial number is 2
>> and
>>> not 1.
>>> Best,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>>> UCSF Computer Graphics Lab and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>                      http://www.cgl.ucsf.edu/home/meng/index.html
>>>
>>>
>>>
>>>
>>> On Jan 11, 2007, at 10:47 AM, Jean-Didier Mar?chal wrote:
>>>
>>>> Hi Everyone,
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> I am desperately trying to select an atom of my pdb by its
>> serial
>>>> number.
>>>>
>>>> Looking at the archives, it seems that I should put something
>> like
>>>> @/serialNumber=525
>>>>
>>>> I tried ?sel #0@/serialNumber=525? in the commandl ine and ?@/
>>>> serialNumber=525? in the Atom Specifier. None of these
>> selections
>>>> worked. Can someone tell me the right way to do this, please ?
>>>>
>>>>
>>>>
>>>> Cheers
>>>>
>>>> JD
>>>>
>>>>
>>>>
>>>> Current running chimera: version 1 build 2309
>>>>
>>>> OS: windows
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>>
>
>




From goddard at cgl.ucsf.edu  Mon Feb 26 14:44:43 2007
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 26 Feb 2007 14:44:43 -0800
Subject: [Chimera-users] Saving model positions
In-Reply-To: <45E34317.1050901@bu.edu>
References: <45DCA890.1040005@bu.edu> <45DCB04B.5020501@cgl.ucsf.edu>
	<45E34317.1050901@bu.edu>
Message-ID: <45E362DB.5070202@cgl.ucsf.edu>

Hi Christopher,

   The problem you have with the Chimera matrixget and matrixset 
commands is that the matrix file lists the model number (0.0, 1.0, 2.0, 
...) with each matrix.  For example,

Model 0.0
	-0.0635922 -0.740419 0.66913 247.807
	-0.979146 -0.0833402 -0.185275 540.192
	0.192946 -0.666958 -0.719679 472.752
Model 1.0
	0.233245 -0.923975 -0.303095 418.621
	0.970522 0.201738 0.131868 -125.304
	-0.0606967 -0.324918 0.943792 100.98

When you open maps and PDB files in a different order they get different 
numbers.  Chimera assigns the lowest available number (starting at 0) 
each time you open a data set.  Then when you use matrixset <filename> 
to get your standard orientation it applies the matrices to the wrong 
models because of the different numbering.  The easiest remedy for this 
is to open your data sets in a fixed order (first large ribosomal map 
(#0), then small ribosomal map (#1), ...).  This can be inconvenient. 
If you save a single positioning matrix in a file there is no current 
command to say to apply that matrix to a model that you specify as a 
command argument (e.g. no command like "matrixset <matrix-file> 
<model-number>" exists).

   There are some other approaches to the problem of getting standard 
orientations.  One method is to save your ribosome large and small 
subunit map positions in a Chimera session.  Then if you want to use 
different maps, open the reference session, then open the new maps and 
use the "matrixcopy" command

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

to position the new maps to match the reference map positions.  Instead 
of using matrixcopy you could use the equivalent Model Panel dialog 
"Transform As" button to apply the positioning matrix of one map to a 
second map.

   Another command that may be helpful is "savepos <name>".

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

It remembers the positions of all currently opened data sets and gives a 
name to that set of positions.  You can later restore those positions 
with the command "reset <name>".  These named positions are saved in 
Chimera session files.  The trouble is that there is not an immediate 
way to apply those positioning matrices to different maps or PDB models. 
  But that could be achieved with the matrixcopy command or Model Panel 
/ Transform As button.

   If this set of capabilities does not let you easily do what you want 
could you describe an exact scenario (how many maps, how many models, 
how are they related) and if possible propose a new command that would 
help you.

   I think it would be great if density map file formats supported 
saving multiple named positioning matrices in their header.  For 
example, you might want to save how a piece of a map is positioned in 
the full source map, and also how a piece of a map fits into different 
map (e.g. at various locations in a tomogram), and your case of just a 
standard orientation ("front view", "top view").  I do not believe any 
of the commonly used density map formats allow this although it may be 
possible to put that info into header comment fields in some map files.

	Tom




Christopher Akey wrote:
> Tom -
> 
> ...
> 
> Chimera is very good, but there are still problems. A new workstation 
> will help and will be here in a few weeks.
> 
> However, one thing is really annoying. It is important to set a 
> particular view for your structure, for example a side-by-side frontal 
> view of the ribosome with regards to the small and large subunits.
> 
> Once you have this in one session it would be useful to be able to 
> recreate this easily in other sessions. (For logistical reasons, it is 
> ofter easier to keep a session for each Figure so that they don't get to 
> crowded.)
> 
> Right now, if you save a matrix (matrixget) and then make a change in 
> the session, ie delete or add a file, you get unpredictable results, but 
> usually, the matrix no longer works or it only works for one volume in 
> the session. This is not good when you have separate vols for the small 
> and large subunits in proper registration, you get a matrix for the 
> front view, and then at a later time, only one subunit will be realigned 
> properly!
> 
> It would be great if you could set a matrix for a particular map as a 
> benchmark, then when you read that map into any other session, you could 
> recreate this orientation using the matrix. I don't understand why this 
> won't work.
> 
> The feature of being able to bring in other maps and align them in 
> CHimera is great and works very well (its in our older test version that 
> we are using, and its very useful as we often have 3 or more structures 
> of the same basic object with minor diffs).
> 
> I hope this makes sense.
> 
> cheers  C Akey
> 


From gregc at cgl.ucsf.edu  Mon Feb 26 16:38:37 2007
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 26 Feb 2007 16:38:37 -0800 (PST)
Subject: [Chimera-users] New chimera development snapshot available
Message-ID: <Pine.OSF.4.63.0702261627160.2086601@guanine.cgl.ucsf.edu>

See <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> for
details (this will be accurate for the next few days, after that read the 
release notes that are bundled into the chimera snapshot).

The snapshot uses NumPy instead of Numeric python, so some third-party 
extensions may break (eg., parts of EMAN).

Other highlights include intial support for PDB 3.0 (remediated PDB) 
format and built-in POV-Ray raytraced image support.

 	Enjoy,

 	Greg Couch
 	UCSF Computer Graphics Lab


From goddard at cgl.ucsf.edu  Tue Feb 27 09:43:32 2007
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 27 Feb 2007 09:43:32 -0800
Subject: [Chimera-users] Saving model positions
In-Reply-To: <45E43C99.20007@bu.edu>
References: <45E43C99.20007@bu.edu>
Message-ID: <45E46DC4.3050609@cgl.ucsf.edu>

Hi Christopher,

  If you have 10 models open in a Chimera session and you close model 
number 7, the session should still save correctly.  If it doesn't please 
report it as a bug.  Unfortunately restoring the session file uses 
different model numbers for the density maps (the lowest available 
numbers).  That is a bug that I need to fix.  It should use all of the 
original model numbers even if there are gaps.  Even though the model 
numbers will change, the orientations of all the models 1-6 and 8-10 
will all be correct in the restored session.

  I sent your earlier email to our Chimera users mailing list.  That is 
why your reply to me went to that mailing list.  I like to post the 
questions to the mailing list so others can benefit from the answer and 
I remove any confidential information (email, phone, signature line, 
research details).  Let me know if you want to keep your questions off 
of the Chimera mailing list.  Here's the message where I posted your 
original question and my reply.

    
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001366.html

  Tom


Christopher Akey wrote:
>
> Thomas -
>
> This went via reply to some kinda list, sorry.
>
> I will try some of these approaches. However, there is a question. If
> you have 10 objects in a session, and decide to delete number 7, then
> sometimes you cannot get the session to save properly with a missing
> number.
>
> In theory, if one could get the session to save, then a matrix for the
> first 6 objects would still work?
>
>
> cheers  C Akey




From gregc at cgl.ucsf.edu  Tue Feb 27 17:21:58 2007
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 27 Feb 2007 17:21:58 -0800 (PST)
Subject: [Chimera-users] 64-bit Linux chimera snapshot available
Message-ID: <Pine.OSF.4.63.0702271716400.1610923@guanine.cgl.ucsf.edu>

If you are running a 64-bit version of Linux with an AMD64, Opteron, or 
Intel Xeon processors, then please try out our new snapshot at 
<http://www.cgl.ucsf.edu/chimera/download.html>.  This platform is now
supported and will have future snapshot and production releases.

 	Greg Couch
 	UCSF Computer Graphics Lab


From eman_ghanem at yahoo.com  Wed Feb 28 14:06:07 2007
From: eman_ghanem at yahoo.com (Eman Ghanem)
Date: Wed, 28 Feb 2007 14:06:07 -0800 (PST)
Subject: [Chimera-users] 2d labels in chimera
Message-ID: <400077.62987.qm@web53313.mail.yahoo.com>

Hi:
I am not able to save an image that contains 2d labels as a Tiff file. Every time I save it, the labels don't show up on the image.  I read on your web site that this only happens if I am trying to save an image that is smaller than the original pixels of the chimera window. However, I tried saving it without changing any specifications. Any idea what I can do??
  thanks,
   
  EG

 
---------------------------------
Don't get soaked.  Take a quick peak at the forecast 
 with theYahoo! Search weather shortcut.
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From meng at cgl.ucsf.edu  Wed Feb 28 14:47:09 2007
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 28 Feb 2007 14:47:09 -0800
Subject: [Chimera-users] 2d labels in chimera
In-Reply-To: <400077.62987.qm@web53313.mail.yahoo.com>
References: <400077.62987.qm@web53313.mail.yahoo.com>
Message-ID: <157739B1-D0B9-4781-9099-358D8788CAA0@cgl.ucsf.edu>

Hi Eman,
We haven't had any reports of 2D label problems when saving at screen  
resolution or higher.  Some things to make sure of:

- are you using a fairly recent version of Chimera?  There used to be  
another problem, but it was fixed a long time ago.
- if you are using the very newest version (Feb 2007) and chose to  
"raytrace with POV-Ray", that definitely wouldn't include the 2D  
Labels.  Only saving the contents of the Chimera graphics window  
(i.e. not ray-tracing) is expected to include labels.
- are you sure that you are not saving fewer pixels than shown in the  
window?  When you choose "File... Save Image" the dimensions are  
initially in inches.  Depending on what "pixels per unit" (inch) is  
set to (shown when you click the Image Setup button), it is possible  
you could be trying to save fewer pixels than shown in the window.   
The simplest test is simply to click Get Pixels (which gives the  
current window dimensions).  Then, with those dimensions or some  
larger number of pixels you type in, save the image and see if the  
labels are there.
- did you mention TIFF because other formats do not have the problem,  
or is that the only one you tried?

It is possible you are finding some problem we didn't know about, of  
course, so if you still have the problem after checking the version  
and trying the "Get Pixels" approach, it would be great if you could  
save a session and mail me the session file.  The session will  
include the 2D labels, allowing us to try to reproduce the problem on  
our computers.
Thanks,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 28, 2007, at 2:06 PM, Eman Ghanem wrote:

> Hi:
> I am not able to save an image that contains 2d labels as a Tiff  
> file. Every time I save it, the labels don't show up on the image.   
> I read on your web site that this only happens if I am trying to  
> save an image that is smaller than the original pixels of the  
> chimera window. However, I tried saving it without changing any  
> specifications. Any idea what I can do??
> thanks,
>
> EG
>
> Don't get soaked. Take a quick peak at the forecast
> with theYahoo! Search weather shortcut.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users