From goddard at cgl.ucsf.edu  Thu May  1 10:53:15 2008
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 01 May 2008 10:53:15 -0700
Subject: [Chimera-users] Moving an ensemble of molecules together
In-Reply-To: <d5dc3ecc0805010159k39d25e5ci93333ece0af70d47@mail.gmail.com>
References: <d5dc3ecc0804281318k25d5d25cifa426b3bcd0e37c9@mail.gmail.com>	
	<4816379C.1040707@cgl.ucsf.edu>	
	<d5dc3ecc0804290453m1480cb39s328ba00dfe8bbcb7@mail.gmail.com>	
	<4818B222.4040208@cgl.ucsf.edu>
	<d5dc3ecc0805010159k39d25e5ci93333ece0af70d47@mail.gmail.com>
Message-ID: <481A038B.9010807@cgl.ucsf.edu>

Hi Miguel,

   If you have two molecules each surrounded by additional molecule 
copies that make crystal contacts you can align the two crystal lattices 
as follows.  Align the two original molecules (e.g. using Match Maker 
dialog or match command).  Then choose all copies of the first molecule 
in Model Panel and use the Transform As button.  You'll be asked to 
choose the molecule to transform these as, so choose the aligned 
molecule.  That will bring all the crystal contact molecules surrounding 
the aligned molecule into correct locations around the aligned molecule.

   This method assumes you have saved the crystal copies to a PDB file 
and have opened that file.  If you simply use the new crystal contacts 
option to make the molecule copies then the Transform As will move all 
those copies to the exact same position as the original molecule -- not 
what you want.  This is because the crystal contacts tool is placing the 
surrounding molecules by adjusting their transformation matrices rather 
than changing their atom coordinates.  If you save all copies to a PDB 
file and read it back in then the atom coordinates of the copies will be 
adjusted and all of the molecules will have the same transformation 
matrix and the above alignment procedure will work.

	Tom


Miguel Ortiz-Lombard?a wrote:
> Hi again!
> 
> I had tried this, yes. But the problem is that when I want to compare 
> crystal packings the procedure is:
> 
>    1. Generate the two ensembles around "central" molecules
>    2. Superpose the "central" molecule (submodel if saved as you say) of
>       the first ensemble to the "central" molecule of the second one
> 
> Doing it this way only the central submodel of the first ensemble moves, 
> not the whole ensemble, as I wish... A single molecule with various 
> chains would move as a whole, as I want. I see the 62 chains limitation, 
> but normally we don't have such enormous amount of molecules contacting 
> an asymmetric unit (of course, with viruses may be different). So, it 
> would be nice (to me, I don't know how generally) to have a way to 
> transform an ensemble of models into an ensemble of chains.
> 
> Thank you for your help!
> 
> 
> Miguel
> 
> 2008/4/30 Tom Goddard <goddard at cgl.ucsf.edu <mailto:goddard at cgl.ucsf.edu>>:
> 
>     Hi Miguel,
> 
>     You mentioned that you would like to be able to save the crystal
>     contact asym units in a single PDB file as separate chains.  Why not
>     save them as multiple models in a single PDB file?  You can do this
>     currently with the Chimera menu entry File / Save PDB....  Making
>     separate chains requires making new chain names and since only one
>     letter names are allowed in PDB format this is limited to about 62
>     chains (a-z, A-Z, 0-9).
> 
>       Tom
> 
> 
> 
> 
> -- 
> http://www.pangea.org/mol/spip.php?rubrique2
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Je suis de la mauvaise herbe,
> Braves gens, braves gens,
> Je pousse en libert?
> Dans les jardins mal fr?quent?s!
> Georges Brassens



From zambonel at gmail.com  Thu May  1 15:37:16 2008
From: zambonel at gmail.com (Carlo Zambonelli)
Date: Thu, 01 May 2008 18:37:16 -0400
Subject: [Chimera-users] adding metal ions
Message-ID: <481A461C.70004@gmail.com>

I have a pdb file with the coordinates of an apo-enzyme. I know Fe3+ and
Zn2+ are essential for catalysis; I also know some of the residues
involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in the
structure so that they are correctly oriented relative to the
coordinating residues? My ultimate goal is to create a PDF file
containing also the metal ions.
Thanks,
Carlo



From meng at cgl.ucsf.edu  Thu May  1 16:13:42 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 1 May 2008 16:13:42 -0700
Subject: [Chimera-users] adding metal ions
In-Reply-To: <481A461C.70004@gmail.com>
References: <481A461C.70004@gmail.com>
Message-ID: <C03D4D46-0144-4B28-A514-7589C9942DC6@cgl.ucsf.edu>

Hi Carlo,
Yes, but I don't think it would be very easy - you would have to do  
most of the work!

Option 1 (recommended):
Try to find another structure with similar coordination environment  
that does contain the metal, match the coordinating residues onto the  
corresponding residues in the structure without the metal, and write  
the metal-containing structure as a PDB file "relative to" the other  
structure.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb
Then I would simply text-edit the metal out of the new PDB and into  
the other PDB that was lacking the metal.  This is by far the easiest  
if you can find such a similar structure that already has the metal ion.

Option 2A (depends how precise the position must be):
Build Structure (under Tools... Structure Editing) allows you to  
"Add" an atom.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ 
editing.html
You would have to put that atom in a "new model" so you could move it  
separately from the structure.  Then you would move it around  
yourself until you think it is in the right place.  Different models  
can be frozen/unfrozen in place using the checkboxes below the  
Command Line or the "Active" checkboxes in the Model Panel.  Then you  
would again write out the "ion" as a PDB file "relative to" the ion- 
lacking structure and then text-edit to add it to that file. I  
wouldn't bother changing the element in the Modify section of Build  
Structure since you can just text-edit the name to the element you  
want when you are doing all that other text-editing.

Option 2B (not recommended):
After you do everything in option 2A, you could read your new PDB  
file back in and attempt to energy-minimize, allowing ONLY the ion to  
move, to get it in a better position.  I am skeptical about this  
option because you have to do a bunch of other stuff before you can  
minimize (fix up the structure by adding missing atoms including  
hydrogens, possibly delete extra hydrogens from histidines  
coordinating the ion, etc.), and currently Fe ions cannot be handled,  
so only Zn++ has any chance of working.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ 
minimize.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 May 1, 2008, at 3:37 PM, Carlo Zambonelli wrote:

> I have a pdb file with the coordinates of an apo-enzyme. I know Fe3 
> + and
> Zn2+ are essential for catalysis; I also know some of the residues
> involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in  
> the
> structure so that they are correctly oriented relative to the
> coordinating residues? My ultimate goal is to create a PDF file
> containing also the metal ions.
> Thanks,
> Carlo
>





From yarbian at gmail.com  Thu May  1 22:08:55 2008
From: yarbian at gmail.com (Ian Yarbrough)
Date: Fri, 2 May 2008 00:08:55 -0500
Subject: [Chimera-users] automated rebuilding of side chains?
Message-ID: <84b4508f0805012208kf154265ub13cc58d1cf75c29@mail.gmail.com>

Hi,

A model that I am working with has several missing or partial side chains,
and I'm dealing with about 80 subunits of this protein (organized into 3
chains).  I am trying to repair these, but don't want to go through the task
of finding every broken chain.  Is there a way to get chimera to locate the
broken ones and repair them all?  I've seen the dock prep feature, but don't
want to change them all to alanines.

Thanks for you help.

Ian Yarbrough
Texas A&M University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080502/8678e855/attachment.html>

From meng at cgl.ucsf.edu  Fri May  2 10:43:28 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 2 May 2008 10:43:28 -0700
Subject: [Chimera-users] automated rebuilding of side chains?
In-Reply-To: <84b4508f0805012208kf154265ub13cc58d1cf75c29@mail.gmail.com>
References: <84b4508f0805012208kf154265ub13cc58d1cf75c29@mail.gmail.com>
Message-ID: <831F09D9-4B7E-4FED-9270-E0184F7E4D5A@cgl.ucsf.edu>

Hi Ian,
Dock Prep now rebuilds  truncated sidechains using data from rotamer  
libraries (Dunbrack or Richardson):

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ 
dockprep.html

It automatically locates the truncated sidechains, retrieves rotamer  
information, and chooses the best rotamer based on clashes, H-bonds,  
and (by default) backbone conformation.  This may take a while... it  
sounds like your system is pretty large. It will not add in missing  
backbone segments or entire residues, however, only sidechains.

Dock Prep was changed after the last production release (Nov 2007),  
so I recommend getting a daily build:
http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

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 May 1, 2008, at 10:08 PM, Ian Yarbrough wrote:

> Hi,
> A model that I am working with has several missing or partial side  
> chains, and I'm dealing with about 80 subunits of this protein  
> (organized into 3 chains).  I am trying to repair these, but don't  
> want to go through the task of finding every broken chain.  Is  
> there a way to get chimera to locate the broken ones and repair  
> them all?  I've seen the dock prep feature, but don't want to  
> change them all to alanines.
> Thanks for you help.
>
> Ian Yarbrough
> Texas A&M University
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080502/992e5af5/attachment.html>

From james.fethiere at umontreal.ca  Fri May  2 14:19:38 2008
From: james.fethiere at umontreal.ca (James Fethiere)
Date: Fri, 02 May 2008 17:19:38 -0400
Subject: [Chimera-users] Sec structure loss
Message-ID: <481B856A.2090201@umontreal.ca>

Hi,

I'm seing something strange with secondary structure assignments in 
peptides. Two examples: PDB 1axc has a peptide bound to PCNA with beta 
strand interactions and chimera doesn't pick it up as a strand. In the 
other example, 1rxz, it picks up the strand in a similar peptide but the 
strand disappear when I run matchmaker with 1ul1 (which also has a 
strand at the c-terminus that is not picked up. Is there any 
explanation? Are the criteria for secondary structure assignments to strict?

One more thing that may have been asked already!!  how does one keeps 
the NH and CO of the peptide bond displayed in the ribbons view?

Thanks

James
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080502/f6b21a6b/attachment.html>

From meng at cgl.ucsf.edu  Fri May  2 16:17:42 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 2 May 2008 16:17:42 -0700
Subject: [Chimera-users] Sec structure loss
In-Reply-To: <481B856A.2090201@umontreal.ca>
References: <481B856A.2090201@umontreal.ca>
Message-ID: <33AEF455-5BBD-4D95-B73F-0CBDD6445286@cgl.ucsf.edu>

Hi James,
There are many different secondary structure assignment methods (and  
sets of parameters), and they often disagree to various extents.   If  
the PDB file has HELIX and SHEET information in it, that will be  
used.  Take a look in the files - if they do have such information,  
it comes from the depositor, and different depositors have used  
different methods.

If files do not have that information, Chimera will perform an  
assignment.  Chimera uses "ksdssp" and there is no other choice of  
method, but you can adjust the parameters that it uses by default by  
choosing "compute SS" from the Model Panel, see:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
modelpanel.html#computess
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html

Also by default, MatchMaker runs "ksdssp" - it uses both sequence and  
secondary structure information to align structures, and we found it  
tends to improve the superpositions when a consistent secondary  
structure assignment method is used on all the structures being  
aligned.  Nevertheless, you can turn off the option to run "ksdssp"  
beforehand.  (Need to re-open the structure files to get back their  
original assignments, however.)

There is no real gold standard of what is a helix and what is a  
strand.  There is no problem when the structure is nearly ideal, only  
as it becomes less regular or shorter.   Thus it is hard to say  
something is definitely wrong.  However, if to your eye you would  
prefer something to be assigned as a strand, you can just set it  
manually with Selection Inspector or "setattr" as described here:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001775.html

To display both backbone atoms and ribbon, use the command  
"ribbackbone" - it may not look very good, however, as the ribbon is  
a smoothed interpolation... the atoms may not fall right on top of  
the ribbon in some places.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html

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 May 2, 2008, at 2:19 PM, James Fethiere wrote:

> Hi,
> I'm seing something strange with secondary structure assignments in  
> peptides. Two examples: PDB 1axc has a peptide bound to PCNA with  
> beta strand interactions and chimera doesn't pick it up as a  
> strand. In the other example, 1rxz, it picks up the strand in a  
> similar peptide but the strand disappear when I run matchmaker with  
> 1ul1 (which also has a strand at the c-terminus that is not picked  
> up. Is there any explanation? Are the criteria for secondary  
> structure assignments to strict?
>
> One more thing that may have been asked already!!  how does one  
> keeps the NH and CO of the peptide bond displayed in the ribbons view?
> Thanks
> James
>



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080502/5e050cd5/attachment.html>

From meng at cgl.ucsf.edu  Sat May  3 09:51:14 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 3 May 2008 09:51:14 -0700
Subject: [Chimera-users] surfaces, electrostatic coloring
In-Reply-To: <481BD657.8060008@umontreal.ca>
References: <481B856A.2090201@umontreal.ca>
	<33AEF455-5BBD-4D95-B73F-0CBDD6445286@cgl.ucsf.edu>
	<481BD657.8060008@umontreal.ca>
Message-ID: <106D2506-8BA0-4CD0-AC43-CDBED1A856EA@cgl.ucsf.edu>


On May 2, 2008, at 8:04 PM, James Fethiere wrote:
>
> Another wquestion.  I managed to display separate surfaces for 2  
> chains in a single model using the surfcat command you've  
> recommended last time.  Is this command accessible through the menu?

There is no menu equivalent to "surfcat," sorry.
>
> However, I can't color each surface separately according to  
> electrostatics.  I know that chimera does not calculate  
> electrostatics. What I tried is to go to tools/surface binding/  
> electrostatic surface coloring, set the palette to radius and set  
> the full range.  What I get when I color is a gradation from red to  
> blue with no atom type discrimination.

When you choose "radius" the coloring is by distance from a point,  
not electrostatics..  To actually color by electrostatics, you would  
have to open an electrostatic potential map and then choose it from  
that menu (the one with "radius" in it).   Also, your two surfaces  
would be two separate entries in the menu listing the surfaces.  You  
would have to choose one, color, and then choose the other, color again.

Perhaps it is misleading to call this tool "Electrostatic Surface  
Coloring" when it is really identical to the "Surface Color" tool:   
it includes options to color by distance from a point, axis, or  
plane.   The radial coloring is used (for example) to color a virus  
capsid by the distance from its center to highlight the contours of  
its surface; see the figure in the man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ 
surfcolor.html

Another possibly confusing thing is that in older versions of  
Chimera, after you use Surface Color, it can be tricky to change the  
color of the surfaces.  In current versions (recent daily builds),  
you should just be able to color the surface with the menu  
(Actions... Color) or commands (color, rangecolor) regardless of  
whether  this tool had been used.

> So I go to the attributes of this map in the model panel, and color  
> source atoms.  Great, I get red for acidic and blue for basics.   
> Now for the other chain, it doesn't work. At the color source atoms  
> step, the whole surface takes one single color.  The other thing is  
> that in the model panel I do not have the small color icon for the  
> two maps!! Is there a better way to do this?

The two surfaces would again be listed separately in the Model Panel,  
and have their own separate attributes dialogs.  I don't know what  
you mean by "doesn't work."  Did you try to use the menu or commands  
to color the surface?  Also, I don't know what other things you did  
in the session, but the red and blue you were seeing were probably  
just the element colors:  surfaces of oxygen atoms (red) and nitrogen  
atoms (blue).  Maybe you had colored the atoms of one chain and not  
the other.  In any case, you could proceed to color the surfaces with  
the menu and/or commands as mentioned above.

If you don't have an electrostatic potential map and don't want to  
color by distance from a point, axis, or plane, there is no reason to  
use Surface Color.   For example, to show the element colors on the  
surface for the two chains in 2zcp:

open 2zcp
surfcat one :.a & protein
surfcat two :.b & protein
surf one
surf two
col byatom                (or "col byhet" to not change carbon color)

Or, instead of using the atomic element colors, you could  
color :asp,glu residues red and :his,arg,lys residues blue.

>
> Can you also tell me how to make the surfaces smoother. Whatever  
> vertex density I give, I see pretty rough edges and it's not very  
> nice.

The vertex density is the only way I know of for making the surface  
smoother.  I am surprised it is not doing that in your case -  it  
definitely works in the molecular surfaces I have tried:  5.0 is a  
lot better, 10.0 even better.  Did you press return?  The main  
drawback I ran into is that it can take a long time to calculate,  
rotate, etc.  Maybe increasing the probe radius would improve your  
surface's appearance.

I hope this helps,
Elaine


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080503/1ff4ce39/attachment.html>

From huy.bui at mol.biol.ethz.ch  Mon May  5 01:11:36 2008
From: huy.bui at mol.biol.ethz.ch (Bui  Khanh Huy)
Date: Mon, 5 May 2008 10:11:36 +0200
Subject: [Chimera-users] Consistency of surface color
Message-ID: <7B0340B3488BF24DAEB8C70665C6B058177D47@EX4.d.ethz.ch>

Hi all,

 

I have a problem with color consistency on Chimera. The surface color of
my model from my Windows server is different than that from my linux
server. Even when I connect from home to the linux server, the color
render is also different from those two above. I use the same session
for all of them but the color comes out quite different on different
machines. Is there anyway to avoid this inconsistency?

 

Regards,

Huy

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080505/87f2e1b7/attachment.html>

From charles.r.midgett at Dartmouth.EDU  Thu May  1 06:46:49 2008
From: charles.r.midgett at Dartmouth.EDU (Charles Midgett)
Date: Thu, 1 May 2008 09:46:49 -0400
Subject: [Chimera-users] transparent surfaces
Message-ID: <88B431AC-3358-4F8C-9CE2-5F13863106DE@dartmouth.edu>

I want to make a transparent surface in volume viewer that can be  
drawn in POVray.  It appears the *.pov and *.ini  files produced by  
Chimera cannot be read by other POVray renders.  Is there some work  
around that will allow me to ray trace a transparent surface  
displayed by the volume viewer?

Charles


From zambonel at fas.harvard.edu  Thu May  1 15:36:07 2008
From: zambonel at fas.harvard.edu (Carlo Zambonelli)
Date: Thu, 01 May 2008 18:36:07 -0400
Subject: [Chimera-users] adding metal ions
Message-ID: <481A45D7.6000705@fas.harvard.edu>

I have a pdb file with the coordinates of an apo-enzyme. I know Fe3+ and 
Zn2+ are essential for catalysis; I also know some of the residues 
involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in the 
structure so that they are correctly oriented relative to the 
coordinating residues? My ultimate goal is to create a PDF file 
containing also the metal ions.
Thanks,
Carlo


From GDeNicola at ind.ucsf.edu  Thu May  1 17:25:11 2008
From: GDeNicola at ind.ucsf.edu (De Nicola, Gian)
Date: Thu, 1 May 2008 17:25:11 -0700
Subject: [Chimera-users] areaSAS_areaSES
Message-ID: <DDE2DE96BDD3A842B73F149913562EA2070F1739@EXVS05.net.ucsf.edu>

To whom it may concern
 
I would like to calculate the areaSAS and areasSES using Chimera.This is
what I do
Load the structure 
tools
Surface Binding Analysis
area/volume from web
I choose the type of surface I want.
Click apply then Ok
 As an output  I get " unexpected output from struc tools server" . 
What am I doing wrong?
Regards
Gian




From meng at cgl.ucsf.edu  Mon May  5 10:50:17 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 May 2008 10:50:17 -0700
Subject: [Chimera-users] areaSAS_areaSES
In-Reply-To: <DDE2DE96BDD3A842B73F149913562EA2070F1739@EXVS05.net.ucsf.edu>
References: <DDE2DE96BDD3A842B73F149913562EA2070F1739@EXVS05.net.ucsf.edu>
Message-ID: <0BE695B3-4761-4491-B04F-65A709BE42A7@cgl.ucsf.edu>

Hi Gian,
To use "Area/Volume from Web" you need to get a newer version of  
Chimera.  That Web server changed and we had to change Chimera  
accordingly.

However, you do not need to use this tool to calculate areaSAS and  
areaSES.  You only need to display molecular surface in Chimera and  
these are automatically computed, as described here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
representation.html#surfaces
Totals are reported in the Reply Log, and values per atom and per  
residue are assigned as the attributes areaSAS and areaSES.

This feature is also newer than the production release from last  
fall, so I recommend you get a daily build:
http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

It sounds like you were looking at documentation newer than the  
version you had installed.  If you use the documentation from the  
Help menu, it should match what you have installed.  However, in this  
case it is good that you found out about the newer features... now  
you just need the version that includes them!

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 May 1, 2008, at 5:25 PM, De Nicola, Gian wrote:

> To whom it may concern
> I would like to calculate the areaSAS and areasSES using  
> Chimera.This is
> what I do
> Load the structure
> tools
> Surface Binding Analysis
> area/volume from web
> I choose the type of surface I want.
> Click apply then Ok
>  As an output  I get " unexpected output from struc tools server" .
> What am I doing wrong?
> Regards
> Gian


From gregc at cgl.ucsf.edu  Mon May  5 11:15:41 2008
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 5 May 2008 11:15:41 -0700 (PDT)
Subject: [Chimera-users] transparent surfaces
In-Reply-To: <88B431AC-3358-4F8C-9CE2-5F13863106DE@dartmouth.edu>
References: <88B431AC-3358-4F8C-9CE2-5F13863106DE@dartmouth.edu>
Message-ID: <Pine.OSF.4.63.0805051106180.1720903@guanine.cgl.ucsf.edu>

On Thu, 1 May 2008, Charles Midgett wrote:

> I want to make a transparent surface in volume viewer that can be
> drawn in POVray.  It appears the *.pov and *.ini  files produced by
> Chimera cannot be read by other POVray renders.  Is there some work
> around that will allow me to ray trace a transparent surface
> displayed by the volume viewer?
>
> Charles

That is news to us.  The chimera povray output was only tested with the 
POV-Ray 3.6.1 renderer that comes with chimera.  Please submit a bug 
report using chimera's Help / Report a Bug dialog and include the name and 
version number of the other POV-ray renderers, as well as the error 
message you get.

 	Thank you,

 	Greg Couch
 	UCSF Computer Graphics Lab


From gregc at cgl.ucsf.edu  Mon May  5 11:31:47 2008
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 5 May 2008 11:31:47 -0700 (PDT)
Subject: [Chimera-users] Consistency of surface color
In-Reply-To: <7B0340B3488BF24DAEB8C70665C6B058177D47@EX4.d.ethz.ch>
References: <7B0340B3488BF24DAEB8C70665C6B058177D47@EX4.d.ethz.ch>
Message-ID: <Pine.OSF.4.63.0805051116080.1720903@guanine.cgl.ucsf.edu>

On Mon, 5 May 2008, Bui  Khanh Huy wrote:

> I have a problem with color consistency on Chimera. The surface color of
> my model from my Windows server is different than that from my linux
> server. Even when I connect from home to the linux server, the color
> render is also different from those two above. I use the same session
> for all of them but the color comes out quite different on different
> machines. Is there anyway to avoid this inconsistency?
>
> Regards,
>
> Huy

In general, the colors you observe on the screen will be different on 
different computers.  If you want them to be the the same, you need to use 
the the same monitor in the same ambient light conditions.  Even two 
different monitors of the same model give different results.

To improve the color consistency of your monitors, you need to calibrate 
them using a colorimeter.  See the wikipedia articles on color 
mananagement[1] and color calibration[2] for more information.  Using a 
color management system and color profiles helps match colors when you 
print too.

 	Good luck,

 	Greg Couch
 	UCSF COmputer Graphics Lab

[1] <http://en.wikipedia.org/wiki/Color_management>
[2] <http://en.wikipedia.org/wiki/Color_calibration>




From gregc at cgl.ucsf.edu  Mon May  5 14:01:27 2008
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 5 May 2008 14:01:27 -0700 (PDT)
Subject: [Chimera-users] transparent surfaces (fwd)
Message-ID: <Pine.OSF.4.63.0805051342001.1807051@guanine.cgl.ucsf.edu>

Just so everyone on the list knows.

Extrapolating from what Charles said, the error was probably that MegaPOV 
wasn't able to include the transforms.inc file because MegaPOV wasn't 
configured properly to include the POV-Ray library files.

And on Mac OS X, Linux, and other UNIX systems, to use the 
CHIMERA/bin/povray.exe program outside of chimera, you need to setup the 
shared library path to include CHIMERA/lib.  Chimera does that setup 
automatically for many of the programs in CHIMERA/bin, so we should 
probably fix it for povray as well, but if you're going to use your own 
POV-Ray anyway, like the multi-threaded 3.7 beta release, then that is 
not an issue.

 	- Greg

---------- Forwarded message ----------
I figured it out.  In MegaPOV you need to set the library path for the render, 
also POVray 3.6 will not work as a standalone application in Mac OS 10.4 and 
higher.

Charles
On May 5, 2008, at 2:15 PM, Greg Couch wrote:

> On Thu, 1 May 2008, Charles Midgett wrote:
> 
>> I want to make a transparent surface in volume viewer that can be
>> drawn in POVray.  It appears the *.pov and *.ini  files produced by
>> Chimera cannot be read by other POVray renders.  Is there some work
>> around that will allow me to ray trace a transparent surface
>> displayed by the volume viewer?
>> 
>> Charles
> 
> That is news to us.  The chimera povray output was only tested with the 
> POV-Ray 3.6.1 renderer that comes with chimera.  Please submit a bug report 
> using chimera's Help / Report a Bug dialog and include the name and version 
> number of the other POV-ray renderers, as well as the error message you get.
>
> 	Thank you,
>
> 	Greg Couch
> 	UCSF Computer Graphics Lab


From meng at cgl.ucsf.edu  Mon May  5 17:15:53 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 May 2008 17:15:53 -0700
Subject: [Chimera-users] solvent-accessible surface area
In-Reply-To: <200805052352.m45NqYD71873692@guanine.cgl.ucsf.edu>
References: <200805052352.m45NqYD71873692@guanine.cgl.ucsf.edu>
Message-ID: <8A70EB2B-A58C-4D0A-8499-909FCDEDA349@cgl.ucsf.edu>

Dear Jose,
Prof. Ferrin forwarded your question to me.  Our program Chimera, the  
successor to MidasPlus, can calculate the solvent-accessible surface  
area.  It is available for download for Windows, Mac OSX, Linux and  
other platforms.  The features I will mention are relatively new, so  
you would need to get a recent version such as the May 1 snapshot:
http://www.cgl.ucsf.edu/chimera/download.html#snapshots

You would first load the structure in Chimera (File... Open for a  
local file, File... Fetch by ID to get it directly from the PDB).   
Then there are a couple of different approaches you could take.

(1) simply show a molecular surface in Chimera (Actions... Surface...  
show) or command "surface".  The total will be reported in the Reply  
Log (under Favorites in the menu).  You can use the solvent- 
accessible value or solvent-excluded as you prefer.  The difference  
is explained here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
representation.html#surfaces

Besides the total, the values per atom and per residue are assigned  
as "attributes" named areaSAS and areaSES for solvent-accessible and  
solvent-excluded, respectively.  You can see a histogram of the  
values by opening "Render by Attribute" (under Tools... Depiction),  
and you can write out the values to a file by choosing File... Save  
Attributes from that dialog's menu.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html#render

The Render dialog can be set to show the values for "atoms" or  
"residues" (simply the sum over the atoms in each residue).  What it  
writes out are the atom (or residue) specifiers and the value for  
each, not a grid.

(2) instead of doing the calculation in Chimera, you can send the  
coordinates to a web server with the tool "Area/Volume from  
Web" (under Tools... Surface/Binding Analysis).  There are various  
options for what you want to calculate.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ 
surfvol.html

Again you get the values assigned as attributes (but this time atoms  
only) and can view and save them in the same way as described for #1  
above.

The help links above are part of the User's Guide, which is also  
accessible from the Help menu of Chimera, once you have downloaded it  
(Help... User's Guide, Search Documentation, Tutorials).  If you  
still have trouble you can send questions to chimera-users at cgl.ucsf.edu

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 May 5, 2008, at 4:52 PM, Tom Ferrin wrote:

> ------- Forwarded Message
>
> Date:    Wed, 30 Apr 2008 17:20:27 -0400
> From:    Jose Gascon <jose.gascon at uconn.edu>
> To:      tef at cgl.ucsf.edu
> Subject: midasplus
>
> Dear Prof. Ferrin
>
> I am an Assistant Professor in the Chemistry Department at UConn, I am
> interested in calculating the solvent accessible area of a protein. I
> looked up on the internet and found that the program midasplus is
> suppose to do that. The links seem to be outdated and I was not been
> able to find the program. I assume that midasplus has probably evolved
> to other programs such as chimera. I understand that you were involved
> in the development of this program.
>
> At the end, given a pdb input file, I am just interested in  
> obtaining a
> grid of x,y,z coordinates representing the SAS.
> Do you know if there is such a program? Is DMS, from midasplus, still
> available somewhere?
>
> Thanks for your help.
>
> Sincerely,
>
> Jose A. Gascon
>
>
> -- 
> Jose A. Gascon - Assistant Professor
> 55 North Eagleville Rd.
> Department of Chemistry
> University of Connecticut - (860) 486-0591
> Storrs, CT 06269
> http://gascon.chem.uconn.edu
>
> ------- End of Forwarded Message
>



From pett at cgl.ucsf.edu  Mon May  5 17:27:32 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 5 May 2008 17:27:32 -0700
Subject: [Chimera-users] solvent-accessible surface area
In-Reply-To: <8A70EB2B-A58C-4D0A-8499-909FCDEDA349@cgl.ucsf.edu>
References: <200805052352.m45NqYD71873692@guanine.cgl.ucsf.edu>
	<8A70EB2B-A58C-4D0A-8499-909FCDEDA349@cgl.ucsf.edu>
Message-ID: <7D77327F-F2EB-4935-9CDA-F4014777FF89@cgl.ucsf.edu>

Hi Jose,
	And if for some reason you still want to use DMS, you can obtain it  
here: http://www.cgl.ucsf.edu/Overview/software.html#dms

--Eric

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


On May 5, 2008, at 5:15 PM, Elaine Meng wrote:

> Dear Jose,
> Prof. Ferrin forwarded your question to me.  Our program Chimera, the
> successor to MidasPlus, can calculate the solvent-accessible surface
> area.  It is available for download for Windows, Mac OSX, Linux and
> other platforms.  The features I will mention are relatively new, so
> you would need to get a recent version such as the May 1 snapshot:
> http://www.cgl.ucsf.edu/chimera/download.html#snapshots
>
> You would first load the structure in Chimera (File... Open for a
> local file, File... Fetch by ID to get it directly from the PDB).
> Then there are a couple of different approaches you could take.
>
> (1) simply show a molecular surface in Chimera (Actions... Surface...
> show) or command "surface".  The total will be reported in the Reply
> Log (under Favorites in the menu).  You can use the solvent-
> accessible value or solvent-excluded as you prefer.  The difference
> is explained here:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/
> representation.html#surfaces
>
> Besides the total, the values per atom and per residue are assigned
> as "attributes" named areaSAS and areaSES for solvent-accessible and
> solvent-excluded, respectively.  You can see a histogram of the
> values by opening "Render by Attribute" (under Tools... Depiction),
> and you can write out the values to a file by choosing File... Save
> Attributes from that dialog's menu.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/
> render.html#render
>
> The Render dialog can be set to show the values for "atoms" or
> "residues" (simply the sum over the atoms in each residue).  What it
> writes out are the atom (or residue) specifiers and the value for
> each, not a grid.
>
> (2) instead of doing the calculation in Chimera, you can send the
> coordinates to a web server with the tool "Area/Volume from
> Web" (under Tools... Surface/Binding Analysis).  There are various
> options for what you want to calculate.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/
> surfvol.html
>
> Again you get the values assigned as attributes (but this time atoms
> only) and can view and save them in the same way as described for #1
> above.
>
> The help links above are part of the User's Guide, which is also
> accessible from the Help menu of Chimera, once you have downloaded it
> (Help... User's Guide, Search Documentation, Tutorials).  If you
> still have trouble you can send questions to chimera- 
> users at cgl.ucsf.edu
>
> 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 May 5, 2008, at 4:52 PM, Tom Ferrin wrote:
>
>> ------- Forwarded Message
>>
>> Date:    Wed, 30 Apr 2008 17:20:27 -0400
>> From:    Jose Gascon <jose.gascon at uconn.edu>
>> To:      tef at cgl.ucsf.edu
>> Subject: midasplus
>>
>> Dear Prof. Ferrin
>>
>> I am an Assistant Professor in the Chemistry Department at UConn,  
>> I am
>> interested in calculating the solvent accessible area of a protein. I
>> looked up on the internet and found that the program midasplus is
>> suppose to do that. The links seem to be outdated and I was not been
>> able to find the program. I assume that midasplus has probably  
>> evolved
>> to other programs such as chimera. I understand that you were  
>> involved
>> in the development of this program.
>>
>> At the end, given a pdb input file, I am just interested in
>> obtaining a
>> grid of x,y,z coordinates representing the SAS.
>> Do you know if there is such a program? Is DMS, from midasplus, still
>> available somewhere?
>>
>> Thanks for your help.
>>
>> Sincerely,
>>
>> Jose A. Gascon
>>
>>
>> -- 
>> Jose A. Gascon - Assistant Professor
>> 55 North Eagleville Rd.
>> Department of Chemistry
>> University of Connecticut - (860) 486-0591
>> Storrs, CT 06269
>> http://gascon.chem.uconn.edu
>>
>> ------- End of Forwarded Message
>>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080505/9bec36cd/attachment.html>

From jparmache at lmb.uni-muenchen.de  Mon May  5 17:20:22 2008
From: jparmache at lmb.uni-muenchen.de (Jean-Paul Armache)
Date: Tue, 06 May 2008 02:20:22 +0200
Subject: [Chimera-users] movie trajectory
Message-ID: <200805060021.m460Lils018859@pluto.lmb.uni-muenchen.de>

hi all,

i have a small question. would any of you know a way to set up a specific trajectory for a camera to move around the molecule? i know you can rotate the whole molecule, but the question is more related to similarity to 3ds max or maya - if you could set up a specific way the camera moves around the molecule (rotation, movement at specific point, zoom, stop, restart, further movement etc) ?
maybe the question is trivial, however i haven't found a way to do it (an easy way - you can do quite a huge script with small movements - one step at a time). my question is more about path drawing and setting stop points.

regards,

jean-paul





From pett at cgl.ucsf.edu  Mon May  5 19:04:41 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 5 May 2008 19:04:41 -0700
Subject: [Chimera-users] movie trajectory
In-Reply-To: <200805060021.m460Lils018859@pluto.lmb.uni-muenchen.de>
References: <200805060021.m460Lils018859@pluto.lmb.uni-muenchen.de>
Message-ID: <75437644-A19B-4CE6-8374-CE10E207C2C1@cgl.ucsf.edu>

Hi Jean-Paul,
	I suppose you're familiar with the page that discusses commands  
relevant to animation in Chimera:

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

	Maybe there are other approaches, but one way to possibly avoid an  
incredibly detailed script is to use the savepos command to save  
views you want to visit and then use the reset command to interpolate  
between these views.  If you find you get unwanted clipping during  
the interpolation, you may have to edit the positions and move the  
clip planes further apart (i.e. reset position-name; use the Side  
View or thickness/clip command to move the clip planes apart; savepos  
position-name).

	Let's say you have an 100-frame trajectory and want to make a 360  
around the molecule as the trajectory plays.  'savepos pos1' as  
whatever you want your starting view to be.  Then 'turn y 180' and  
'savepos pos2'.  The use MD Movie's per-frame script dialog (set to  
Python scripting) and enter this:

from chimera import runCommand
frame = mdInfo['frame']
if frame == 1:
	runCommand('reset pos2 50')
elif frame == 51:
	runCommand('reset pos1 50')

and click Apply or OK.  You will get some motion of the trajectory  
right away (assuming you were sitting on frame 1).  Now type 'reset  
pos1' and record your trajectory.  _Playing_ your trajectory won't  
work right until it's looped once since it's already executed the  
frame 1 reset command, though if you back up to the _last_ frame, do  
"reset pos1" and then play it will work immediately.

	You may or may not want to also smooth your trajectory, as described  
here:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-April/002496.html

--Eric

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


On May 5, 2008, at 5:20 PM, Jean-Paul Armache wrote:

> hi all,
>
> i have a small question. would any of you know a way to set up a  
> specific trajectory for a camera to move around the molecule? i  
> know you can rotate the whole molecule, but the question is more  
> related to similarity to 3ds max or maya - if you could set up a  
> specific way the camera moves around the molecule (rotation,  
> movement at specific point, zoom, stop, restart, further movement  
> etc) ?
> maybe the question is trivial, however i haven't found a way to do  
> it (an easy way - you can do quite a huge script with small  
> movements - one step at a time). my question is more about path  
> drawing and setting stop points.
>
> regards,
>
> jean-paul
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080505/788c2421/attachment.html>

From meng at cgl.ucsf.edu  Mon May  5 20:52:29 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 May 2008 20:52:29 -0700
Subject: [Chimera-users] movie trajectory
In-Reply-To: <75437644-A19B-4CE6-8374-CE10E207C2C1@cgl.ucsf.edu>
References: <200805060021.m460Lils018859@pluto.lmb.uni-muenchen.de>
	<75437644-A19B-4CE6-8374-CE10E207C2C1@cgl.ucsf.edu>
Message-ID: <E8DD96DF-1BBF-431A-A1FE-B7D968478411@cgl.ucsf.edu>

Hi Jean-Paul,
I wanted to explain that many of the movie-related commands listed in

> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html

have a "number of frames" argument.   For example, the command

roll y 1 360

performs a 1-degree rotation around the Y axis in each of 360 frames  
- you don't have to repeat a 1-degree rotation command 360 times!     
There are similar commands for scaling, translation, and  
interpolating between previously saved positions, as Eric  
mentioned.   The page also links to some example command files.
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 May 5, 2008, at 7:04 PM, Eric Pettersen wrote:

> Hi Jean-Paul,
> 	I suppose you're familiar with the page that discusses commands  
> relevant to animation in Chimera:
>
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html
>
> 	Maybe there are other approaches, but one way to possibly avoid an  
> incredibly detailed script is to use the savepos command to save  
> views you want to visit and then use the reset command to  
> interpolate between these views.  If you find you get unwanted  
> clipping during the interpolation, you may have to edit the  
> positions and move the clip planes further apart (i.e. reset  
> position-name; use the Side View or thickness/clip command to move  
> the clip planes apart; savepos position-name).
>
>
> On May 5, 2008, at 5:20 PM, Jean-Paul Armache wrote:
>
>> hi all,
>> i have a small question. would any of you know a way to set up a  
>> specific trajectory for a camera to move around the molecule? i  
>> know you can rotate the whole molecule, but the question is more  
>> related to similarity to 3ds max or maya - if you could set up a  
>> specific way the camera moves around the molecule (rotation,  
>> movement at specific point, zoom, stop, restart, further movement  
>> etc) ?
>> maybe the question is trivial, however i haven't found a way to do  
>> it (an easy way - you can do quite a huge script with small  
>> movements - one step at a time). my question is more about path  
>> drawing and setting stop points.
>> regards,
>> jean-paul
>>



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080505/9d0c6204/attachment.html>

From jparmache at lmb.uni-muenchen.de  Mon May  5 22:36:54 2008
From: jparmache at lmb.uni-muenchen.de (Jean-Paul Armache)
Date: Tue, 06 May 2008 07:36:54 +0200
Subject: [Chimera-users] movie trajectory
Message-ID: <200805060538.m465cBA0021015@pluto.lmb.uni-muenchen.de>

Hi Elaine, Eric,

Thanks for the answer - I know the webpage for the movies, but it will be helpful to use the savepos command. I will let you know whether this produces the desired effect or further help will be needed.
Best regards,

Jean-Paul




From esanzgar at terra.es  Tue May  6 12:51:12 2008
From: esanzgar at terra.es (Eduardo Sanz-Garcia)
Date: Tue, 06 May 2008 13:51:12 -0600
Subject: [Chimera-users] Tile structure request
Message-ID: <4820B6B0.4090309@terra.es>

I noticed that the tile structure option arranges the models logically 
when there are 5 or less models opened.
When there are 6 or more, the arrangement is a little bit chaotic, the 
models are not placed sequentially.
Could this option be improved so the sequence is more logical?

Thank you very much.
Chimera is great!!

PS: I am used to work with EM models, I don't know if the previously 
described behaviour also applies to atomic coordinates models.


From goddard at cgl.ucsf.edu  Tue May  6 17:20:17 2008
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 06 May 2008 17:20:17 -0700
Subject: [Chimera-users] Tile structure request
In-Reply-To: <4820B6B0.4090309@terra.es>
References: <4820B6B0.4090309@terra.es>
Message-ID: <4820F5C1.2000200@cgl.ucsf.edu>

Hi Eduardo,

   I made a mistake in the tiling code that caused them to be placed in 
random order.  I've fixed that so they will now be ordered according to 
their model id numbers starting at the top row going left to right, then 
the second row, ....

   The fixed code will be in tonight's daily Chimera builds if they succeed.

	http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

We've made a major upgrade in the windowing toolkit Tk 8.4 to 8.5 so the 
  daily builds may have problems.

	Tom


From ibdeno at gmail.com  Wed May  7 06:40:32 2008
From: ibdeno at gmail.com (=?ISO-8859-1?Q?Miguel_Ortiz-Lombard=EDa?=)
Date: Wed, 7 May 2008 15:40:32 +0200
Subject: [Chimera-users] how to use hbonds spec
Message-ID: <d5dc3ecc0805070640o71ec1b08s646019ae6418dfa6@mail.gmail.com>

Hello,

I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I
would like to run a 'per frame' script with something like:

hbonds spec :100 selRestrict cross relax false

However, this fails because apparently no atoms are selected. This fails as
well:

hbonds spec #0:100 selRestrict cross relax false

I can only see the hydrogen bonds if insert a

select :100

before the hbonds command. I wouldn't like to see the green 'aura' of the
selection, that's why I would like to make the selection within the hbonds
command. I'm probably missing something, but cannot figure out what.

Thank you!


Miguel
-- 
http://www.pangea.org/mol/spip.php?rubrique2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en libert?
Dans les jardins mal fr?quent?s!
Georges Brassens
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080507/37fb8185/attachment.html>

From meng at cgl.ucsf.edu  Wed May  7 08:59:36 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 7 May 2008 08:59:36 -0700
Subject: [Chimera-users] how to use hbonds spec
In-Reply-To: <d5dc3ecc0805070640o71ec1b08s646019ae6418dfa6@mail.gmail.com>
References: <d5dc3ecc0805070640o71ec1b08s646019ae6418dfa6@mail.gmail.com>
Message-ID: <94C9DF9A-5D0C-4CE7-B5D4-11C865E7A0BC@cgl.ucsf.edu>

Hi Miguel,
The "selRestrict" keyword only works on the selection (what is  
outlined with green).  It sounds like you already figured out that  
the selection must be done in a separate command, since "hbonds"  
doesn't select atoms.  The "spec" keyword can be used to specify a  
particular model but not anything smaller (i.e. not a particular  
residue or set of atoms, only the whole model), and it does not  
select anything.

The remaining issue is how to prevent the selection outline from  
appearing.  In MD Movie, the display is only updated after the per- 
frame script is executed, so you just need to add a command to turn  
off the selection after the hbonds are calculated:

select :100
hbonds selRestrict cross relax false
~select

If this was done in a command script outside of MD Movie, the way to  
suppress intermediate display is to string commands together with  
semicolons:

select :100; hbonds selRestrict cross relax false; ~select

(that should be all one line even if the annoying mail program breaks  
it up!)

It does seem a bit inefficient to keep selecting/deselecting the same  
thing, but that is the only method I can think of currently.   I will  
ask the others about perhaps adding a preference option to suppress  
the selection highlighting.

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 May 7, 2008, at 6:40 AM, Miguel Ortiz-Lombard?a wrote:
>
> I'm trying to follow hydrogen bonds in a trajectory from amber. To  
> do so, I would like to run a 'per frame' script with something like:
>
> hbonds spec :100 selRestrict cross relax false
>
> However, this fails because apparently no atoms are selected. This  
> fails as well:
>
> hbonds spec #0:100 selRestrict cross relax false
>
> I can only see the hydrogen bonds if insert a
>
> select :100
>
> before the hbonds command. I wouldn't like to see the green 'aura'  
> of the selection, that's why I would like to make the selection  
> within the hbonds command. I'm probably missing something, but  
> cannot figure out what.
> Thank you!



From jose.gascon at uconn.edu  Tue May  6 06:44:25 2008
From: jose.gascon at uconn.edu (Jose Gascon)
Date: Tue, 06 May 2008 09:44:25 -0400
Subject: [Chimera-users] solvent-accessible surface area
In-Reply-To: <8A70EB2B-A58C-4D0A-8499-909FCDEDA349@cgl.ucsf.edu>
References: <200805052352.m45NqYD71873692@guanine.cgl.ucsf.edu>
	<8A70EB2B-A58C-4D0A-8499-909FCDEDA349@cgl.ucsf.edu>
Message-ID: <1210081465.14938.313.camel@borges.chem.uconn.edu>

Dear Elaine and Tom,

Thanks for the thorough answer. 
This is exactly what I was looking for. I appreciate the time you took
to write this.

With best regards,

Jose.

On Mon, 2008-05-05 at 17:15 -0700, Elaine Meng wrote:
> Dear Jose,
> Prof. Ferrin forwarded your question to me.  Our program Chimera, the  
> successor to MidasPlus, can calculate the solvent-accessible surface  
> area.  It is available for download for Windows, Mac OSX, Linux and  
> other platforms.  The features I will mention are relatively new, so  
> you would need to get a recent version such as the May 1 snapshot:
> http://www.cgl.ucsf.edu/chimera/download.html#snapshots
> 
> You would first load the structure in Chimera (File... Open for a  
> local file, File... Fetch by ID to get it directly from the PDB).   
> Then there are a couple of different approaches you could take.
> 
> (1) simply show a molecular surface in Chimera (Actions... Surface...  
> show) or command "surface".  The total will be reported in the Reply  
> Log (under Favorites in the menu).  You can use the solvent- 
> accessible value or solvent-excluded as you prefer.  The difference  
> is explained here:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
> representation.html#surfaces
> 
> Besides the total, the values per atom and per residue are assigned  
> as "attributes" named areaSAS and areaSES for solvent-accessible and  
> solvent-excluded, respectively.  You can see a histogram of the  
> values by opening "Render by Attribute" (under Tools... Depiction),  
> and you can write out the values to a file by choosing File... Save  
> Attributes from that dialog's menu.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
> render.html#render
> 
> The Render dialog can be set to show the values for "atoms" or  
> "residues" (simply the sum over the atoms in each residue).  What it  
> writes out are the atom (or residue) specifiers and the value for  
> each, not a grid.
> 
> (2) instead of doing the calculation in Chimera, you can send the  
> coordinates to a web server with the tool "Area/Volume from  
> Web" (under Tools... Surface/Binding Analysis).  There are various  
> options for what you want to calculate.


http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html

> 
> Again you get the values assigned as attributes (but this time atoms  
> only) and can view and save them in the same way as described for #1  
> above.
> 
> The help links above are part of the User's Guide, which is also  
> accessible from the Help menu of Chimera, once you have downloaded it  
> (Help... User's Guide, Search Documentation, Tutorials).  If you  
> still have trouble you can send questions to chimera-users at cgl.ucsf.edu
> 
> 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 May 5, 2008, at 4:52 PM, Tom Ferrin wrote:
> 
> > ------- Forwarded Message
> >
> > Date:    Wed, 30 Apr 2008 17:20:27 -0400
> > From:    Jose Gascon <jose.gascon at uconn.edu>
> > To:      tef at cgl.ucsf.edu
> > Subject: midasplus
> >
> > Dear Prof. Ferrin
> >
> > I am an Assistant Professor in the Chemistry Department at UConn, I am
> > interested in calculating the solvent accessible area of a protein. I
> > looked up on the internet and found that the program midasplus is
> > suppose to do that. The links seem to be outdated and I was not been
> > able to find the program. I assume that midasplus has probably evolved
> > to other programs such as chimera. I understand that you were involved
> > in the development of this program.
> >
> > At the end, given a pdb input file, I am just interested in  
> > obtaining a
> > grid of x,y,z coordinates representing the SAS.
> > Do you know if there is such a program? Is DMS, from midasplus, still
> > available somewhere?
> >
> > Thanks for your help.
> >
> > Sincerely,
> >
> > Jose A. Gascon
> >
> >
> > -- 
> > Jose A. Gascon - Assistant Professor
> > 55 North Eagleville Rd.
> > Department of Chemistry
> > University of Connecticut - (860) 486-0591
> > Storrs, CT 06269
> > http://gascon.chem.uconn.edu
> >
> > ------- End of Forwarded Message
> >
> 
-- 
Jose A. Gascon - Assistant Professor 
55 North Eagleville Rd.
Department of Chemistry 
University of Connecticut - (860) 486-0591 
Storrs, CT 06269
http://gascon.chem.uconn.edu



From pett at cgl.ucsf.edu  Wed May  7 16:32:42 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 7 May 2008 16:32:42 -0700
Subject: [Chimera-users] MemoryError restoring session
In-Reply-To: <200805072323.m47NNk1s1625093@guanine.cgl.ucsf.edu>
References: <200805072323.m47NNk1s1625093@guanine.cgl.ucsf.edu>
Message-ID: <50C3193F-4A2C-4C5A-A807-4DAFE4DD43A8@cgl.ucsf.edu>

Christian Rickert wrote:

> At the university, I saved a huge project of mine containing a  
> density map and multiple (!) rigid-body fitted pdbs.
> Although this system is a 32-bit Kubuntu 8.04 only (4 Gig of RAM  
> installed), I observed the same problems with my 64-bit SUSE 10.3  
> (4 Gig of RAM installed as well) at work.
>
> Creating this project took me two days in total, so I really would  
> appreciate any suggestions from you ...

Hi Christian,
	It's possible that your shell is imposing a limit on memory use by a  
single process.  Before starting Chimera, remove the memory limit of  
your shell by typing:

csh-type shell:  unlimit

sh-type shell: ulimit -v unlimited

	Let me know if this helps or not.

--Eric

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080507/ceec5772/attachment.html>

From cong at bcm.edu  Wed May  7 23:18:29 2008
From: cong at bcm.edu (Yao Cong)
Date: Thu, 8 May 2008 01:18:29 -0500
Subject: [Chimera-users] color scale bar
Message-ID: <FA25B18F-DC4D-473B-A37D-62649158B508@bcm.edu>

Hello Chimera developer,

I am rendering a PDB file colored according to B-factor value by  
"render by attribute" tool. How can I generate a color scale bar  
besides the structure labeling the color scale used?

Many thanks,
Yao Cong



From I.moustafa at psu.edu  Thu May  8 14:03:27 2008
From: I.moustafa at psu.edu (Ibrahim Moustafa)
Date: Thu, 08 May 2008 17:03:27 -0400
Subject: [Chimera-users] Selected residues already shown on the screen
Message-ID: <C448E2DF.E5C%I.moustafa@psu.edu>

   Dear Chimera team,

    How to include residues previously selected and shown on the screen with
a new selection?
  For example, I did a selection for few residues and displayed them on the
screen; then removed the selection.
I wanted to run hbond on those residues already on display. How to do that?

  Thanks,
 Ibrahim
-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080508/1cec5fd6/attachment.html>

From meng at cgl.ucsf.edu  Thu May  8 15:34:09 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 8 May 2008 15:34:09 -0700
Subject: [Chimera-users] Selected residues already shown on the screen
In-Reply-To: <C448E2DF.E5C%I.moustafa@psu.edu>
References: <C448E2DF.E5C%I.moustafa@psu.edu>
Message-ID: <14036F11-5B59-4E0A-9F1F-4C007C0A53EF@cgl.ucsf.edu>

Dear Ibrahim,
If I understand correctly, you want to get back the selection you had  
before, which is the same as the atoms that are displayed.

If that selection was the most recent, "Select... Undo" would restore  
it.  The same thing is accomplished by pressing the left arrow key  
after clicking into the graphics window.

If that doesn't work (if you did some other selections in between),  
you can re-select just the displayed atoms with the command:

select @/display

Then you can proceed with hbond and one of its "selRestrict" options.

For future reference, you can name and save a selection ("Select...  
Name Selection" in the menu or the command "namesel") and then later  
restore that selection by choosing its name from the menu under  
"Select... Named Selections".
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.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 May 8, 2008, at 2:03 PM, Ibrahim Moustafa wrote:

>   Dear Chimera team,
>     How to include residues previously selected and shown on the  
> screen with a new selection?
>   For example, I did a selection for few residues and displayed  
> them on the screen; then removed the selection.
> I wanted to run hbond on those residues already on display. How to  
> do that?
>
>   Thanks,
>  Ibrahim


From pett at cgl.ucsf.edu  Thu May  8 17:17:58 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 8 May 2008 17:17:58 -0700
Subject: [Chimera-users] color scale bar
In-Reply-To: <FA25B18F-DC4D-473B-A37D-62649158B508@bcm.edu>
References: <FA25B18F-DC4D-473B-A37D-62649158B508@bcm.edu>
Message-ID: <D73005AF-9C67-471E-A3C7-E1513EE6A241@cgl.ucsf.edu>

On May 7, 2008, at 11:18 PM, Yao Cong wrote:

> Hello Chimera developer,
>
> I am rendering a PDB file colored according to B-factor value by
> "render by attribute" tool. How can I generate a color scale bar
> besides the structure labeling the color scale used?

Hi Yao,
	There's no way to do this directly in Chimera now, though I am  
working on a tool that will make it easy to produce such a key -- but  
it's not ready yet.  For now you will have to use an external image- 
processing program such as GIMP or photoshop to add the key.  There  
is some basic advice for doing this in this message:  http:// 
www.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000878.html

--Eric

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080508/a217ea46/attachment.html>

From I.moustafa at psu.edu  Fri May  9 08:58:06 2008
From: I.moustafa at psu.edu (Ibrahim Moustafa)
Date: Fri, 09 May 2008 11:58:06 -0400
Subject: [Chimera-users] Dashed H-bond
Message-ID: <C449ECCE.E91%I.moustafa@psu.edu>

    Dear Chimera Team,

  Few weeks ago I asked about how to make H-bonds with dashed line style, I
got your great help in that.

 So, I can make the H-bond with the color and style I want; however, when
saving the image (with POV true)

I got the H-bond appeared with the new chosen color but not as dashed line
shown in the display.

 But, if I save the image with POVray option false, I got the same style
shown in the display (new color and dashed line).

  The question is why saving the image using ?POV true? does not give the
image as it appears in the display? Again, it accepts the new color but not
the dashed style.

  Thanks for your great help,

  Ibrahim
-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927
 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080509/e9405e99/attachment.html>

From meng at cgl.ucsf.edu  Fri May  9 09:20:07 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 May 2008 09:20:07 -0700
Subject: [Chimera-users] Dashed H-bond
In-Reply-To: <C449ECCE.E91%I.moustafa@psu.edu>
References: <C449ECCE.E91%I.moustafa@psu.edu>
Message-ID: <C865549B-EC87-4331-9B6E-2B3B8DBB0CAD@cgl.ucsf.edu>

Dear Ibraham,
That is a known problem - the result from raytracing may be different  
from the Chimera display in some ways, as listed in the Limitations  
section of this page:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html

This problem is "pseudobonds always shown as sticks, even if shown as  
dashed lines in Chimera"

When you save an image in Chimera without raytracing, it will match  
the display, except the resolution is whatever you specified (usually  
better than the display).  However, when you turn on raytracing (POV- 
Ray option), Chimera writes a separate file describing the display,  
and that separate file is sent to the POV-Ray program.  The  
limitations reflect what information has been written to that  
separate file.  I am guessing it should be possible to describe the  
line as dashed in the file, but we have not written the code to do  
that yet.

In the image-saving dialog, when you turn on "raytrace with POV-Ray"  
there will also be a button "POV-Ray Options" - if you click that,  
there is an option to "Keep POV-Ray input files" if you want to see  
what that separate file looks like.  It is usually quite large.  It  
gets the same name as the saved image except ending in ".pov"  If you  
know a lot about POV-Ray, you could edit the file to contain the  
information you want and run POV-Ray on it separately, but it would  
not be easy.

Currently I can only recommend turning off raytracing to show dashed  
lines.  Also, if your display has a lot of details in it, often the  
image looks better without raytracing, in my opinion.
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 May 9, 2008, at 8:58 AM, Ibrahim Moustafa wrote:

>    Dear Chimera Team,
>   Few weeks ago I asked about how to make H-bonds with dashed line  
> style, I got your great help in that.
>   So, I can make the H-bond with the color and style I want;  
> however, when saving the image (with POV true)
>  I got the H-bond appeared with the new chosen color but not as  
> dashed line shown in the display.
>   But, if I save the image with POVray option false, I got the same  
> style shown in the display (new color and dashed line).
>
>   The question is why saving the image using ?POV true? does not  
> give the image as it appears in the display? Again, it accepts the  
> new color but not the dashed style.
>
>   Thanks for your great help,
>   Ibrahim



From meng at cgl.ucsf.edu  Fri May  9 09:30:57 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 May 2008 09:30:57 -0700
Subject: [Chimera-users] saving a stereo image
In-Reply-To: <54652.160.129.14.233.1210349061.squirrel@vuwebmail.vanderbilt.edu>
References: <1537.160.129.14.81.1209581823.squirrel@vuwebmail.vanderbilt.edu>
	<8A6717DD-3514-477E-8E81-E73E9154E8AD@cgl.ucsf.edu>
	<54652.160.129.14.233.1210349061.squirrel@vuwebmail.vanderbilt.edu>
Message-ID: <611CCD19-63FD-4955-93E9-DD080841D01E@cgl.ucsf.edu>

On May 9, 2008, at 9:04 AM, Pallan, Pradeep S wrote:
>
> Hi Elaine,
> I am trying to save a generate a stereo image by following the  
> instructions:
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ 
> frameimages.html
>
> I captured left eye and right eye images separately, pasted
> them side by side ~65 mm apart, and I see this do not appear as
> stereo. Any comments and instructions? I can send you the image
> if you want to take a look at it.
>
> Thank you very much,
> Pradeep Pallan


Hi Pradeep,
I think you are looking at old documentation.  I don't think the  
current documentation says anything about saving separate images for  
left eye and right eye.

This is the current page:
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ 
print.html#stereo

Here is the blurb from that page, but it is probably better to go to  
the URL because there are helpful hyperlinks:

Stereo. Wall-eye, cross-eye, and red-cyan stereo images can be saved  
by changing the graphics window to the corresponding camera mode with  
the Camera tool (or the command stereo) and using the "same as  
screen" Image camera mode in the Save Image dialog. Another way to  
save cross-eye stereo images is with the "stereo pair" Image camera  
mode; in that case, it does not matter what camera mode is being used  
in the graphics window, but the resulting image will be twice as wide  
as the specified size.

Those approaches should work, assuming you also have a recent version  
of Chimera!
(last production release Nov 2007 or newer)
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




From gregc at cgl.ucsf.edu  Fri May  9 11:23:31 2008
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 9 May 2008 11:23:31 -0700 (PDT)
Subject: [Chimera-users] Dashed H-bond
In-Reply-To: <C865549B-EC87-4331-9B6E-2B3B8DBB0CAD@cgl.ucsf.edu>
References: <C449ECCE.E91%I.moustafa@psu.edu>
	<C865549B-EC87-4331-9B6E-2B3B8DBB0CAD@cgl.ucsf.edu>
Message-ID: <Pine.OSF.4.63.0805091022060.1643258@guanine.cgl.ucsf.edu>

POV-Ray does not support dashed lines directly.  There is a POV-Ray macro 
for dashed lines called Stippellijn described in 
<http://www.stack.nl/~brian/LookingAtNothing_WordPress/wp-content/uploads/2007/08/povray_workshop_snippets.pdf>
that you might try.  I'll look into adding something like that to 
chimera's POV-ray 
output.

 	Greg Couch
 	UCSF Computer Graphics Lab

On Fri, 9 May 2008, Elaine Meng wrote:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sender: chimera-users-bounces at cgl.ucsf.edu
> To: Ibrahim Moustafa <I.moustafa at psu.edu>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Date: Fri, 9 May 2008 09:20:07 -0700
> Subject: Re: [Chimera-users] Dashed H-bond
> Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted
>     mechanism)
> Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted
>     mechanism)
> 
> Dear Ibraham,
> That is a known problem - the result from raytracing may be different
> from the Chimera display in some ways, as listed in the Limitations
> section of this page:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html
>
> This problem is "pseudobonds always shown as sticks, even if shown as
> dashed lines in Chimera"
>
> When you save an image in Chimera without raytracing, it will match
> the display, except the resolution is whatever you specified (usually
> better than the display).  However, when you turn on raytracing (POV-
> Ray option), Chimera writes a separate file describing the display,
> and that separate file is sent to the POV-Ray program.  The
> limitations reflect what information has been written to that
> separate file.  I am guessing it should be possible to describe the
> line as dashed in the file, but we have not written the code to do
> that yet.
>
> In the image-saving dialog, when you turn on "raytrace with POV-Ray"
> there will also be a button "POV-Ray Options" - if you click that,
> there is an option to "Keep POV-Ray input files" if you want to see
> what that separate file looks like.  It is usually quite large.  It
> gets the same name as the saved image except ending in ".pov"  If you
> know a lot about POV-Ray, you could edit the file to contain the
> information you want and run POV-Ray on it separately, but it would
> not be easy.
>
> Currently I can only recommend turning off raytracing to show dashed
> lines.  Also, if your display has a lot of details in it, often the
> image looks better without raytracing, in my opinion.
> 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 May 9, 2008, at 8:58 AM, Ibrahim Moustafa wrote:
>
>>    Dear Chimera Team,
>>   Few weeks ago I asked about how to make H-bonds with dashed line
>> style, I got your great help in that.
>>   So, I can make the H-bond with the color and style I want;
>> however, when saving the image (with POV true)
>>  I got the H-bond appeared with the new chosen color but not as
>> dashed line shown in the display.
>>   But, if I save the image with POVray option false, I got the same
>> style shown in the display (new color and dashed line).
>>
>>   The question is why saving the image using ?POV true? does not
>> give the image as it appears in the display? Again, it accepts the
>> new color but not the dashed style.
>>
>>   Thanks for your great help,
>>   Ibrahim
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

From Steven.J.Kolodziej at uth.tmc.edu  Fri May  9 15:20:11 2008
From: Steven.J.Kolodziej at uth.tmc.edu (Kolodziej, Steven J)
Date: Fri, 9 May 2008 17:20:11 -0500
Subject: [Chimera-users] Number of voxels?
Message-ID: <1F423A0A78EC5442A3DE45AF10059EAE0557A8F1@UTHEVS3.mail.uthouston.edu>

I was wondering if anyone knows how to tell how many voxels within a bounding box can be assigned to protein signal instead of "empty space" at any given contour/density level?

Thanks,
Steve Kolodziej


From goddard at cgl.ucsf.edu  Fri May  9 15:28:26 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 09 May 2008 15:28:26 -0700
Subject: [Chimera-users] Number of voxels?
In-Reply-To: <1F423A0A78EC5442A3DE45AF10059EAE0557A8F1@UTHEVS3.mail.uthouston.edu>
References: <1F423A0A78EC5442A3DE45AF10059EAE0557A8F1@UTHEVS3.mail.uthouston.edu>
Message-ID: <4824D00A.7070108@cgl.ucsf.edu>

Hi Steve,

  Chimera can measure the volume enclosed in a contour surface using 
menu entry

    Tools / Volume Data / Measure Volume and Area

If the density map has a correct grid spacing set (called voxel size in 
volume viewer dialog Coordinates panel) then the reported volume will be 
in physical units, e.g. cubic Angstroms.  If the grid spacing is set to 
1 or you divide the reported volume by the voxel volume you can get a 
count of the voxels inside the contour.

    Tom




From gregc at cgl.ucsf.edu  Fri May  9 19:20:34 2008
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 9 May 2008 19:20:34 -0700 (PDT)
Subject: [Chimera-users] Dashed H-bond
In-Reply-To: <Pine.OSF.4.63.0805091022060.1643258@guanine.cgl.ucsf.edu>
References: <C449ECCE.E91%I.moustafa@psu.edu>
	<C865549B-EC87-4331-9B6E-2B3B8DBB0CAD@cgl.ucsf.edu>
	<Pine.OSF.4.63.0805091022060.1643258@guanine.cgl.ucsf.edu>
Message-ID: <Pine.OSF.4.63.0805091919340.1643258@guanine.cgl.ucsf.edu>

Dashed line support for POV-Ray will be in the next successful daily 
build.

 	- Greg

On Fri, 9 May 2008, Greg Couch wrote:

> POV-Ray does not support dashed lines directly.  There is a POV-Ray macro for 
> dashed lines called Stippellijn described in 
> <http://www.stack.nl/~brian/LookingAtNothing_WordPress/wp-content/uploads/2007/08/povray_workshop_snippets.pdf>
> that you might try.  I'll look into adding something like that to chimera's 
> POV-ray output.
>
> 	Greg Couch
> 	UCSF Computer Graphics Lab


From hbahudha at fau.edu  Sat May 10 10:27:39 2008
From: hbahudha at fau.edu (Harinathachari Bahudhanapati)
Date: Sat, 10 May 2008 13:27:39 -0400 (EDT)
Subject: [Chimera-users] Renaming chains in a PDB file with two chains
Message-ID: <7968456.1210440459493.JavaMail.hbahudha@fau.edu>

Hi Elaine, 
               Thanks for all the answers you give to our questions. 
They are very helpful as I learn more everyday. I have a question. 

Is there anyway to rename a chain in a PDB file through the GUI? I have 
a few PATCHDOCK generated PDB files with two different chains named 
under  Chain 'A' as #0.1 and #0.2. When I try to get the list of 
hydrogen bonds between these two chains, the chain name 'A'  appears 
for all of the h-bonding pairs. So, I want to have them named Chain A 
and Chain B for easier analysis than scratching my head figuring out 
which h-bond pair is between the chains or with in the chain. I am 
attaching the pdb file. Please help me.

(I thought of renaming the chains in the PDB file going through the PDB 
header (text file) and manually changing the name. But I am not a 
expert if anything goes wrong.)

Sincerely
Hari


From meng at cgl.ucsf.edu  Sat May 10 11:35:36 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 10 May 2008 11:35:36 -0700
Subject: [Chimera-users] Renaming chains in a PDB file with two chains
In-Reply-To: <7968456.1210440459493.JavaMail.hbahudha@fau.edu>
References: <7968456.1210440459493.JavaMail.hbahudha@fau.edu>
Message-ID: <2538BCB8-A331-45D6-B947-206178503ED0@cgl.ucsf.edu>

Hi Hari,
You're welcome!

There is no way to change the chain ID in Chimera.  The only way I  
know is to just text-edit the PDB file.  However, the two chains are  
already distinguishable by their model ID numbers #0.1 and #0.2, so  
there is no reason to give them different chain IDs.

FindHBond ignores interactions between models with the same first  
number and different second numbers, so now you are only getting the  
H-bonds within each chain anyway.  In the PDB, multi-model files like  
that are only used to describe multiple conformations of the same  
structure that are on top of each other (such as from NMR), where you  
wouldn't want them to "see" each other.

So there are two issues, (1) how to find H-bonds between them and (2)  
how to separate the results for H-bonds between the structures and  
within each structure.

(1) You cannot find H-bonds between #0.1 and #0.2 with the FindHBond  
graphical interface (GUI) and your current file.  However, the  
"findhbond" command has an option "interSubmodels true" to include  
those interactions:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html

Alternatively, you can edit your file into two separate files; then  
you could use either the GUI or the command.

(2) You can do separate calculations of inter-model and intra-model H- 
bonds, so you do not have to postprocess the combined results.  Both  
the GUI and the command have options to do those calculations  
separately:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ 
findhbond.html

If you did not edit the file, you have to use the command to  
calculate the H-bonds between the structures, as mentioned above.   
For example, these keywords would give only the H-bonds between the  
structures:

hb intersub true intermod false

You could use either GUI or command to calculate H-bonds within each  
structure.
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 May 10, 2008, at 10:27 AM, Harinathachari Bahudhanapati wrote:

> Hi Elaine,
>                Thanks for all the answers you give to our questions.
> They are very helpful as I learn more everyday. I have a question.
>
> Is there anyway to rename a chain in a PDB file through the GUI? I  
> have
> a few PATCHDOCK generated PDB files with two different chains named
> under  Chain 'A' as #0.1 and #0.2. When I try to get the list of
> hydrogen bonds between these two chains, the chain name 'A'  appears
> for all of the h-bonding pairs. So, I want to have them named Chain A
> and Chain B for easier analysis than scratching my head figuring out
> which h-bond pair is between the chains or with in the chain. I am
> attaching the pdb file. Please help me.
>
> (I thought of renaming the chains in the PDB file going through the  
> PDB
> header (text file) and manually changing the name. But I am not a
> expert if anything goes wrong.)
>
> Sincerely
> Hari



From meng at cgl.ucsf.edu  Sat May 10 11:45:16 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 10 May 2008 11:45:16 -0700
Subject: [Chimera-users] Renaming chains in a PDB file with two chains
In-Reply-To: <2538BCB8-A331-45D6-B947-206178503ED0@cgl.ucsf.edu>
References: <7968456.1210440459493.JavaMail.hbahudha@fau.edu>
	<2538BCB8-A331-45D6-B947-206178503ED0@cgl.ucsf.edu>
Message-ID: <98756E68-6032-4EE3-96B8-E0A758542838@cgl.ucsf.edu>

Whoops!! should be

hb intersub true intramod false

I tried both and then copied the wrong one.  "intermod" instead of  
"intramod" would give only the H-bonds within structures, using  
neither of those keywords would give the total.

On May 10, 2008, at 11:35 AM, Elaine Meng wrote:

> For example, these keywords would give only the H-bonds between the
> structures:
>
> hb intersub true intermod false
>



From arlamber at fhcrc.org  Thu May  8 14:34:47 2008
From: arlamber at fhcrc.org (Abigail Lambert)
Date: Thu, 08 May 2008 14:34:47 -0700
Subject: [Chimera-users] Program won't open
Message-ID: <C448C007.219%arlamber@fhcrc.org>

Hello - 

I'm using a MacBook Pro, OS X (10.4.11), and I had been successfully using
Chimera for a while.  Then all of sudden, the program will no longer open.
The Chimera icon blinks once in the taskbar, and then it disappears and the
program does NOT open.  I tried uninstalling and re-installing, but this
does not help. 

Any suggestions?
 
Thanks!

 - Abbie - 





From meng at cgl.ucsf.edu  Mon May 12 09:41:48 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 May 2008 09:41:48 -0700
Subject: [Chimera-users] Program won't open
In-Reply-To: <C448C007.219%arlamber@fhcrc.org>
References: <C448C007.219%arlamber@fhcrc.org>
Message-ID: <8552D095-D059-4432-99A8-AFAB87762F6F@cgl.ucsf.edu>

Hi Abigail,
There was a daily build from last week that had this problem,  
resulting from the switch to a new version of Tk.   However, the  
problem has been fixed - if you get the most recent daily build (from  
last night), it should work - I'm using it now on my 10.4.11 Mac!
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 May 8, 2008, at 2:34 PM, Abigail Lambert wrote:

> Hello -
>
> I'm using a MacBook Pro, OS X (10.4.11), and I had been  
> successfully using
> Chimera for a while.  Then all of sudden, the program will no  
> longer open.
> The Chimera icon blinks once in the taskbar, and then it disappears  
> and the
> program does NOT open.  I tried uninstalling and re-installing, but  
> this
> does not help.
>
> Any suggestions?
>
> Thanks!
>
>  - Abbie -
>


From goddard at cgl.ucsf.edu  Mon May 12 10:12:39 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Mon, 12 May 2008 10:12:39 -0700
Subject: [Chimera-users] Encoding movie by hand
In-Reply-To: <web-4053253@guppy.mail.virginia.edu>
References: <200805072107.m47L7CVl1827393@guanine.cgl.ucsf.edu>
	<48224067.90604@cgl.ucsf.edu> <web-4053253@guppy.mail.virginia.edu>
Message-ID: <48287A87.1030007@cgl.ucsf.edu>

Anindito Sen wrote:
>
> Hi Tom
>
> How can we make a movie (not morphing) out of several still snaps 
> (.jpg) saved from  of many density maps.
> using chimera.
>
> Thanks
> qandy
>
> Dr. Anindito Sen (Ph.D)
> Research Associate , Dept. of Biochemistry and Molecular Genetics 
> University of Virginia
> Box 800733 Charlottesville, VA 22908



Hi Qandy,

  You can create a movie directly from a set of images using the ffmpeg 
executable included in the Chimera distribution.  When you make a movie 
using Chimera it runs the ffmpeg executable to make the movie file and 
the options used are printed to the Chimera reply log (Favorites / Reply 
Log).  For example, in the reply log I see

ARG_LIST IS  ['-r', '25', '-i', '/tmp/chimovie_JgKl-%05d.ppm', '-y', 
'-f', 'mov', '-b', '2000', '-bufsize', '200', 
'/Users/goddard/chimera_movie.mov']
Movie saved to /Users/goddard/chimera_movie.mov

so the ffmpeg command used was:

ffmpeg -r 25 -i /tmp/chimovie_JgK1-%05d.ppm -y -f mov -b 2000 -bufsize 200

You could run a similar command from a shell to encode a movie outside 
of Chimera.  The files are specified by the "-i" option.  In the example 
they are ppm format but jpg will work too.   The %05d means that the 
file names ended in a 5-digit number with leading zeros (e.g. 
chimovie_JgK1-00000.ppm, chimovie_JgK1-00001.ppm, ...).  The -r option 
indicates frame rate (25 frames per second).  The -f option is output 
format (mov = quicktime).  The -b option is bit rate (Kbits/sec) and 
controls output quality.  The -y option means to overwrite the output 
file if it already exists.  For complete ffmpeg options see online docs:

    http://ffmpeg.mplayerhq.hu/ffmpeg-doc.html

The Chimera copy of ffmpeg is in the distribution in chimera/bin (or on 
Mac in Chimera.app/Contents/Resources/bin).

    Tom



From goddard at cgl.ucsf.edu  Mon May 12 11:19:09 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Mon, 12 May 2008 11:19:09 -0700
Subject: [Chimera-users] measure volume area request
In-Reply-To: <558F6B7F5360E046B597A008686EAFBF51A0B6@EXCHV1.lj.ad.scripps.edu>
References: <47FA3213.1020304@ebi.ac.uk> <47FA6E38.6080006@cgl.ucsf.edu>
	<558F6B7F5360E046B597A008686EAFBF51A0B6@EXCHV1.lj.ad.scripps.edu>
Message-ID: <48288A1D.7070103@cgl.ucsf.edu>

Edward Brignole wrote:
> Tom,
>  
> I have a request for display of the measure volume area tool - can it 
> be moved from "tools" to "features" such that it is displayed in the 
> volume viewer along with color, voxel size, etc.  The problem I have 
> is that frequently I have 30 or so volumes to open at once and then 
> need to independently go through them and set density thresholds.  
> It's really a pain to have to select the volume once in the volume 
> viewer and then again select the same volume in the measure tool then 
> go back to the viewer and adjust threshold.  After doing this 30 
> times, you'll find that most of the effort is spent making sure to 
> select the same volume in both menus so that the selected volume that 
> you are adjusting is the same volume being measured.
>  
> Thankfully, I did however find a python script that you emailed a year 
> ago that I can steal a few lines out of to adjust the thresholds 
> automatically so that the enclosed surface of each model has the 
> appropriate volume in A^3.  BTW, I really like your hidedust.py as 
> well, however once I've executed that script adjusting the threshold 
> in the volume viewer does nothing to the displayed or measured volumes 
> - I'm using the snapshot from a week or so ago.
>  
> Ed
>  
> Ed Brignole
> Asturias Lab, CB227
> The Scripps Research Institute
>  
Hi Ed,

  I agree it would be helpful to have a measured volume/area panel in 
the volume dialog.  I'll add that to our requested features list.

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

It still needs to be a separate dialog too because it works on surfaces 
that are not from volume data (e.g. molecular surfaces).

  The hidedust.py script hides connected components smaller than a 
specified volume.  But the Measure Volume and Area dialog displays 
values for the entire surface, hidden or not.  So those values don't 
change.  Currently there is no provision in the volume/area measurement 
to exclude the hidden part of the surface.  You also say that changing 
the contour level does not change the displayed surface.  As soon as you 
change the contour level the whole surface is replaced.  The hidedust.py 
script only acts on the surface that is shown at the time you run it, 
not on future surfaces, so all the dust should come back.  You seem to 
say this is not what happens in your use.  I've attached the hidedust.py 
script to this email in case you are using a different version.

    Tom


-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: hidedust.py
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080512/af92abff/attachment.ksh>

From goddard at cgl.ucsf.edu  Mon May 12 12:02:57 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Mon, 12 May 2008 12:02:57 -0700
Subject: [Chimera-users] Drawing a circle or square
In-Reply-To: <8A6717DD-3514-477E-8E81-E73E9154E8AD@cgl.ucsf.edu>
References: <1537.160.129.14.81.1209581823.squirrel@vuwebmail.vanderbilt.edu>
	<8A6717DD-3514-477E-8E81-E73E9154E8AD@cgl.ucsf.edu>
Message-ID: <48289461.6020609@cgl.ucsf.edu>

Hi Pradeep,

  Here's a Python script to draw a circle.   The inner/outer radius, 
subdivisions, color are set at the bottom of the script and you can edit 
those.  You just open the script with File / Open to create the circle.  
Use the "active" buttons in Model Panel to move the circle to the 
desired position and orientation.

  This script works with Chimera 1.2502 and other recent daily builds.  
It will not work with the Nov 2007 production release.

    Tom

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: circle.py
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080512/24dad366/attachment.ksh>

From pett at cgl.ucsf.edu  Tue May 13 09:11:51 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 13 May 2008 09:11:51 -0700
Subject: [Chimera-users] Fwd: Help needed
References: <20080513115815.y1ylp6sag0kccgkk@webmail.iu.edu>
Message-ID: <6EE1C9AD-7A4E-4FF0-83C4-2AEEA1656940@cgl.ucsf.edu>



Begin forwarded message:

> From: "Bagchi,  Angshuman" <abagchi at iupui.edu>
> Date: May 13, 2008 8:58:15 AM PDT
> To: chimera-users at cgl.ucsf.edu
> Cc: chimera-bugs at cgl.ucsf.edu
> Subject: Help needed
>
> Hi,
> I am a student of IUPUI (indiana-University-Purdue University- 
> Indianapolis). I would like to know how chimera can be used to  
> select the amino acid residues of one chain of a protein, which are  
> within a certain distance (say 10A) of another chain of the same  
> protein.
> For example, the pdb 1o6s has two chains A and B. I would like to  
> find what amino acid residues of A chain of 1o6s are within 10A of B  
> chain of 1o6s.
> I am eagerly expecting a reply from your end.
> Thanks
> Ang
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080513/9fbc894e/attachment.html>

From meng at cgl.ucsf.edu  Tue May 13 09:35:44 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 13 May 2008 09:35:44 -0700
Subject: [Chimera-users] Fwd: Help needed
In-Reply-To: <6EE1C9AD-7A4E-4FF0-83C4-2AEEA1656940@cgl.ucsf.edu>
References: <20080513115815.y1ylp6sag0kccgkk@webmail.iu.edu>
	<6EE1C9AD-7A4E-4FF0-83C4-2AEEA1656940@cgl.ucsf.edu>
Message-ID: <4574DACF-53F6-410C-AF94-3040C1622098@cgl.ucsf.edu>

>
> Begin forwarded message:
>> From: "Bagchi,  Angshuman" <abagchi at iupui.edu>
>> Date: May 13, 2008 8:58:15 AM PDT
>> To: chimera-users at cgl.ucsf.edu
>> Subject: Help needed
>> Hi,
>> I am a student of IUPUI (indiana-University-Purdue University- 
>> Indianapolis). I would like to know how chimera can be used to  
>> select the amino acid residues of one chain of a protein, which  
>> are within a certain distance (say 10A) of another chain of the  
>> same protein.
>> For example, the pdb 1o6s has two chains A and B. I would like to  
>> find what amino acid residues of A chain of 1o6s are within 10A of  
>> B chain of 1o6s.
>> I am eagerly expecting a reply from your end.
>> Thanks
>> Ang


Hi Ang,
Sure, it is quite simple.  You can do it with a command or with menu  
operations.

(A) Command (show command line with "Favorites... Command Line" in  
the menu):
select :.a & :.b z<10
(use "z" to get whole residues, "za" to get just atoms)

Command-line specifications including zones are documented here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
frameatom_spec.html

(B) Menu:
Select... Chain... B
Select... Zone     (specify <10 angstroms and whether you want whole  
residues or not, click OK)
Select... Selection Mode     (change to "intersect")
Select... Chain... A
(change selection mode back to "replace" so you don't get confused  
later)

Either way, you can then write a list of the residues in the current  
selection with "Actions... Write List" in the menu - in the resulting  
dialog, indicate you want "selected residues."

In fact you can do more sophisticated things such as identify  
contacts using VDW radii and identify H-bonding residues, and write  
out atom-atom distances.  I am in the middle of writing a tutorial  
that includes all this stuff, but it is not done yet.  In the  
meanwhile, this previous chimera-users message has some additional  
information:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002425.html

See also "Find Clashes/Contacts"
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ 
findclash.html
and "FindHBond"
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ 
findhbond.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




From abagchi at iupui.edu  Tue May 13 08:58:15 2008
From: abagchi at iupui.edu (Bagchi,  Angshuman)
Date: Tue, 13 May 2008 11:58:15 -0400
Subject: [Chimera-users] Help needed
Message-ID: <20080513115815.y1ylp6sag0kccgkk@webmail.iu.edu>

Hi,
I am a student of IUPUI (indiana-University-Purdue 
University-Indianapolis). I would like to know how chimera can be used 
to select the amino acid residues of one chain of a protein, which are 
within a certain distance (say 10A) of another chain of the same 
protein.
For example, the pdb 1o6s has two chains A and B. I would like to find 
what amino acid residues of A chain of 1o6s are within 10A of B chain 
of 1o6s.
I am eagerly expecting a reply from your end.
Thanks
Ang



From ibdeno at gmail.com  Thu May 15 00:43:25 2008
From: ibdeno at gmail.com (=?ISO-8859-1?Q?Miguel_Ortiz-Lombard=EDa?=)
Date: Thu, 15 May 2008 09:43:25 +0200
Subject: [Chimera-users] electrostatic potential colored surfaces script
Message-ID: <d5dc3ecc0805150043h3b50afdev95ab93c28a6208a1@mail.gmail.com>

Dear all,

I wonder if someone has written and would share a script to sequentially
read a pdb file, show its molecular surface and color it by the
electrostatic potential from an appropriate .dx file.

Cheers,


Miguel
-- 
http://www.pangea.org/mol/spip.php?rubrique2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en libert?
Dans les jardins mal fr?quent?s!
Georges Brassens
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080515/8339bffc/attachment.html>

From goddard at cgl.ucsf.edu  Thu May 15 11:58:58 2008
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 15 May 2008 11:58:58 -0700
Subject: [Chimera-users] electrostatic potential colored surfaces script
In-Reply-To: <d5dc3ecc0805150043h3b50afdev95ab93c28a6208a1@mail.gmail.com>
References: <d5dc3ecc0805150043h3b50afdev95ab93c28a6208a1@mail.gmail.com>
Message-ID: <482C87F2.5030508@cgl.ucsf.edu>

Hi Miguel,

   Unfortunately we do not yet have a Chimera command equivalent of the 
Surface Color dialog which does the coloring by electrostatic potential. 
  So it requires a Python script to do that step.  I've attached a 
Python script that opens a PDB, makes the molecular surface, opens the 
electrostatic potential map and colors the surface.

   I hope to add the Chimera command that does the coloring soon which 
will make this much simpler.

	Tom


From goddard at cgl.ucsf.edu  Thu May 15 12:06:12 2008
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 15 May 2008 12:06:12 -0700
Subject: [Chimera-users] electrostatic potential colored surfaces script
In-Reply-To: <d5dc3ecc0805150043h3b50afdev95ab93c28a6208a1@mail.gmail.com>
References: <d5dc3ecc0805150043h3b50afdev95ab93c28a6208a1@mail.gmail.com>
Message-ID: <482C89A4.3080602@cgl.ucsf.edu>

Hi Miguel,

   Guess it would help if I really attached the script.

   You open the script with File/Open... to run it.  The paths to the 
files appear in the script and you'll need to edit those.

	Tom
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: escolor.py
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080515/39d2ffba/attachment.ksh>

From goddard at cgl.ucsf.edu  Thu May 15 18:08:24 2008
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 15 May 2008 18:08:24 -0700
Subject: [Chimera-users] Action  focus
Message-ID: <482CDE88.1000101@cgl.ucsf.edu>

I made Action / Focus work on selected surfaces.  Also I made the 
none-implies-all rule include surfaces in the "all".  So Actions / Color 
/ green will color everything green including surfaces if nothing is 
selected.  I fear this a bit because volume user often have tens of maps 
and pdb models open and could shoot themselves in the foot pretty 
easily.  These changes were a bit more complicated than expected and may 
be a buggy.  Report anything suspicious or wait until next week when I 
shake it down a bit more.

	Tom


From fabian.glaser at gmail.com  Sun May 18 04:20:07 2008
From: fabian.glaser at gmail.com (Fabian Gmail)
Date: Sun, 18 May 2008 14:20:07 +0300
Subject: [Chimera-users] building linker peptide
Message-ID: <483010E7.5070603@gmail.com>

Dear Chimera experts,

I am willing to build a peptide "linker" connecting two different pdb 
chains, that is to connect two existing pdb chains with a new peptide 
chain, and if possible minimize it. Is it possible to do that wich 
chimera? I know the command addaa, but to my best understanding this 
command it's not able to connect the end of the new peptide with the 
beginning of the second chain.

Any suggestions will be greatly appreciated.

Best regards and thanks a lot in advance,

Fabian

-- 
Fabian Glaser, PhD

Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

Web:   http://bku.technion.ac.il
Email: fglaser at tx.technion.ac.il
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396



From meng at cgl.ucsf.edu  Sun May 18 09:38:01 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 18 May 2008 09:38:01 -0700
Subject: [Chimera-users] building linker peptide
In-Reply-To: <483010E7.5070603@gmail.com>
References: <483010E7.5070603@gmail.com>
Message-ID: <7217A6E5-86B3-4C49-A714-AD47699DD97E@cgl.ucsf.edu>

Dear Fabian,
You can add the final bond with the "Build Structure" tool (under  
Tools... Structure Editing) or the command "bond":
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#addbond
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html

You may want to rotate torsions to get the ends closer together before  
adding the bond:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#adjust

You may already know about the "Minimize Structure" tool and  
"minimize" command.  You can allow only parts of the structure to move  
during minimization.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html

However, this process will not likely generate a high-quality model,  
as minimization only goes so far in removing strain and will not cross  
barriers to find more likely conformations.  It may suffice if you are  
aware (and don't mind) that it is a rough model, or you may use the  
structure as a starting point for MD or MC simulations with another  
program.  Alternatively, you could look into other approaches to  
building the linker.  A few programs that might do that are Modeller,  
MolIDE, RAPPER:
http://salilab.org/modeller/index.html
http://dunbrack.fccc.edu/molide/molide.php
http://mordred.bioc.cam.ac.uk/~rapper/
(I haven't tried to use any of these for de novo loop building,  
however).

I should also mention that "addaa", unlike "swapaa", currently doesn't  
use rotamer libraries, so it may not give the best sidechain  
conformations.

There is a little more discussion about Chimera and protein modeling  
in this post:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-January/002202.html

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 May 18, 2008, at 4:20 AM, Fabian Gmail wrote:

> Dear Chimera experts,
> I am willing to build a peptide "linker" connecting two different pdb
> chains, that is to connect two existing pdb chains with a new peptide
> chain, and if possible minimize it. Is it possible to do that wich
> chimera? I know the command addaa, but to my best understanding this
> command it's not able to connect the end of the new peptide with the
> beginning of the second chain.
>
> Any suggestions will be greatly appreciated.
> Best regards and thanks a lot in advance,
> Fabian


From odonnell at chem.fsu.edu  Mon May 19 06:30:34 2008
From: odonnell at chem.fsu.edu (odonnell at chem.fsu.edu)
Date: Mon, 19 May 2008 09:30:34 -0400
Subject: [Chimera-users] saving multiple maps
Message-ID: <20080519093034.k1kt0n5m0ocg4s4s@webmail.chem.fsu.edu>

Similar to saving multiple PDB's as a single PDB file, is there a way  
to save multiple  maps (e.g mrc or ccp4) as a single map file. Thanks  
in advance for anything which could help me out!!
-Jason

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.



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



From goddard at cgl.ucsf.edu  Mon May 19 14:30:18 2008
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 19 May 2008 14:30:18 -0700
Subject: [Chimera-users] saving multiple maps
In-Reply-To: <20080519093034.k1kt0n5m0ocg4s4s@webmail.chem.fsu.edu>
References: <20080519093034.k1kt0n5m0ocg4s4s@webmail.chem.fsu.edu>
Message-ID: <4831F16A.2020408@cgl.ucsf.edu>

Hi Jason,

   Saving multiple maps in a single file is possible with a file format 
that is only used by Chimera.  I don't recommend it.  Maybe you are 
interested in adding one map to another.  Chimera doesn't do that 
currently though I could add it.

   Chimera does allow you to recalculate a map at the grid points of a 
second map using interpolation, called "resampling".  The resulting map 
can be saved and can be added point-wise to other maps having the same 
grid using other software (e.g. EMAN).  To resample a volume  use the 
"vop" command (volume operation) with the resample option, for example,

	volume #1 resample onGrid #0

calculates the map with model id 1 on the grid of map with id 0 and 
creates a new map.

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

   If your goal is just to save the fitting of one map into a second map 
then you can save the Chimera session.  But if you want to be able to 
open those maps in another program and have them align you would need to 
do the above resampling so that both maps have the same grid and save 
the resulting map.  Then other programs will show both maps with the 
desired alignment.

   Here are more details about the Chimera format the can handle 
multiple maps in one file.  First, there are no commonly used file 
formats that I know of for x-ray or EM maps that hold multiple maps. 
Some formats of this sort are used in light microscopy for handling 
multi-wavelength images.  There is a prototype file format called 
"Chimera map" based on HDF5 that can do keep many maps in one file, but 
only Chimera reads and writes this format.  You write multiple maps to 
one cmap file with the "volume" command with "saveFormat cmap".  The 
"append True" option allows you to append to an existing file.  I don't 
recommend using this as it was written just to explore desirable 
capabilities for a new EM file format.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output


	Tom


From dchen at caltech.edu  Tue May 20 14:43:44 2008
From: dchen at caltech.edu (David Chenoweth)
Date: Tue, 20 May 2008 14:43:44 -0700
Subject: [Chimera-users] reporting sigma values for electron density maps
Message-ID: <6AC3326C-DAF7-4B82-8D61-BD8D1910366C@caltech.edu>

Hi!

Can you please let me know if there is a way to report or set the  
sigma value for an electron density map from a high resolution crystal  
structure. I am using a ccp4 FWT.map and DELFWT.map file for  
structures <1.2 angstrom resolution. Can I somehow find the sigma  
value that corresponds to the Level setting in the Volume viewer?

Thanks,
Dave Chenoweth

**********************************************
David M. Chenoweth
California Institute of Technology
Division of Chemistry and Chemical Engineering
Mail Code: 164-30
1200 California Boulevard, 91125 Pasadena
California, USA

Phone: 626-395-6074
Email: dchen at caltech.edu
**********************************************




From meng at cgl.ucsf.edu  Tue May 20 15:49:39 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 20 May 2008 15:49:39 -0700
Subject: [Chimera-users] reporting sigma values for electron density maps
In-Reply-To: <6AC3326C-DAF7-4B82-8D61-BD8D1910366C@caltech.edu>
References: <6AC3326C-DAF7-4B82-8D61-BD8D1910366C@caltech.edu>
Message-ID: <2176D8A1-DF71-4566-A4DB-A25DC71E29D7@cgl.ucsf.edu>

Hi David,
The Tools menu in Volume Viewer includes "Volume Mean, SD, RMS" to  
report statistics for the current set of data.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ 
volstats.html

You probably want to make sure the whole map is displayed with step  
size 1 beforehand.
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 May 20, 2008, at 2:43 PM, David Chenoweth wrote:

> Hi!
>
> Can you please let me know if there is a way to report or set the
> sigma value for an electron density map from a high resolution crystal
> structure. I am using a ccp4 FWT.map and DELFWT.map file for
> structures <1.2 angstrom resolution. Can I somehow find the sigma
> value that corresponds to the Level setting in the Volume viewer?
>
> Thanks,
> Dave Chenoweth
>


From goddard at cgl.ucsf.edu  Tue May 20 15:54:10 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Tue, 20 May 2008 15:54:10 -0700
Subject: [Chimera-users] reporting sigma values for electron density maps
In-Reply-To: <6AC3326C-DAF7-4B82-8D61-BD8D1910366C@caltech.edu>
References: <6AC3326C-DAF7-4B82-8D61-BD8D1910366C@caltech.edu>
Message-ID: <48335692.9060409@cgl.ucsf.edu>

Hi Dave,

  Chimera can report the mean, standard deviation and root mean square 
map value using menu entry

    Tools / Volume Data / Volume Mean, SD, RMS

The values using whatever normalization the map file has.  If you divide 
the threshold level you set in the volume dialog by the RMS value you 
will get a sigma value.  Actually I'm not sure if that is correct -- 
depends on the definition of sigma.  Maybe you have to take the volume 
dialog number, subtract the mean and divide by the SD.  The reported SD 
and RMS differ only in that the SD is the standard deviation of the map 
about the mean while the RMS is the standard deviation about 0.

  Allowing the volume dialog to show the sigma values directly is on our 
requested features list (item 88) but has not yet been implemented.

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

    Tom


David Chenoweth wrote:
> Hi!
>
> Can you please let me know if there is a way to report or set the  
> sigma value for an electron density map from a high resolution crystal  
> structure. I am using a ccp4 FWT.map and DELFWT.map file for  
> structures <1.2 angstrom resolution. Can I somehow find the sigma  
> value that corresponds to the Level setting in the Volume viewer?
>
> Thanks,
> Dave Chenoweth
>   



From meng at cgl.ucsf.edu  Wed May 21 09:27:11 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 21 May 2008 09:27:11 -0700
Subject: [Chimera-users] Low resolution surface model
In-Reply-To: <4833B149.6000405@fourmentinguilbert.org>
References: <4833B149.6000405@fourmentinguilbert.org>
Message-ID: <083DFD5F-1651-4449-938F-54779EE10675@cgl.ucsf.edu>


On May 20, 2008, at 10:21 PM, Damien Larivi?re wrote:
> Dear Elaine,
> Here is what I would like to do with Chimera :
>
> From Tools/Structure analysis/sequence, it is possible to copy a  
> portion of the aminoacid sequence of a protein and then to  
> highlight in an other color this portion of sequence in a high  
> resolution surface model (Actions / surface / show).
>
> I would like to highlight a given portion of sequence but in a low  
> resolution surface model. I tried High-Order Structure / Multiscale  
> models with no success.
>
> Thanks for you help and congratulations for the work you perform.
> Damien
> ------------------------------------------
> Damien Larivi?re
> Fourmentin-Guilbert Scientific Foundation
> 2 Av. du Pav? Neuf, 93160 Noisy-le-Grand, France
> Phone : + 33 1 43 03 06 20
> Cell phone : +33 6 82 19 81 32
> damien.lariviere at fourmentinguilbert.org
>

Hi Damien,
You can color a low-resolution surface for certain residues, but it  
takes an additional step as compared to coloring the high-resolution  
surface.  Another difference is that it is done by distance cutoff,  
because it is no longer clear exactly which atom goes with which  
point on the surface.

(1) First create the low-resolution surface.  I can think of two  
different ways:

   (a) Multiscale Models - click "Make Models" and that will create a  
separate low-res surface for each chain.  In that dialog, if you  
select "All" chains you can then edit the resolution value for those  
surfaces.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ 
framemulti.html

   (b) command "molmap" - it makes a density map from the atomic  
coordinates, which you can then display as an isosurface.  The Volume  
Viewer tool is automatically opened to show the density; in that  
tool, you can drag a bar on the histogram to change the contour  
level.  In this case, all the atoms in the structure are used, and so  
you would get one "blob" (depending on contour level, though) rather  
than separate surfaces per chain.  Volume Viewer has many additional  
options including surface smoothing (see Features... Surface and Mesh  
options).
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ 
framevolumeviewer.html

(2) Select the residues and perform the coloring.  This can be done  
exactly the same as for the high-resolution surface, and there are  
many different ways.  To select the residues, you can use the  
Sequence tool (as you described), or the Select menu, or commands; to  
perform the coloring, you can use Actions...Color or the "color"  
command.  However, the low-res surface will not be colored yet...

(3) Use Color Zone (under Tools.... Volume Data) to color the surface  
to match the atoms you just colored.  This just uses a simple  
distance cutoff and colors parts of the surface to match the closest  
atoms.  After clicking Color, you can just drag the slider to change  
the distance cutoff.

You're welcome!  I hope this helps,
Elaine

P.S. we are working on better integration of different kinds of  
surfaces, so this procedure may change in the future
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html





From meng at cgl.ucsf.edu  Wed May 21 09:59:48 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 21 May 2008 09:59:48 -0700
Subject: [Chimera-users] building linker peptide
In-Reply-To: <4833DD54.3080806@technion.ac.il>
References: <483010E7.5070603@gmail.com>
	<7217A6E5-86B3-4C49-A714-AD47699DD97E@cgl.ucsf.edu>
	<4833DD54.3080806@technion.ac.il>
Message-ID: <21800AD8-5DD9-4B7C-9DDB-B5ACD075B368@cgl.ucsf.edu>

On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
> Another question regarding this issue, I succeded to make a new  
> bond and minimize it between two chains, A and B, in the same pdb.  
> But this created apparently a problem with the residue numbering  
> and Nterm recognition, since when I tried to add an additional  
> linker to the chimera I created, I got the following error message:
>
> "No MMTK name for atom "H" in standard residue ALA"
>
> I suspect that this is related to the fact that I still have two  
> chains, and Chimera does not identified the new bond, or something  
> similar.
>
> Is there a way to automatically rename the newly unified chains?
> Any suggetion will be highly appreciated.

Hi Fabian,
There is no automatic way to change chain ID.  Only the ugly manual  
text-editing way, sorry!  I guess that the ATOM part of the file no  
longer agreed with the SEQRES part of the file.

It might work to simply delete that atom, if it looks like it is extra.

However, I would probably go back to a PDB file saved after you added  
all your linker residues and edit it to remove all the lines except  
the coordinates (the ATOM and HETATM lines), remove the chain IDs,  
and renumber all the residues.  It is necessary to renumber the  
residues because there may be residues with the same number in the  
different chains, and now there would be no way to tell them apart  
(for example, two different residues numbered 10, which used to be  
residue 10 in A and residue 10 in B).   Unfortunately you will lose  
the ability to use the "familiar" residue numbering within the second  
chain.

I attached a fortran (f77) program to do this editing, but I realize  
you may not be able to use it depending on your computing  
environment.  If you are on some unix-type computer you would just  
compile it with something like:

f77 renum2.f -o renum

Then execute it with

renum

It would ask for the names of the input and output PDB files and what  
residue number to start with.

Then you would have to do the addh/addcharge/minimization stuff  
again, sorry.  I think it would already have the bond you wanted,  
however.

Maybe someone else can think of a more elegant approach.
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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: renum2.f
Type: application/octet-stream
Size: 1889 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080521/59173ecc/attachment.obj>
-------------- next part --------------




From pett at cgl.ucsf.edu  Wed May 21 11:34:27 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 21 May 2008 11:34:27 -0700
Subject: [Chimera-users] building linker peptide
In-Reply-To: <21800AD8-5DD9-4B7C-9DDB-B5ACD075B368@cgl.ucsf.edu>
References: <483010E7.5070603@gmail.com>
	<7217A6E5-86B3-4C49-A714-AD47699DD97E@cgl.ucsf.edu>
	<4833DD54.3080806@technion.ac.il>
	<21800AD8-5DD9-4B7C-9DDB-B5ACD075B368@cgl.ucsf.edu>
Message-ID: <0CB10640-4BA8-4F68-A2C6-148708636B84@cgl.ucsf.edu>

Just deleting the SEQRES records _might_ be good enough.  Otherwise  
go with what Elaine wrote.

--Eric

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

On May 21, 2008, at 9:59 AM, Elaine Meng wrote:

> On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
>> Another question regarding this issue, I succeded to make a new  
>> bond and minimize it between two chains, A and B, in the same pdb.  
>> But this created apparently a problem with the residue numbering  
>> and Nterm recognition, since when I tried to add an additional  
>> linker to the chimera I created, I got the following error message:
>>
>> "No MMTK name for atom "H" in standard residue ALA"
>>
>> I suspect that this is related to the fact that I still have two  
>> chains, and Chimera does not identified the new bond, or something  
>> similar.
>>
>> Is there a way to automatically rename the newly unified chains?
>> Any suggetion will be highly appreciated.
>
> Hi Fabian,
> There is no automatic way to change chain ID.  Only the ugly manual  
> text-editing way, sorry!  I guess that the ATOM part of the file no  
> longer agreed with the SEQRES part of the file.
>
> It might work to simply delete that atom, if it looks like it is  
> extra.
>
> However, I would probably go back to a PDB file saved after you  
> added all your linker residues and edit it to remove all the lines  
> except the coordinates (the ATOM and HETATM lines), remove the  
> chain IDs, and renumber all the residues.  It is necessary to  
> renumber the residues because there may be residues with the same  
> number in the different chains, and now there would be no way to  
> tell them apart (for example, two different residues numbered 10,  
> which used to be residue 10 in A and residue 10 in B).    
> Unfortunately you will lose the ability to use the "familiar"  
> residue numbering within the second chain.
>
> I attached a fortran (f77) program to do this editing, but I  
> realize you may not be able to use it depending on your computing  
> environment.  If you are on some unix-type computer you would just  
> compile it with something like:
>
> f77 renum2.f -o renum
>
> Then execute it with
>
> renum
>
> It would ask for the names of the input and output PDB files and  
> what residue number to start with.
>
> Then you would have to do the addh/addcharge/minimization stuff  
> again, sorry.  I think it would already have the bond you wanted,  
> however.
>
> Maybe someone else can think of a more elegant approach.
> 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
>
> <renum2.f>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080521/fde548f3/attachment.html>

From mc3077 at columbia.edu  Wed May 21 13:06:07 2008
From: mc3077 at columbia.edu (Magali Cottevieille)
Date: Wed, 21 May 2008 16:06:07 -0400
Subject: [Chimera-users] Stereo projection
Message-ID: <483480AF.9020604@columbia.edu>

Hi,

Is there any way, with two projectors piloted by two graphic cards, to 
send from Chimera the stereo left eye view onto one, and the stereo 
right eye view onto the other one ? These two projectors are meant to be 
used with filters and special glasses to create a 3D view.
Thanks for your help!

-- 
Magali Cottevieille, Ph.D.
Howard Hughes Medical Institute,
Department of Biochemistry and Molecular Biophysics,
630 W 168th St, P&S Black Building 2-221
New York, NY 10032 

Ph:  (+1) 212-305-9521
Fax: (+1) 212-305-9500

Email: mc3077 at columbia.edu
       magali.cottevieille at gmail.com



From sludtke at bcm.edu  Wed May 21 14:18:26 2008
From: sludtke at bcm.edu (Steven Ludtke)
Date: Wed, 21 May 2008 16:18:26 -0500
Subject: [Chimera-users] Stereo projection
Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C@bcm.edu>

Yes, we have done this before, though I don't remember with absolute  
certainty if we
did it with chimera. You don't use 2 video cards normally, but rather  
1 card with 2
outputs. Also, you will need one of the 'professional' cards where the  
driver supports
stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea  
stereo drivers then
have a mode for this type of stereo, or at least that's my memory, it  
was a year or two
ago when we demonstrated this. You need:

2 identical projectors which permit geometry correction so their  
corners can be exactly aligned
2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj-pfilt-3x3.html 
) for $20 a pair
linear polarizing glasses (from the same site)
Quadro or similar GFX card

Note that with this type of stereo, you could technically make this  
work with any old dual
output 3-D card, but you would have to write the visualization  
software so it would open
2 display windows with slightly different orientations that you could  
then manually (or
automatically) position on each of the 2 projectors.

We did this just as an initial proof of concept, and haven't managed  
to get back to it again,
though we keep meaning to, as it is MUCH cheaper than the commercial  
solutions. Oh, one warning,
the polarizer plates mentioned above are plastic, and the light energy  
put out by your typical
projector is quite substantial. We actually melted one of the  
polarizers on our first attempt,
despite using much of it's 3x3 inch surface area. ie - use a low power  
projector, or put the
polarizer between thick glass plates or somesuch...

> From: Magali Cottevieille <mc3077 at columbia.edu>
> Date: May 21, 2008 3:06:07 PM CDT
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Stereo projection
>
> Hi,
>
> Is there any way, with two projectors piloted by two graphic cards, to
> send from Chimera the stereo left eye view onto one, and the stereo
> right eye view onto the other one ? These two projectors are meant  
> to be
> used with filters and special glasses to create a 3D view.
> Thanks for your help!
>
> -- 
> Magali Cottevieille, Ph.D.
> Howard Hughes Medical Institute,
> Department of Biochemistry and Molecular Biophysics,
> 630 W 168th St, P&S Black Building 2-221
> New York, NY 10032
>
> Ph:  (+1) 212-305-9521
> Fax: (+1) 212-305-9500
>
> Email: mc3077 at columbia.edu
>       magali.cottevieille at gmail.com
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
----------------------------------------------------------------------------
Steven Ludtke, PhD              |        Baylor College of Medicine
sludtke at bcm.tmc.edu             |     Associate Professor & Co-Director
stevel at alumni.caltech.edu       | National Center For Macromolecular  
Imaging
V: (713)798-9020                |    Dept of Biochemistry and Mol. Biol.
F: (713)798-1625                |
                                 |             Those who Do, Are
http://ncmi.bcm.edu/~stevel     |         The converse also applies





From gregc at cgl.ucsf.edu  Wed May 21 14:25:09 2008
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Wed, 21 May 2008 14:25:09 -0700 (PDT)
Subject: [Chimera-users] Stereo projection
In-Reply-To: <483480AF.9020604@columbia.edu>
References: <483480AF.9020604@columbia.edu>
Message-ID: <Pine.OSF.4.63.0805211409520.1818353@guanine.cgl.ucsf.edu>

On Wed, 21 May 2008, Magali Cottevieille wrote:

> Hi,
>
> Is there any way, with two projectors piloted by two graphic cards, to
> send from Chimera the stereo left eye view onto one, and the stereo
> right eye view onto the other one ? These two projectors are meant to be
> used with filters and special glasses to create a 3D view.
> Thanks for your help!

Chimera supports stereo using workstation graphics cards, i.e., NVidia 
Quadro FX and ATI/AMD FireGL cards.  We don't have a recent FireGL card 
(and driver), so the rest of this email will be about the NVidia Quadro FX 
cards and driver.

The Quadro FX graphics cards have two video outputs and the driver lets 
you display the left eye on one output and the right eye on the other. 
The higher end cards have SLI support (on FireGL it's called CrossFire) 
which lets you use two matched graphics cards together.  It is unclear to 
me how or if SLI/CrossFire and stereo work together, but I would expect 
them to.

 	Greg


From pett at cgl.ucsf.edu  Thu May 22 10:51:29 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 22 May 2008 10:51:29 -0700
Subject: [Chimera-users] findhbond/5750 (FindHBond failure)
In-Reply-To: <A2540AFE-35C2-4A7A-8A72-CB47E4856DEB@gmail.com>
References: <200805221713.m4MHDBAm2092851@guanine.cgl.ucsf.edu>
	<CFE0ABCB-C22B-4BD2-B964-8858228C2637@cgl.ucsf.edu>
	<A2540AFE-35C2-4A7A-8A72-CB47E4856DEB@gmail.com>
Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0@cgl.ucsf.edu>

Hi Tyler,
	The problem is that Chimera "knows" the atom types of standard  
residues and doesn't try to compute them from scratch.  Therefore it  
assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the  
find-hbond computation as it looks for the planarity of the ND1 and  
sees it bonded to nothing!
	For what you want to do, you want to get that atom's residue  
changed.  Do this:

1) Control-double click on the ND1 atom
2) Chose "Modify Atom" from the resulting popup menu.
3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral"
4) Change "Bonds" to 3
5) In the "Residue Name" section, use the "new residue" option with  
"NH3" as the name and chain "het"
5) Click the Change button

That should give you what you want.

--Eric

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

On May 22, 2008, at 10:25 AM, Tyler Arbour wrote:

> Wow, I didn't expect a response for this...great!  I was actually  
> just trying to create a figure representing a computational model  
> that I am using.  Starting from the crystal structure, I wanted to  
> actually change the histidinal N to a simple NH3 molecule.  I am  
> just trying to get familiar with Chimera--I usually use DS  
> Viewerpro for modifying structures, and it doesn't seem like  
> Chimera is well-suited to this type of modification.  If you have  
> any advice on an easy way to make this conversion so that I have a  
> nice figure, I'd greatly appreciate it!  Thanks.
>
> Tyler
>
> On May 22, 2008, at 11:17 AM, Eric Pettersen wrote:
>
>> Hi Tyler,
>> 	Your structure seems to have a histidine residue (residue 159 in  
>> chain A) that consists solely of an ND1 atom!  How did you manage  
>> that?
>>
>> --Eric
>>
>>
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu
>>
>>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080522/72231393/attachment.html>

From JeanDidier.Marechal at uab.es  Thu May 22 13:12:53 2008
From: JeanDidier.Marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=)
Date: Thu, 22 May 2008 22:12:53 +0200
Subject: [Chimera-users] displacing atoms following a given vector
In-Reply-To: <mailman.1.1211482802.1815858.chimera-users@cgl.ucsf.edu>
References: <mailman.1.1211482802.1815858.chimera-users@cgl.ucsf.edu>
Message-ID: <1211487173.7435.4.camel@AMD3800>

Dear All,

I have been flying through the developer's guide but can't find what I
look for, sorry.

I have a given molecule and a vector in cartesian coordinates (e.g.  a
normal mode but not necessarily) indicating a direction of displacement
for the different atoms of the molecules. I would like to write a script
that displaces the atoms following this vector. I am prettysure that
some modules of chimera should allow me to do that, but I can't find
which ones. Could you give me a hand on this please?

ALl the best
JD
 

El jue, 22-05-2008 a las 12:00 -0700, chimera-users-request at cgl.ucsf.edu
escribi?:
> Send Chimera-users mailing list submissions to
> 	chimera-users at cgl.ucsf.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> or, via email, send a message with subject or body 'help' to
> 	chimera-users-request at cgl.ucsf.edu
> 
> You can reach the person managing the list at
> 	chimera-users-owner at cgl.ucsf.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Stereo projection (Magali Cottevieille)
>    2. Stereo projection (Steven Ludtke)
>    3. Re: Stereo projection (Greg Couch)
>    4. Re: findhbond/5750 (FindHBond failure) (Eric Pettersen)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 21 May 2008 16:06:07 -0400
> From: Magali Cottevieille <mc3077 at columbia.edu>
> Subject: [Chimera-users] Stereo projection
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <483480AF.9020604 at columbia.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi,
> 
> Is there any way, with two projectors piloted by two graphic cards, to 
> send from Chimera the stereo left eye view onto one, and the stereo 
> right eye view onto the other one ? These two projectors are meant to be 
> used with filters and special glasses to create a 3D view.
> Thanks for your help!
> 
> -- 
> Magali Cottevieille, Ph.D.
> Howard Hughes Medical Institute,
> Department of Biochemistry and Molecular Biophysics,
> 630 W 168th St, P&S Black Building 2-221
> New York, NY 10032 
> 
> Ph:  (+1) 212-305-9521
> Fax: (+1) 212-305-9500
> 
> Email: mc3077 at columbia.edu
>        magali.cottevieille at gmail.com
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 21 May 2008 16:18:26 -0500
> From: Steven Ludtke <sludtke at bcm.edu>
> Subject: [Chimera-users] Stereo projection
> To: chimera-users at cgl.ucsf.edu
> Cc: mc3077 at columbia.edu
> Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C at bcm.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> Yes, we have done this before, though I don't remember with absolute  
> certainty if we
> did it with chimera. You don't use 2 video cards normally, but rather  
> 1 card with 2
> outputs. Also, you will need one of the 'professional' cards where the  
> driver supports
> stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea  
> stereo drivers then
> have a mode for this type of stereo, or at least that's my memory, it  
> was a year or two
> ago when we demonstrated this. You need:
> 
> 2 identical projectors which permit geometry correction so their  
> corners can be exactly aligned
> 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj-pfilt-3x3.html 
> ) for $20 a pair
> linear polarizing glasses (from the same site)
> Quadro or similar GFX card
> 
> Note that with this type of stereo, you could technically make this  
> work with any old dual
> output 3-D card, but you would have to write the visualization  
> software so it would open
> 2 display windows with slightly different orientations that you could  
> then manually (or
> automatically) position on each of the 2 projectors.
> 
> We did this just as an initial proof of concept, and haven't managed  
> to get back to it again,
> though we keep meaning to, as it is MUCH cheaper than the commercial  
> solutions. Oh, one warning,
> the polarizer plates mentioned above are plastic, and the light energy  
> put out by your typical
> projector is quite substantial. We actually melted one of the  
> polarizers on our first attempt,
> despite using much of it's 3x3 inch surface area. ie - use a low power  
> projector, or put the
> polarizer between thick glass plates or somesuch...
> 
> > From: Magali Cottevieille <mc3077 at columbia.edu>
> > Date: May 21, 2008 3:06:07 PM CDT
> > To: chimera-users at cgl.ucsf.edu
> > Subject: [Chimera-users] Stereo projection
> >
> > Hi,
> >
> > Is there any way, with two projectors piloted by two graphic cards, to
> > send from Chimera the stereo left eye view onto one, and the stereo
> > right eye view onto the other one ? These two projectors are meant  
> > to be
> > used with filters and special glasses to create a 3D view.
> > Thanks for your help!
> >
> > -- 
> > Magali Cottevieille, Ph.D.
> > Howard Hughes Medical Institute,
> > Department of Biochemistry and Molecular Biophysics,
> > 630 W 168th St, P&S Black Building 2-221
> > New York, NY 10032
> >
> > Ph:  (+1) 212-305-9521
> > Fax: (+1) 212-305-9500
> >
> > Email: mc3077 at columbia.edu
> >       magali.cottevieille at gmail.com
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> ----------------------------------------------------------------------------
> Steven Ludtke, PhD              |        Baylor College of Medicine
> sludtke at bcm.tmc.edu             |     Associate Professor & Co-Director
> stevel at alumni.caltech.edu       | National Center For Macromolecular  
> Imaging
> V: (713)798-9020                |    Dept of Biochemistry and Mol. Biol.
> F: (713)798-1625                |
>                                  |             Those who Do, Are
> http://ncmi.bcm.edu/~stevel     |         The converse also applies
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 21 May 2008 14:25:09 -0700 (PDT)
> From: Greg Couch <gregc at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Stereo projection
> To: Magali Cottevieille <mc3077 at columbia.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <Pine.OSF.4.63.0805211409520.1818353 at guanine.cgl.ucsf.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> 
> On Wed, 21 May 2008, Magali Cottevieille wrote:
> 
> > Hi,
> >
> > Is there any way, with two projectors piloted by two graphic cards, to
> > send from Chimera the stereo left eye view onto one, and the stereo
> > right eye view onto the other one ? These two projectors are meant to be
> > used with filters and special glasses to create a 3D view.
> > Thanks for your help!
> 
> Chimera supports stereo using workstation graphics cards, i.e., NVidia 
> Quadro FX and ATI/AMD FireGL cards.  We don't have a recent FireGL card 
> (and driver), so the rest of this email will be about the NVidia Quadro FX 
> cards and driver.
> 
> The Quadro FX graphics cards have two video outputs and the driver lets 
> you display the left eye on one output and the right eye on the other. 
> The higher end cards have SLI support (on FireGL it's called CrossFire) 
> which lets you use two matched graphics cards together.  It is unclear to 
> me how or if SLI/CrossFire and stereo work together, but I would expect 
> them to.
> 
>  	Greg
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Thu, 22 May 2008 10:51:29 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure)
> To: Tyler Arbour <tyler.arbour at gmail.com>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Tyler,
> 	The problem is that Chimera "knows" the atom types of standard  
> residues and doesn't try to compute them from scratch.  Therefore it  
> assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the  
> find-hbond computation as it looks for the planarity of the ND1 and  
> sees it bonded to nothing!
> 	For what you want to do, you want to get that atom's residue  
> changed.  Do this:
> 
> 1) Control-double click on the ND1 atom
> 2) Chose "Modify Atom" from the resulting popup menu.
> 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral"
> 4) Change "Bonds" to 3
> 5) In the "Residue Name" section, use the "new residue" option with  
> "NH3" as the name and chain "het"
> 5) Click the Change button
> 
> That should give you what you want.
> 
> --Eric
> 
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu
> 
> On May 22, 2008, at 10:25 AM, Tyler Arbour wrote:
> 
> > Wow, I didn't expect a response for this...great!  I was actually  
> > just trying to create a figure representing a computational model  
> > that I am using.  Starting from the crystal structure, I wanted to  
> > actually change the histidinal N to a simple NH3 molecule.  I am  
> > just trying to get familiar with Chimera--I usually use DS  
> > Viewerpro for modifying structures, and it doesn't seem like  
> > Chimera is well-suited to this type of modification.  If you have  
> > any advice on an easy way to make this conversion so that I have a  
> > nice figure, I'd greatly appreciate it!  Thanks.
> >
> > Tyler
> >
> > On May 22, 2008, at 11:17 AM, Eric Pettersen wrote:
> >
> >> Hi Tyler,
> >> 	Your structure seems to have a histidine residue (residue 159 in  
> >> chain A) that consists solely of an ND1 atom!  How did you manage  
> >> that?
> >>
> >> --Eric
> >>
> >>
> >>                         Eric Pettersen
> >>                         UCSF Computer Graphics Lab
> >>                         http://www.cgl.ucsf.edu
> >>
> >>
> >
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080522/72231393/attachment-0001.html 
> 
> ------------------------------
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> End of Chimera-users Digest, Vol 61, Issue 20
> *********************************************



From pett at cgl.ucsf.edu  Thu May 22 15:18:52 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 22 May 2008 15:18:52 -0700
Subject: [Chimera-users] displacing atoms following a given vector
In-Reply-To: <1211487173.7435.4.camel@AMD3800>
References: <mailman.1.1211482802.1815858.chimera-users@cgl.ucsf.edu>
	<1211487173.7435.4.camel@AMD3800>
Message-ID: <39E344AA-509F-4E37-9423-6C6C71464CCA@cgl.ucsf.edu>

Hi JD,
	You would displace the atoms of molecule 'm' by the vector (1,2,3)  
like so:

v = chimera.Vector(1,2,3)
for a in m.atoms:
	a.setCoord(a.coord() + v)

--Eric

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


On May 22, 2008, at 1:12 PM, Jean-Didier Mar?chal wrote:

> Dear All,
>
> I have been flying through the developer's guide but can't find what I
> look for, sorry.
>
> I have a given molecule and a vector in cartesian coordinates (e.g.  a
> normal mode but not necessarily) indicating a direction of  
> displacement
> for the different atoms of the molecules. I would like to write a  
> script
> that displaces the atoms following this vector. I am prettysure that
> some modules of chimera should allow me to do that, but I can't find
> which ones. Could you give me a hand on this please?
>
> ALl the best
> JD
>
>
> El jue, 22-05-2008 a las 12:00 -0700, chimera-users- 
> request at cgl.ucsf.edu
> escribi?:
>> Send Chimera-users mailing list submissions to
>> 	chimera-users at cgl.ucsf.edu
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> or, via email, send a message with subject or body 'help' to
>> 	chimera-users-request at cgl.ucsf.edu
>>
>> You can reach the person managing the list at
>> 	chimera-users-owner at cgl.ucsf.edu
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Chimera-users digest..."
>>
>>
>> Today's Topics:
>>
>>    1. Stereo projection (Magali Cottevieille)
>>    2. Stereo projection (Steven Ludtke)
>>    3. Re: Stereo projection (Greg Couch)
>>    4. Re: findhbond/5750 (FindHBond failure) (Eric Pettersen)
>>
>>
>> --------------------------------------------------------------------- 
>> -
>>
>> Message: 1
>> Date: Wed, 21 May 2008 16:06:07 -0400
>> From: Magali Cottevieille <mc3077 at columbia.edu>
>> Subject: [Chimera-users] Stereo projection
>> To: chimera-users at cgl.ucsf.edu
>> Message-ID: <483480AF.9020604 at columbia.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi,
>>
>> Is there any way, with two projectors piloted by two graphic  
>> cards, to
>> send from Chimera the stereo left eye view onto one, and the stereo
>> right eye view onto the other one ? These two projectors are meant  
>> to be
>> used with filters and special glasses to create a 3D view.
>> Thanks for your help!
>>
>> -- 
>> Magali Cottevieille, Ph.D.
>> Howard Hughes Medical Institute,
>> Department of Biochemistry and Molecular Biophysics,
>> 630 W 168th St, P&S Black Building 2-221
>> New York, NY 10032
>>
>> Ph:  (+1) 212-305-9521
>> Fax: (+1) 212-305-9500
>>
>> Email: mc3077 at columbia.edu
>>        magali.cottevieille at gmail.com
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 21 May 2008 16:18:26 -0500
>> From: Steven Ludtke <sludtke at bcm.edu>
>> Subject: [Chimera-users] Stereo projection
>> To: chimera-users at cgl.ucsf.edu
>> Cc: mc3077 at columbia.edu
>> Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C at bcm.edu>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> Yes, we have done this before, though I don't remember with absolute
>> certainty if we
>> did it with chimera. You don't use 2 video cards normally, but rather
>> 1 card with 2
>> outputs. Also, you will need one of the 'professional' cards where  
>> the
>> driver supports
>> stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea
>> stereo drivers then
>> have a mode for this type of stereo, or at least that's my memory, it
>> was a year or two
>> ago when we demonstrated this. You need:
>>
>> 2 identical projectors which permit geometry correction so their
>> corners can be exactly aligned
>> 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj- 
>> pfilt-3x3.html
>> ) for $20 a pair
>> linear polarizing glasses (from the same site)
>> Quadro or similar GFX card
>>
>> Note that with this type of stereo, you could technically make this
>> work with any old dual
>> output 3-D card, but you would have to write the visualization
>> software so it would open
>> 2 display windows with slightly different orientations that you could
>> then manually (or
>> automatically) position on each of the 2 projectors.
>>
>> We did this just as an initial proof of concept, and haven't managed
>> to get back to it again,
>> though we keep meaning to, as it is MUCH cheaper than the commercial
>> solutions. Oh, one warning,
>> the polarizer plates mentioned above are plastic, and the light  
>> energy
>> put out by your typical
>> projector is quite substantial. We actually melted one of the
>> polarizers on our first attempt,
>> despite using much of it's 3x3 inch surface area. ie - use a low  
>> power
>> projector, or put the
>> polarizer between thick glass plates or somesuch...
>>
>>> From: Magali Cottevieille <mc3077 at columbia.edu>
>>> Date: May 21, 2008 3:06:07 PM CDT
>>> To: chimera-users at cgl.ucsf.edu
>>> Subject: [Chimera-users] Stereo projection
>>>
>>> Hi,
>>>
>>> Is there any way, with two projectors piloted by two graphic  
>>> cards, to
>>> send from Chimera the stereo left eye view onto one, and the stereo
>>> right eye view onto the other one ? These two projectors are meant
>>> to be
>>> used with filters and special glasses to create a 3D view.
>>> Thanks for your help!
>>>
>>> -- 
>>> Magali Cottevieille, Ph.D.
>>> Howard Hughes Medical Institute,
>>> Department of Biochemistry and Molecular Biophysics,
>>> 630 W 168th St, P&S Black Building 2-221
>>> New York, NY 10032
>>>
>>> Ph:  (+1) 212-305-9521
>>> Fax: (+1) 212-305-9500
>>>
>>> Email: mc3077 at columbia.edu
>>>       magali.cottevieille at gmail.com
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>> --------------------------------------------------------------------- 
>> -------
>> Steven Ludtke, PhD              |        Baylor College of Medicine
>> sludtke at bcm.tmc.edu             |     Associate Professor & Co- 
>> Director
>> stevel at alumni.caltech.edu       | National Center For Macromolecular
>> Imaging
>> V: (713)798-9020                |    Dept of Biochemistry and Mol.  
>> Biol.
>> F: (713)798-1625                |
>>                                  |             Those who Do, Are
>> http://ncmi.bcm.edu/~stevel     |         The converse also applies
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 21 May 2008 14:25:09 -0700 (PDT)
>> From: Greg Couch <gregc at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] Stereo projection
>> To: Magali Cottevieille <mc3077 at columbia.edu>
>> Cc: chimera-users at cgl.ucsf.edu
>> Message-ID: <Pine.OSF. 
>> 4.63.0805211409520.1818353 at guanine.cgl.ucsf.edu>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>> On Wed, 21 May 2008, Magali Cottevieille wrote:
>>
>>> Hi,
>>>
>>> Is there any way, with two projectors piloted by two graphic  
>>> cards, to
>>> send from Chimera the stereo left eye view onto one, and the stereo
>>> right eye view onto the other one ? These two projectors are  
>>> meant to be
>>> used with filters and special glasses to create a 3D view.
>>> Thanks for your help!
>>
>> Chimera supports stereo using workstation graphics cards, i.e.,  
>> NVidia
>> Quadro FX and ATI/AMD FireGL cards.  We don't have a recent FireGL  
>> card
>> (and driver), so the rest of this email will be about the NVidia  
>> Quadro FX
>> cards and driver.
>>
>> The Quadro FX graphics cards have two video outputs and the driver  
>> lets
>> you display the left eye on one output and the right eye on the  
>> other.
>> The higher end cards have SLI support (on FireGL it's called  
>> CrossFire)
>> which lets you use two matched graphics cards together.  It is  
>> unclear to
>> me how or if SLI/CrossFire and stereo work together, but I would  
>> expect
>> them to.
>>
>>  	Greg
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 22 May 2008 10:51:29 -0700
>> From: Eric Pettersen <pett at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure)
>> To: Tyler Arbour <tyler.arbour at gmail.com>
>> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
>> Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0 at cgl.ucsf.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi Tyler,
>> 	The problem is that Chimera "knows" the atom types of standard
>> residues and doesn't try to compute them from scratch.  Therefore it
>> assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the
>> find-hbond computation as it looks for the planarity of the ND1 and
>> sees it bonded to nothing!
>> 	For what you want to do, you want to get that atom's residue
>> changed.  Do this:
>>
>> 1) Control-double click on the ND1 atom
>> 2) Chose "Modify Atom" from the resulting popup menu.
>> 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral"
>> 4) Change "Bonds" to 3
>> 5) In the "Residue Name" section, use the "new residue" option with
>> "NH3" as the name and chain "het"
>> 5) Click the Change button
>>
>> That should give you what you want.
>>
>> --Eric
>>
>>                          Eric Pettersen
>>                          UCSF Computer Graphics Lab
>>                          http://www.cgl.ucsf.edu
>>
>> On May 22, 2008, at 10:25 AM, Tyler Arbour wrote:
>>
>>> Wow, I didn't expect a response for this...great!  I was actually
>>> just trying to create a figure representing a computational model
>>> that I am using.  Starting from the crystal structure, I wanted to
>>> actually change the histidinal N to a simple NH3 molecule.  I am
>>> just trying to get familiar with Chimera--I usually use DS
>>> Viewerpro for modifying structures, and it doesn't seem like
>>> Chimera is well-suited to this type of modification.  If you have
>>> any advice on an easy way to make this conversion so that I have a
>>> nice figure, I'd greatly appreciate it!  Thanks.
>>>
>>> Tyler
>>>
>>> On May 22, 2008, at 11:17 AM, Eric Pettersen wrote:
>>>
>>>> Hi Tyler,
>>>> 	Your structure seems to have a histidine residue (residue 159 in
>>>> chain A) that consists solely of an ND1 atom!  How did you manage
>>>> that?
>>>>
>>>> --Eric
>>>>
>>>>
>>>>                         Eric Pettersen
>>>>                         UCSF Computer Graphics Lab
>>>>                         http://www.cgl.ucsf.edu
>>>>
>>>>
>>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/ 
>> 20080522/72231393/attachment-0001.html
>>
>> ------------------------------
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>> End of Chimera-users Digest, Vol 61, Issue 20
>> *********************************************
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080522/ba7c6670/attachment.html>

From bokcmho at ust.hk  Thu May 22 22:03:46 2008
From: bokcmho at ust.hk (Maurice Ho)
Date: Fri, 23 May 2008 13:03:46 +0800
Subject: [Chimera-users] rotate a helix
Message-ID: <48365032.4070409@ust.hk>

Hi there,
I would like to rotate a helix at a particular angle.  How could I 
accomplish the following?
1. How to define the central axis of the helix in chimera?
2. How to set a particular angle to rotate?
3. I do this on a helix belonging to a GPCR, with the loops firstly 
broken for rotation and then perhaps need to rejoin them.  How to join 
them back?
4. After joining, should I just redo energy minimization for the loops 
concerned?
Much thanks!
-------------- next part --------------
A non-text attachment was scrubbed...
Name: bokcmho.vcf
Type: text/x-vcard
Size: 315 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080523/6be7c7a8/attachment.vcf>

From meng at cgl.ucsf.edu  Fri May 23 11:59:52 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 23 May 2008 11:59:52 -0700
Subject: [Chimera-users] rotate a helix
In-Reply-To: <48365032.4070409@ust.hk>
References: <48365032.4070409@ust.hk>
Message-ID: <D2B0E3B7-E17B-4F7D-AB44-C18706405A39@cgl.ucsf.edu>

Hi Maurice,
Firstly, I would only recommend this type of work for generating a  
crude model, such as for a figure.  I doubt that the quality would be  
high enough for work that depends on the detailed atomic  
coordinates.  Energy minimization can only "rescue" local strains and  
conflicts, so if you start with something ridiculous you will still  
have something ridiculous after minimization!  For a higher-quality  
model you would need to do more complicated conformational sampling  
and energy evaluation, either by creating it with some other program  
that includes such calculations, or by performing such calculations  
with another program after building the initial model in Chimera.

Given those caveats, however, here are some ideas:

(A) use Movement Mouse Mode (under Tools... Movement) set to "Move  
helix, strand, or turn" - this lets you move interactively whichever  
unit of secondary structure you "grab" with the mouse.  You do not  
have to break any bonds, they will just distort.  You can still move  
the entire structure when the cursor is in the window but not on top  
of any atoms.  The drawback here is that instead of entering a  
specific angle you would have to approximate the amount of movement  
interactively.  Before moving the helix, specify the center of  
rotation, for example by selecting one or more atoms and choosing  
Actions... Set Pivot or using the command cofr and specifying those  
atoms.  The Movement Mouse Mode tool includes an "Undo Move" button  
so you can recover from mistakes.  Save a PDB file of the result.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/ 
movemode.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb

If you have a recent version of Chimera, you can measure the crossing  
angle of the original and modeled helices using the Axes tool (under  
Tools... Structure Analysis).
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
structuremeas/structuremeas.html#axes

(B) if you really want to rotate the helix exactly X degrees, the  
only way I know of is to put that helix in a separate file.  You  
could open the original file with the whole structure for comparison,  
and then a second file with just the helix.  Move the structures in  
tandem to get a position where the rotation you want is around the  
screen axis X (horizontal in plane of screen), Y (vertical in plane  
of screen), or Z (normal to screen).  Then freeze the original  
structure (for example by unchecking its Active box in the Model  
Panel, which is under Favorites), specify the center of rotation as  
in (A), and then use a command to rotate the helix:
   turn y 45
(or x or z depending on how you set up the view).  Then save the PDB  
file of the helix "relative to" the original structure.  To merge the  
helix back in, you would have to text-edit the whole structure file  
to replace the old coordinates with the new coordinates.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html

After (A) or (B) and making sure you have saved those results to a  
file, you can consider whether or not minimization will improve the  
structure.  I am skeptical that it would help very much.  You would  
probably want to freeze some parts of the structure and do it in  
different stages freezing different sets of atoms to lessen  
distortions and keep the helix approximately in the intended  
orientation.

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 May 22, 2008, at 10:03 PM, Maurice Ho wrote:

> Hi there,
> I would like to rotate a helix at a particular angle.  How could I  
> accomplish the following?
> 1. How to define the central axis of the helix in chimera?
> 2. How to set a particular angle to rotate?
> 3. I do this on a helix belonging to a GPCR, with the loops firstly  
> broken for rotation and then perhaps need to rejoin them.  How to  
> join them back?
> 4. After joining, should I just redo energy minimization for the  
> loops concerned?
> Much thanks!


From goddard at cgl.ucsf.edu  Fri May 23 16:26:13 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 23 May 2008 16:26:13 -0700
Subject: [Chimera-users] map 3d pdf
In-Reply-To: <483670A1.9090807@ebi.ac.uk>
References: <456AC346.4050404@ebi.ac.uk>
	<200611272251.kARMpmUR1684943@guanine.cgl.ucsf.edu>
	<456BFDF8.2050508@ebi.ac.uk>
	<200611281859.kASIxgO31604823@guanine.cgl.ucsf.edu>
	<456D4E42.5010606@ebi.ac.uk>
	<200611291639.kATGdh601954828@guanine.cgl.ucsf.edu>
	<456E9F93.4020006@ebi.ac.uk>
	<200701022232.l02MWZF31803339@guanine.cgl.ucsf.edu>
	<45C1EBBD.9000002@ebi.ac.uk> <45C29CD5.4010008@cgl.ucsf.edu>
	<462DD2AE.9070908@ebi.ac.uk> <462E274B.3010207@cgl.ucsf.edu>
	<47319AE5.6080400@ebi.ac.uk> <4731F17A.6040405@cgl.ucsf.edu>
	<483670A1.9090807@ebi.ac.uk>
Message-ID: <48375295.6070808@cgl.ucsf.edu>

Richard Newman wrote:
> Hi Tom
>
> Does CHIMERA have the ability to export a map format which can be used 
> by 3D PDF?
>
> We would like to make the EMDB maps available in this format.
>
> All the best
> Richard

Hi Richard,

  Chimera can export map surfaces in several 3-D file formats Wavefront 
OBJ, POV-Ray, RenderMan, VRML, or X3D using menu entry File / Export 
Scene....  The format for objects embedded in 3D PDF is called U3D which 
Chimera does not export.  I used a program called MeshLab to read OBJ 
format produced by Chimera and write U3D format, then used another 
program to convert LaTeX to PDF (pdflatex).  Here's an example showing 
EMDB map 1356.  It requires Adobe Acrobat Reader 8.0.  It will not 
display on Mac OS 10.4 Preview.

    http://www.cgl.ucsf.edu/home/goddard/temp/emd_1356.pdf

Producing the file was painful and Chimera can't export the surface 
coloring in OBJ format.  I think it would be more interesting for the EM 
Databank to show 3D models in the web browser like JMol shows PDB 
models.  I don't know if a java applet has been written to do that.  
Perhaps JMol could do it.

    Tom



From goddard at cgl.ucsf.edu  Fri May 23 16:34:48 2008
From: goddard at cgl.ucsf.edu (Tom Goddard)
Date: Fri, 23 May 2008 16:34:48 -0700
Subject: [Chimera-users] Replacing lysine with alanine
In-Reply-To: <464122.33311.qm@web35408.mail.mud.yahoo.com>
References: <464122.33311.qm@web35408.mail.mud.yahoo.com>
Message-ID: <48375498.2040807@cgl.ucsf.edu>

Hi Neville,

  You can replace all lysine residues in a molecule with alanines using 
the Chimera command

    swapaa ALA #0:LYS

The #0 refers to the molecule id number shown in model panel.  Here is 
further documentation on swapaa.

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

  Tom


yimnai forlemu wrote:
> Hi Tom
> I have a quick question about chimera.
> Can you perform multi amino acid residue mutation
> using chimera. For example lets say you have a protein
> of 340 amino acids with about 100 lysine, and you want
> all the lysines to become say ALaninis. Is that
> possible
> Thanks
> Neville
>   



From fglaser at technion.ac.il  Thu May 22 05:56:59 2008
From: fglaser at technion.ac.il (Fabian Glaser)
Date: Thu, 22 May 2008 15:56:59 +0300
Subject: [Chimera-users] building linker peptide
In-Reply-To: <0CB10640-4BA8-4F68-A2C6-148708636B84@cgl.ucsf.edu>
References: <483010E7.5070603@gmail.com>
	<7217A6E5-86B3-4C49-A714-AD47699DD97E@cgl.ucsf.edu>
	<4833DD54.3080806@technion.ac.il>
	<21800AD8-5DD9-4B7C-9DDB-B5ACD075B368@cgl.ucsf.edu>
	<0CB10640-4BA8-4F68-A2C6-148708636B84@cgl.ucsf.edu>
Message-ID: <48356D9B.20502@technion.ac.il>

Dear Elaine and Eric,

Elaine program worked beautifully, and it's in any case better to have a 
renumbered PDB,

Thanks a lot!!

Fabian

Eric Pettersen said the following on 21/05/08 21:34:
> Just deleting the SEQRES records _might_ be good enough.  Otherwise go 
> with what Elaine wrote.
>
> --Eric
>
>                         Eric Pettersen
>
>                         UCSF Computer Graphics Lab
>
>                         http://www.cgl.ucsf.edu
>
>
> On May 21, 2008, at 9:59 AM, Elaine Meng wrote:
>
>> On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
>>> Another question regarding this issue, I succeded to make a new bond 
>>> and minimize it between two chains, A and B, in the same pdb. But 
>>> this created apparently a problem with the residue numbering and 
>>> Nterm recognition, since when I tried to add an additional linker to 
>>> the chimera I created, I got the following error message:
>>>
>>> "No MMTK name for atom "H" in standard residue ALA"
>>>
>>> I suspect that this is related to the fact that I still have two 
>>> chains, and Chimera does not identified the new bond, or something 
>>> similar.
>>>
>>> Is there a way to automatically rename the newly unified chains?
>>> Any suggetion will be highly appreciated.
>>
>> Hi Fabian,
>> There is no automatic way to change chain ID.  Only the ugly manual 
>> text-editing way, sorry!  I guess that the ATOM part of the file no 
>> longer agreed with the SEQRES part of the file.
>>
>> It might work to simply delete that atom, if it looks like it is extra.
>>
>> However, I would probably go back to a PDB file saved after you added 
>> all your linker residues and edit it to remove all the lines except 
>> the coordinates (the ATOM and HETATM lines), remove the chain IDs, 
>> and renumber all the residues.  It is necessary to renumber the 
>> residues because there may be residues with the same number in the 
>> different chains, and now there would be no way to tell them apart 
>> (for example, two different residues numbered 10, which used to be 
>> residue 10 in A and residue 10 in B).   Unfortunately you will lose 
>> the ability to use the "familiar" residue numbering within the second 
>> chain.
>>
>> I attached a fortran (f77) program to do this editing, but I realize 
>> you may not be able to use it depending on your computing 
>> environment.  If you are on some unix-type computer you would just 
>> compile it with something like:
>>
>> f77 renum2.f -o renum
>>
>> Then execute it with
>>
>> renum
>>
>> It would ask for the names of the input and output PDB files and what 
>> residue number to start with.
>>
>> Then you would have to do the addh/addcharge/minimization stuff 
>> again, sorry.  I think it would already have the bond you wanted, 
>> however.
>>
>> Maybe someone else can think of a more elegant approach.
>> Best,
>> Elaine
>> --------
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu 
>> <mailto: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
>>
>> <renum2.f>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

-- 
Fabian Glaser, PhD

Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

Web:   http://bku.technion.ac.il
Email: fglaser at tx.technion.ac.il
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396



From fabian.glaser at gmail.com  Mon May 26 02:41:37 2008
From: fabian.glaser at gmail.com (Fabian Gmail)
Date: Mon, 26 May 2008 12:41:37 +0300
Subject: [Chimera-users] povray problem
Message-ID: <483A85D1.6050000@gmail.com>

Dear chimera team,

I have a recurrent problem with the povray facility for saving high 
quality figures, in many cases I get a black-white figures like the 
attached. Is there a way to  avoid that ?

Thanks a lot in advance,

FAbian


-- 
Fabian Glaser, PhD

Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

Web:   http://bku.technion.ac.il
Email: fglaser at tx.technion.ac.il
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396


 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: struct_align_tranx_translin_human.png
Type: image/png
Size: 128129 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080526/ef180a4e/attachment.png>

From meng at cgl.ucsf.edu  Tue May 27 10:40:56 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 27 May 2008 10:40:56 -0700
Subject: [Chimera-users] povray problem
In-Reply-To: <483A85D1.6050000@gmail.com>
References: <483A85D1.6050000@gmail.com>
Message-ID: <123549E9-63F4-4754-B148-C1E8E69D5A85@cgl.ucsf.edu>

Dear Fabian,
We cannot tell how to fix the problem without more information.   
Please use Help... Report a Bug from the Chimera menu.  This includes  
information about your computer and what version of Chimera you are  
using.  Also, if you could attach a session file to the bug report  
(File... Save Session As) for a Chimera session that has this  
problem, that would help even more.

If you instead send email about a bug, the better address is chimera- 
bugs at cgl.ucsf.edu but usually the method above is best of all.
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 May 26, 2008, at 2:41 AM, Fabian Gmail wrote:

> Dear chimera team,
>
> I have a recurrent problem with the povray facility for saving high  
> quality figures, in many cases I get a black-white figures like the  
> attached. Is there a way to  avoid that ?
>
> Thanks a lot in advance,
>
> FAbian
>
>
> -- 
> Fabian Glaser, PhD
>
> Bioinformatics Knowledge Unit,
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
>
> Web:   http://bku.technion.ac.il
> Email: fglaser at tx.technion.ac.il
> Tel:   +972-(0)4-8293701
> Cel:   +972-(0)54-4772396
>


From heiland at indiana.edu  Tue May 27 10:56:54 2008
From: heiland at indiana.edu (Randy Heiland)
Date: Tue, 27 May 2008 13:56:54 -0400
Subject: [Chimera-users] H bonds
Message-ID: <952527C5-75BD-4BF0-B5B7-58892AA2F698@indiana.edu>

I have a naive question - given the following pdb file:

ATOM      1  CA  ALA     0       1.125   1.534   0.000  0.00   
0.00      0    C
ATOM      2  C   ALA     0       0.000   0.514   0.000  0.00   
0.00      0    C
ATOM      3  O   ALA     0      -1.173   0.853   0.000  0.00   
0.00      0    O
ATOM      4  N   ALA     1       0.394  -0.796   0.000  0.00   
0.00      0    N
ATOM      5  CA  ALA     1      -0.546  -1.905   0.000  0.00   
0.00      0    C
ATOM      6  H1  ALA     1       1.017   2.171   0.880  0.00   
0.00      0    H
ATOM      7  H2  ALA     1       1.017   2.171  -0.880  0.00   
0.00      0    H
ATOM      8  H3  ALA     1       1.381  -0.999   0.000  0.00   
0.00      0    H
ATOM      9  H4  ALA     1      -1.551  -1.486   0.000  0.00   
0.00      0    H
ATOM     10  H5  ALA     1      -0.420  -2.528  -0.890  0.00   
0.00      0    H
ATOM     11  H6  ALA     1       2.123   1.091   0.000  0.00   
0.00      0    H
ATOM     12  H7  ALA     1      -0.420  -2.528   0.890  0.00   
0.00      0    H

when I display it in Chimera, there are 3 unbonded hydrogens - why is  
that and is there a menu item to create/display the bonds?

thanks, Randy


From pett at cgl.ucsf.edu  Tue May 27 11:25:47 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 27 May 2008 11:25:47 -0700
Subject: [Chimera-users] H bonds
In-Reply-To: <952527C5-75BD-4BF0-B5B7-58892AA2F698@indiana.edu>
References: <952527C5-75BD-4BF0-B5B7-58892AA2F698@indiana.edu>
Message-ID: <F3788C58-1722-4FFB-9A9C-CEC59BF6640C@cgl.ucsf.edu>

Hi Randy,
	The disconnected hydrogens (H1, H2, H6) look like they should be  
bonded to the CA in residue 0.  The problem is that the hydrogens are  
in residue 1 and Chimera will never form cross-residue bonds that  
involve hydrogen unless there are explicit connect records.  Your  
options to fix this are:

	1) add CONECT records
	2) put those hydrogens in residue 0 and reorder the PDB file
	3) put all the atoms in residue 1 and give the CAs unique names.  I  
recommend changing the residue name to something other than ALA in  
this case.

As a footnote for option 3, you don't actually _have_ to give the CAs  
unique names.  You could still distinguish them in commands by serial  
number, e.g. color red @/serialNumber=1.  It's just a whole lot  
easier to give them unique names.  :-)

--Eric

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

On May 27, 2008, at 10:56 AM, Randy Heiland wrote:

> I have a naive question - given the following pdb file:
>
> ATOM      1  CA  ALA     0       1.125   1.534   0.000  0.00
> 0.00      0    C
> ATOM      2  C   ALA     0       0.000   0.514   0.000  0.00
> 0.00      0    C
> ATOM      3  O   ALA     0      -1.173   0.853   0.000  0.00
> 0.00      0    O
> ATOM      4  N   ALA     1       0.394  -0.796   0.000  0.00
> 0.00      0    N
> ATOM      5  CA  ALA     1      -0.546  -1.905   0.000  0.00
> 0.00      0    C
> ATOM      6  H1  ALA     1       1.017   2.171   0.880  0.00
> 0.00      0    H
> ATOM      7  H2  ALA     1       1.017   2.171  -0.880  0.00
> 0.00      0    H
> ATOM      8  H3  ALA     1       1.381  -0.999   0.000  0.00
> 0.00      0    H
> ATOM      9  H4  ALA     1      -1.551  -1.486   0.000  0.00
> 0.00      0    H
> ATOM     10  H5  ALA     1      -0.420  -2.528  -0.890  0.00
> 0.00      0    H
> ATOM     11  H6  ALA     1       2.123   1.091   0.000  0.00
> 0.00      0    H
> ATOM     12  H7  ALA     1      -0.420  -2.528   0.890  0.00
> 0.00      0    H
>
> when I display it in Chimera, there are 3 unbonded hydrogens - why is
> that and is there a menu item to create/display the bonds?
>
> thanks, Randy
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080527/777d7168/attachment.html>

From meng at cgl.ucsf.edu  Tue May 27 11:34:29 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 27 May 2008 11:34:29 -0700
Subject: [Chimera-users] H bonds
In-Reply-To: <952527C5-75BD-4BF0-B5B7-58892AA2F698@indiana.edu>
References: <952527C5-75BD-4BF0-B5B7-58892AA2F698@indiana.edu>
Message-ID: <B40528A1-9ACE-4973-8D89-0FFDDCB05D7E@cgl.ucsf.edu>

Hi Randy,
Oh, H bonds, not H-bonds!  I see what you mean.  I am guessing it is  
because you have all the hydrogens in residue 1, whereas the CA that  
they are supposed to be attached to are in residue 0.  However,  
simply changing everything to residue 1 causes trouble because what  
you have is not really ALA but some other thing with an extra methyl  
group.  If you change the residue name to something nonstandard, say  
UNK, and residue 1, the structure is bonded as it should be when  
opened in Chimera.  (file attached)

If you don't do any file editing, however, you can add the bonds in  
Chimera by choosing Tools... Structure Editing... Build Structure and  
going to the Add/Delete Bonds tab.  Then, select the 4 atoms and  
click the button to add all reasonable bonds.

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: randy3.pdb
Type: application/octet-stream
Size: 732 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080527/a731a6bb/attachment.obj>
-------------- next part --------------



From pett at cgl.ucsf.edu  Tue May 27 17:18:27 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 27 May 2008 17:18:27 -0700
Subject: [Chimera-users] preferences - povray - keep input files doesn't
Message-ID: <DCA648E3-82D1-40DD-AE63-BFF16CA21259@cgl.ucsf.edu>

> We're thinking of adding some generic per-frame hook as a command so
> that you don't have to use Movie Recorder at all to generate a series
> of POVray files that you want to post-process before rendering (you
> would use the not-yet-documented "export" command to generate them).
>
> --Eric

This hook, a command named "perframe", is now in there.  It will be  
available in tomorrow's build if that works.  There is documentation  
here:

http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/perframe.html

>
> On Mar 17, 2008, at 11:00 AM, Thomas Goddard wrote:
>
> > Hi Klaas,
> >
> >    You can make the Chimera movie recorder use your preference for
> > keeping POVray files by editing file
> >
> > 	chimera/share/MovieRecorder/RecorderHandler.py
> >
> > changing line 120 from
> >
> >                        raytraceKeepInput = False,
> >
> > to
> >
> >                        # raytraceKeepInput = False,
> >
> > Then restart Chimera.
> >
> >    Perhaps we should change the Chimera default for the "keep POVray
> > input files" to false and have movie recorder respect the preference
> > setting.
> >
> > 	Tom
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080527/23b1b438/attachment.html>

From I.moustafa at psu.edu  Thu May 29 10:08:01 2008
From: I.moustafa at psu.edu (Ibrahim Moustafa)
Date: Thu, 29 May 2008 13:08:01 -0400
Subject: [Chimera-users] Plotting modes from PCA onto the structure
Message-ID: <C4645B32.132A%I.moustafa@psu.edu>

Dear Chimera support,

  I hope Chimera (with  supporting scripts) can be used to make the figures
described below:

     I want to make a figure to display the different modes obtained from
PCA analysis (on MD trajectory obtained from AMBER) as different snapshots
of the structure under study.
 
 To explain it more, I have a file containing the displacement in X, Y, Z
for each C-alpha in a column format. Is there a simple script that can add
the displacement vectors to the x, y, z coordinates of the original
structure? So the new structure with modified C-alpha can be plotted
representing a particular mode in Chimera.

   Also, related to the same point, is it possible to represent the vectors
at each C-alpha as arrows/porcupine needle in Chimera?

P.S. It would be great if Chimera can add features to represent these kind
of figures from PTRAJ output or similar analysis programs used in MD
simulation. Especially, Chimera support analysis of AMBER trajectory.

  Thanks in advance for your great support,
     Ibrahim


-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080529/219675f5/attachment.html>

From meng at cgl.ucsf.edu  Thu May 29 10:44:34 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 29 May 2008 10:44:34 -0700
Subject: [Chimera-users] Plotting modes from PCA onto the structure
In-Reply-To: <C4645B32.132A%I.moustafa@psu.edu>
References: <C4645B32.132A%I.moustafa@psu.edu>
Message-ID: <BACB5EBE-BA74-44EA-B798-38A27406E8F5@cgl.ucsf.edu>

Hi Ibrahim,
I don't write code myself and cannot promise (given time constraints)  
that others will work on this, but it would help if you could send us  
some example files:  perhaps a PCA file and the structure snapshot  
that is the basis for the displacements, and any other files that you  
think are relevant (are the trajectory and prmtop also needed to show  
the results?).  You could send them just to me and I would share them  
as needed.

Are your PCA results from PTRAJ?  I know that several programs and  
web servers do similar PCA or NM calculations, and probably each  
produces a different output format.

You may want to take a look at converting your PCA results file into  
lines and arrows in the BILD format. Simply opening the file in  
Chimera displays the objects.  This format is extremely simple and is  
documented here, including an example file:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html

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 May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote:

> Dear Chimera support,
>
>   I hope Chimera (with  supporting scripts) can be used to make the  
> figures described below:
>
>      I want to make a figure to display the different modes  
> obtained from PCA analysis (on MD trajectory obtained from AMBER)  
> as different snapshots of the structure under study.
>
>  To explain it more, I have a file containing the displacement in  
> X, Y, Z for each C-alpha in a column format. Is there a simple  
> script that can add the displacement vectors to the x, y, z  
> coordinates of the original structure? So the new structure with  
> modified C-alpha can be plotted representing a particular mode in  
> Chimera.
>
>    Also, related to the same point, is it possible to represent the  
> vectors at each C-alpha as arrows/porcupine needle in Chimera?
>
> P.S. It would be great if Chimera can add features to represent  
> these kind of figures from PTRAJ output or similar analysis  
> programs used in MD simulation. Especially, Chimera support  
> analysis of AMBER trajectory.
>
>   Thanks in advance for your great support,
>      Ibrahim
> -- 
> Ibrahim M. Moustafa, Ph.D.
> Biochemistry and Molecular Biology Dept.
> 201 Althouse Lab., University Park,
> Pennsylvania State University
> PA 16802
>
> Tel. (814) 863-8703
> Fax (814) 865-7927
>


From A00775435 at itesm.mx  Fri May 30 01:30:24 2008
From: A00775435 at itesm.mx (A00775435 at itesm.mx)
Date: Fri, 30 May 2008 03:30:24 -0500
Subject: [Chimera-users] Help Installing Chimera in Ubunty Hardy already
	read and google a lot.
Message-ID: <483DF6700000135D@mailserver1.itesm.mx>


Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for
6 gb of ram that couldn't be used in XP 32 bits. I need help installing
Linux version of Chimera, I have read and goggled web for instructions,
and none of them seems to work, I run .exe in terminal (knowing linux
doesn't use .exe i find this confusing) and nothing happens, I try that
Chmod command and running again and nothing too... Im a really beginner
here in linux, also browsed Ubuntu forums for help and at least till
today have got no answer. All help would be greatly appreciated.

sincerely,
David Bulnes Abundis



From heiland at indiana.edu  Fri May 30 05:05:39 2008
From: heiland at indiana.edu (Randy Heiland)
Date: Fri, 30 May 2008 08:05:39 -0400
Subject: [Chimera-users] Help Installing Chimera in Ubunty Hardy already
	read and google a lot.
In-Reply-To: <483DF6700000135D@mailserver1.itesm.mx>
References: <483DF6700000135D@mailserver1.itesm.mx>
Message-ID: <7B98BF99-9543-46F4-9B50-DD4DC78BFB76@indiana.edu>

David,

The only thing I did to install on my Ubuntu was:

chmod +x chimera-xxx.exe
sudo ./chimera-xxx.exe

-Randy

On May 30, 2008, at 4:30 AM, A00775435 at itesm.mx wrote:

>
> Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu  
> for
> 6 gb of ram that couldn't be used in XP 32 bits. I need help  
> installing
> Linux version of Chimera, I have read and goggled web for  
> instructions,
> and none of them seems to work, I run .exe in terminal (knowing linux
> doesn't use .exe i find this confusing) and nothing happens, I try  
> that
> Chmod command and running again and nothing too... Im a really  
> beginner
> here in linux, also browsed Ubuntu forums for help and at least till
> today have got no answer. All help would be greatly appreciated.
>
> sincerely,
> David Bulnes Abundis
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From bala at igib.res.in  Fri May 30 05:31:16 2008
From: bala at igib.res.in (bala)
Date: Fri, 30 May 2008 18:01:16 +0530
Subject: [Chimera-users] Chimera-users Digest, Vol 61, Issue 27
References: <mailman.1.1212087602.1836222.chimera-users@cgl.ucsf.edu>
Message-ID: <7E7071C8392C6E41916C9A6AE2843C7F10AA30@n1ex>

Dear Ibrahim,

Try to use IED Plugin in VMD to analyze your PCA output. In fact there is a server that can produce the arrows (you want) that can show the direction and magnitude of the displacement along a Eigen vector. But i guess the server works on gromacs output only. 

A month ago, i posted the same query to Chimera (Analyzing PCA with chimera). I thank Elaine for his support. I would surely send some samples files of PCA analysis done with PTRAJ. I think addition of this analysis facility in Chimera is surely going to help all chimeran's a lot.

Bala 


-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu on behalf of chimera-users-request at cgl.ucsf.edu
Sent: Fri 5/30/2008 12:30 AM
To: chimera-users at cgl.ucsf.edu
Subject: Chimera-users Digest, Vol 61, Issue 27
 
Send Chimera-users mailing list submissions to
	chimera-users at cgl.ucsf.edu

To subscribe or unsubscribe via the World Wide Web, visit
	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
or, via email, send a message with subject or body 'help' to
	chimera-users-request at cgl.ucsf.edu

You can reach the person managing the list at
	chimera-users-owner at cgl.ucsf.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Chimera-users digest..."


Today's Topics:

   1. Plotting modes from PCA onto the structure (Ibrahim Moustafa)
   2. Re: Plotting modes from PCA onto the structure (Elaine Meng)


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

Message: 1
Date: Thu, 29 May 2008 13:08:01 -0400
From: Ibrahim Moustafa <I.moustafa at psu.edu>
Subject: [Chimera-users] Plotting modes from PCA onto the structure
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Message-ID: <C4645B32.132A%I.moustafa at psu.edu>
Content-Type: text/plain; charset="us-ascii"

Dear Chimera support,

  I hope Chimera (with  supporting scripts) can be used to make the figures
described below:

     I want to make a figure to display the different modes obtained from
PCA analysis (on MD trajectory obtained from AMBER) as different snapshots
of the structure under study.
 
 To explain it more, I have a file containing the displacement in X, Y, Z
for each C-alpha in a column format. Is there a simple script that can add
the displacement vectors to the x, y, z coordinates of the original
structure? So the new structure with modified C-alpha can be plotted
representing a particular mode in Chimera.

   Also, related to the same point, is it possible to represent the vectors
at each C-alpha as arrows/porcupine needle in Chimera?

P.S. It would be great if Chimera can add features to represent these kind
of figures from PTRAJ output or similar analysis programs used in MD
simulation. Especially, Chimera support analysis of AMBER trajectory.

  Thanks in advance for your great support,
     Ibrahim


-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080529/219675f5/attachment-0001.html 

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

Message: 2
Date: Thu, 29 May 2008 10:44:34 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Plotting modes from PCA onto the
	structure
To: Ibrahim Moustafa <I.moustafa at psu.edu>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Message-ID: <BACB5EBE-BA74-44EA-B798-38A27406E8F5 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi Ibrahim,
I don't write code myself and cannot promise (given time constraints)  
that others will work on this, but it would help if you could send us  
some example files:  perhaps a PCA file and the structure snapshot  
that is the basis for the displacements, and any other files that you  
think are relevant (are the trajectory and prmtop also needed to show  
the results?).  You could send them just to me and I would share them  
as needed.

Are your PCA results from PTRAJ?  I know that several programs and  
web servers do similar PCA or NM calculations, and probably each  
produces a different output format.

You may want to take a look at converting your PCA results file into  
lines and arrows in the BILD format. Simply opening the file in  
Chimera displays the objects.  This format is extremely simple and is  
documented here, including an example file:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html

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 May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote:

> Dear Chimera support,
>
>   I hope Chimera (with  supporting scripts) can be used to make the  
> figures described below:
>
>      I want to make a figure to display the different modes  
> obtained from PCA analysis (on MD trajectory obtained from AMBER)  
> as different snapshots of the structure under study.
>
>  To explain it more, I have a file containing the displacement in  
> X, Y, Z for each C-alpha in a column format. Is there a simple  
> script that can add the displacement vectors to the x, y, z  
> coordinates of the original structure? So the new structure with  
> modified C-alpha can be plotted representing a particular mode in  
> Chimera.
>
>    Also, related to the same point, is it possible to represent the  
> vectors at each C-alpha as arrows/porcupine needle in Chimera?
>
> P.S. It would be great if Chimera can add features to represent  
> these kind of figures from PTRAJ output or similar analysis  
> programs used in MD simulation. Especially, Chimera support  
> analysis of AMBER trajectory.
>
>   Thanks in advance for your great support,
>      Ibrahim
> -- 
> Ibrahim M. Moustafa, Ph.D.
> Biochemistry and Molecular Biology Dept.
> 201 Althouse Lab., University Park,
> Pennsylvania State University
> PA 16802
>
> Tel. (814) 863-8703
> Fax (814) 865-7927
>


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

_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


End of Chimera-users Digest, Vol 61, Issue 27
*********************************************

-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 5539 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/bb628cad/attachment.bin>

From lionel.nauton at univ-bpclermont.fr  Fri May 30 05:52:04 2008
From: lionel.nauton at univ-bpclermont.fr (Lionel Nauton)
Date: Fri, 30 May 2008 14:52:04 +0200
Subject: [Chimera-users] add atom type in MMTK
Message-ID: <483FF874.5020709@univ-bpclermont.fr>

hello everybody

this is my first question since I use chimera, more than 3 years ago, 
and I would like to know
if is it possible to add atom type in the MMTK basis set ?
I actually work on a molecule containing platinium, and I can't run mopac
because there is no description.
I'm looking for some description files , and I found this : 
/antechamber/dat/antechamber/*****.DAT
which is the good one and which is the way to modify it ?
thank's for your answer and excuse me for my english.....
best regards

-- 

=================================================


NAUTON Lionel

Ing?nieur d'?tudes.

Laboratoire de Synth?se Et Etude de Syst?mes ? Int?r?t Biologique

UMR6504 : universit? Blaise Pascal ? CNRS

24, avenue des Landais ? Campus des C?zeaux

63177 AUBIERE Cedex

France

Tel : 04 73 40 55 06

m?l : lionel.nauton at univ-bpclermont.fr 
<mailto:lionel.nauton at univ-bpclermont.fr>

site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm 
<http://seesib.univ-bpclermont.fr/site_web/pageaccueil.html>


=================================================



From pett at cgl.ucsf.edu  Fri May 30 15:15:02 2008
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 30 May 2008 15:15:02 -0700
Subject: [Chimera-users] Plotting modes from PCA onto the structure
In-Reply-To: <C4645B32.132A%I.moustafa@psu.edu>
References: <C4645B32.132A%I.moustafa@psu.edu>
Message-ID: <476E9F7A-2FDD-4558-8053-5345D9995A02@cgl.ucsf.edu>

Hi Ibrahim,
	As Bala pointed out, IED in VMD may well be the way to go for now.   
Also, the "porcupine needles" can be accomplished with BILD, as  
Elaine mentioned.  I've attached a script that reads a file of  
displacements and applies them to the CAs of a structure.  Obviously,  
there should be as many lines in the file as there are CAs in the  
structure.  Each line should consist of 3 numbers, the X, Y, and Z  
displacements.  Since the script only modifies the CAs, you should  
probably only be displaying the CAs -- the rest of the structure will  
be out of position.  You may need to edit the script to put in the  
name of the file with the displacements, otherwise it will use a file  
named "displacements" in the same directory as the script.  You run  
the script by simply opening it with File...Open or the "open" command.
	We are working on closer coordination between Amber and Chimera,  
with the help of Wei Zhang.  He has already contributed one tool,  
Solvate, which uses sleap to solvate a system.  Solvate is available  
in daily builds.  In the short term he hopes to write tools to add  
ions and write parmtop files.  Longer term goals are to include the  
minimization and MD functionality of NAB, and ptraj trajectory analysis.

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

?
On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote:

> Dear Chimera support,
>
>   I hope Chimera (with  supporting scripts) can be used to make the  
> figures described below:
>
>      I want to make a figure to display the different modes  
> obtained from PCA analysis (on MD trajectory obtained from AMBER)  
> as different snapshots of the structure under study.
>
>  To explain it more, I have a file containing the displacement in  
> X, Y, Z for each C-alpha in a column format. Is there a simple  
> script that can add the displacement vectors to the x, y, z  
> coordinates of the original structure? So the new structure with  
> modified C-alpha can be plotted representing a particular mode in  
> Chimera.
>
>    Also, related to the same point, is it possible to represent the  
> vectors at each C-alpha as arrows/porcupine needle in Chimera?
>
> P.S. It would be great if Chimera can add features to represent  
> these kind of figures from PTRAJ output or similar analysis  
> programs used in MD simulation. Especially, Chimera support  
> analysis of AMBER trajectory.
>
>   Thanks in advance for your great support,
>      Ibrahim
>
>
> -- 
> Ibrahim M. Moustafa, Ph.D.
> Biochemistry and Molecular Biology Dept.
> 201 Althouse Lab., University Park,
> Pennsylvania State University
> PA 16802
>
> Tel. (814) 863-8703
> Fax (814) 865-7927
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/66de27cf/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pca.py
Type: text/x-python-script
Size: 682 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/66de27cf/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080530/66de27cf/attachment-0001.html>

From meng at cgl.ucsf.edu  Fri May 30 17:34:49 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 30 May 2008 17:34:49 -0700
Subject: [Chimera-users] add atom type in MMTK
In-Reply-To: <483FF874.5020709@univ-bpclermont.fr>
References: <483FF874.5020709@univ-bpclermont.fr>
Message-ID: <7F83CFB3-19E1-4C36-9C28-5BE5B55DB005@cgl.ucsf.edu>

Hello Lionel,
Are you trying to run "addcharge" or "minimize"?

If "addcharge" to calculate partial charges on some Pt complex (e.g.  
cisplatin or carboplatin):

Nonstandard residues are sent to Antechamber, but that program is  
only meant to be used on organic molecules (C,H,O,N,S,P,F,Cl,Br,I),  
not metal complexes or inorganic species.  See the antechamber site:  
http://amber.scripps.edu/antechamber/tips.html
I think you have to use some other program that can handle metal  
complexes to derive partial charges.  I don't think it is possible to  
simply edit some antechamber data files to get it to work on such  
compounds.

If "minimize" and you just wanted to treat the Pt as a monatomic ion  
with integer charge:

I had thought it possible to add a metal ion type by editing a  
parameter file.  However, I have not been successful at minimizing a  
structure with the "new" type even when the file appears to include  
the necessary parameters.  Maybe there is an additional step that I  
don't know about.  So currently my best answer is that it is not  
possible, but if we find a way, we will send another message. (I may  
be wrong given my lack of success, but I think the relevant parameter  
file within the Chimera installation is lib/python2.5/site-packages/ 
MMTK/ForceFields/amber/amber_parm99 )

Sorry about that,
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 May 30, 2008, at 5:52 AM, Lionel Nauton wrote:

> hello everybody
> this is my first question since I use chimera, more than 3 years ago,
> and I would like to know
> if is it possible to add atom type in the MMTK basis set ?
> I actually work on a molecule containing platinium, and I can't run  
> mopac
> because there is no description.
> I'm looking for some description files , and I found this :
> /antechamber/dat/antechamber/*****.DAT
> which is the good one and which is the way to modify it ?
> thank's for your answer and excuse me for my english.....
> best regards
>


From brucedray at yahoo.com  Sat May 31 08:50:53 2008
From: brucedray at yahoo.com (Bruce D. Ray)
Date: Sat, 31 May 2008 08:50:53 -0700 (PDT)
Subject: [Chimera-users]  Import error with chimera-1.2509-osx_x11.dmg,
	May 01, 2008
Message-ID: <640107.47762.qm@web35804.mail.mud.yahoo.com>

I have a Mac G4 PPC running OS X 10.3.9 on which
previous versions of chimera have run without
incident.
I installed chimera-1.2509 of May 01, 2008 after
removing the chimera-1.2492 of Feb 11, 2008 I had been
using.  However, when I attempted to run
chimera-1.2509
it did not start and the following error messages were
written to the console.log file accessible by
console.app rather than to the X-terminal:

     Traceback (most recent call last):

       File
"/Applications/Chimera.app/Contents/Resources/share/__main__.py",
  line 65, in <module>

         value = chimeraInit.init(sys.argv)

       File
"/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py",
line 279, in init

         import chimera

       File
"/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",
line 15, in <module>

         from _chimera import *

     ImportError: dynamic module does not define init
function (init_chimera)



This appears to be specific to the Mac OS X version
as the Windows version of chimera-1.2509 works.
Obviously, I removed chimera-1.2509 from the Mac and
reinstalled chimera-1.2492 of Feb 11, 2008 which does
work on this Mac.


Sincerely,




-- 
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


      


From heiland at indiana.edu  Sat May 31 09:54:04 2008
From: heiland at indiana.edu (Randy Heiland)
Date: Sat, 31 May 2008 12:54:04 -0400
Subject: [Chimera-users] Import error with chimera-1.2509-osx_x11.dmg,
	May 01, 2008
In-Reply-To: <640107.47762.qm@web35804.mail.mud.yahoo.com>
References: <640107.47762.qm@web35804.mail.mud.yahoo.com>
Message-ID: <C7183562-073B-43DC-AFC5-0D8FE142DF17@indiana.edu>

I was going to try to reproduce your problem, but it looks like  
they've already updated that snapshot since there is no 1.2509 now:

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

You might try the latest, 1.2524, snapshot if you really need  
something newer than the production release.

-Randy

On May 31, 2008, at 11:50 AM, Bruce D. Ray wrote:

> I have a Mac G4 PPC running OS X 10.3.9 on which
> previous versions of chimera have run without
> incident.
> I installed chimera-1.2509 of May 01, 2008 after
> removing the chimera-1.2492 of Feb 11, 2008 I had been
> using.  However, when I attempted to run
> chimera-1.2509
> it did not start and the following error messages were
> written to the console.log file accessible by
> console.app rather than to the X-terminal:
>
>      Traceback (most recent call last):
>
>        File
> "/Applications/Chimera.app/Contents/Resources/share/__main__.py",
>   line 65, in <module>
>
>          value = chimeraInit.init(sys.argv)
>
>        File
> "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py",
> line 279, in init
>
>          import chimera
>
>        File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/ 
> __init__.py",
> line 15, in <module>
>
>          from _chimera import *
>
>      ImportError: dynamic module does not define init
> function (init_chimera)
>
>
>
> This appears to be specific to the Mac OS X version
> as the Windows version of chimera-1.2509 works.
> Obviously, I removed chimera-1.2509 from the Mac and
> reinstalled chimera-1.2492 of Feb 11, 2008 which does
> work on this Mac.
>
>
> Sincerely,
>
>
>
>
> -- 
> Bruce D. Ray, Ph.D.
> Associate Scientist, and Operations Director
> NMR Center
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN  46202-3273
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080531/e8cc81a7/attachment.html>

From brucedray at yahoo.com  Sat May 31 11:24:29 2008
From: brucedray at yahoo.com (Bruce D. Ray)
Date: Sat, 31 May 2008 11:24:29 -0700 (PDT)
Subject: [Chimera-users] Import error with chimera-1.2509-osx_x11.dmg,
	May 01, 2008
In-Reply-To: <C7183562-073B-43DC-AFC5-0D8FE142DF17@indiana.edu>
Message-ID: <533863.58573.qm@web35804.mail.mud.yahoo.com>


--- Randy Heiland <heiland at indiana.edu> wrote:

> I was going to try to reproduce your problem, but it
> looks like  
> they've already updated that snapshot since there is
> no 1.2509 now:
> 
> http://www.cgl.ucsf.edu/chimera/download.html
> 
> You might try the latest, 1.2524, snapshot if you
> really need  
> something newer than the production release.

Well, I just tried that version and I get the exact
same error.


Error messages to console log are:

     Traceback (most recent call last):

       File
"/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/share/__main__.py",
line 65, in <module>

         value = chimeraInit.init(sys.argv)

  File
"/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/share/chimeraInit.py",
line 279, in init

              import chimera

       File
"/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/share/chimera/__init__.py",
line 15, in <module>

    from _chimera import *

     ImportError: dynamic module does not define init
function (init_chimera)



Sincerely,





-- 
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


      


From heiland at indiana.edu  Sat May 31 12:34:44 2008
From: heiland at indiana.edu (Randy Heiland)
Date: Sat, 31 May 2008 15:34:44 -0400
Subject: [Chimera-users] Import error with chimera-1.2509-osx_x11.dmg,
	May 01, 2008
In-Reply-To: <533863.58573.qm@web35804.mail.mud.yahoo.com>
References: <533863.58573.qm@web35804.mail.mud.yahoo.com>
Message-ID: <BD4F6268-FECB-4F37-91F4-5305B5F7041F@indiana.edu>

I just successfully installed/ran 1.2524 on my Intel Mac running OSX  
10.4.11  The only minor hiccup I had were the following warnings spit  
out when I executed chimera and a lengthier-than-usual first-time  
hesitation before the gui appeared (presumably due to these fonts -  
which by the way look *much* nicer than those in the production  
release):

~/dev/Chimera-1.2524.app/Contents/MacOS$ ./chimera
Fontconfig warning: no <cachedir> elements found. Check configuration.
Fontconfig warning: adding <cachedir>//var/cache/fontconfig</cachedir>
Fontconfig warning: adding <cachedir>~/.fontconfig</cachedir>

It just dawned on me that maybe you have a powerpc machine (uname - 
a)?  I'm guessing that the Chimera developers need to recompile that  
snapshot with some different env flags.  There's some info on google  
about the error msg you're seeing.  I just went through this slightly  
painful exercise for a guy running osx 10.3.x/ppc for some Python  
eggs we distribute as extensions to Chimera.

I also noticed this snapshot is now using Python 2.5, fwiw.

-Randy


On May 31, 2008, at 2:24 PM, Bruce D. Ray wrote:

>
> --- Randy Heiland <heiland at indiana.edu> wrote:
>
>> I was going to try to reproduce your problem, but it
>> looks like
>> they've already updated that snapshot since there is
>> no 1.2509 now:
>>
>> http://www.cgl.ucsf.edu/chimera/download.html
>>
>> You might try the latest, 1.2524, snapshot if you
>> really need
>> something newer than the production release.
>
> Well, I just tried that version and I get the exact
> same error.
>
>
> Error messages to console log are:
>
>      Traceback (most recent call last):
>
>        File
> "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/share/ 
> __main__.py",
> line 65, in <module>
>
>          value = chimeraInit.init(sys.argv)
>
>   File
> "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/share/ 
> chimeraInit.py",
> line 279, in init
>
>               import chimera
>
>        File
> "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/share/ 
> chimera/__init__.py",
> line 15, in <module>
>
>     from _chimera import *
>
>      ImportError: dynamic module does not define init
> function (init_chimera)
>
>
>
> Sincerely,
>
>
>
>
>
> -- 
> Bruce D. Ray, Ph.D.
> Associate Scientist, and Operations Director
> NMR Center
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN  46202-3273
>
>
>



From meng at cgl.ucsf.edu  Sat May 31 13:54:12 2008
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 31 May 2008 13:54:12 -0700
Subject: [Chimera-users] Import error with chimera-1.2509-osx_x11.dmg,
	May 01, 2008
In-Reply-To: <C7183562-073B-43DC-AFC5-0D8FE142DF17@indiana.edu>
References: <640107.47762.qm@web35804.mail.mud.yahoo.com>
	<C7183562-073B-43DC-AFC5-0D8FE142DF17@indiana.edu>
Message-ID: <16B835EF-DB1D-4E35-8C68-9700515D645B@cgl.ucsf.edu>

Hello,
As you have found, the most recent versions of Chimera do not support  
Mac OSX 10.3.  We had a "news" item on the home page last fall, which  
has since been displaced by newer messages, but here is the text:

November 16, 2007
Chimera production release v1.2470 is available. This is the last  
release to officially support Mac OS 10.3.  There have been several  
changes since the previous production release (v1.2422, June 2007).

Platform support depends on the availability of such machines to our  
group, and "older" systems may be dropped as most users migrate to  
newer OS versions.  It is always a balancing act as to where time/ 
effort should be spent.  Sorry about that,
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 May 31, 2008, at 9:54 AM, Randy Heiland wrote:

> I was going to try to reproduce your problem, but it looks like  
> they've already updated that snapshot since there is no 1.2509 now:
>
> http://www.cgl.ucsf.edu/chimera/download.html
>
> You might try the latest, 1.2524, snapshot if you really need  
> something newer than the production release.
>
> -Randy
>
> On May 31, 2008, at 11:50 AM, Bruce D. Ray wrote:
>
>> I have a Mac G4 PPC running OS X 10.3.9 on which
>> previous versions of chimera have run without
>> incident.
>> I installed chimera-1.2509 of May 01, 2008 after
>> removing the chimera-1.2492 of Feb 11, 2008 I had been
>> using.  However, when I attempted to run
>> chimera-1.2509
>> it did not start and the following error messages were
>> written to the console.log file accessible by
>> console.app rather than to the X-terminal:
>>
>>      Traceback (most recent call last):
>>
>>        File
>> "/Applications/Chimera.app/Contents/Resources/share/__main__.py",
>>   line 65, in <module>
>>
>>          value = chimeraInit.init(sys.argv)
>>
>>        File
>> "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py",
>> line 279, in init
>>
>>          import chimera
>>
>>        File
>> "/Applications/Chimera.app/Contents/Resources/share/chimera/ 
>> __init__.py",
>> line 15, in <module>
>>
>>          from _chimera import *
>>
>>      ImportError: dynamic module does not define init
>> function (init_chimera)
>>
>>
>>
>> This appears to be specific to the Mac OS X version
>> as the Windows version of chimera-1.2509 works.
>> Obviously, I removed chimera-1.2509 from the Mac and
>> reinstalled chimera-1.2492 of Feb 11, 2008 which does
>> work on this Mac.
>>
>>
>> Sincerely,
>>
>>
>>
>>
>> -- 
>> Bruce D. Ray, Ph.D.
>> Associate Scientist, and Operations Director
>> NMR Center
>> IUPUI
>> Physics Dept.
>> 402 N. Blackford St.
>> Indianapolis, IN  46202-3273
>>
>>
>>
>> _______________________________________________
>> 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 a00775435 at itesm.mx  Thu May 29 23:53:41 2008
From: a00775435 at itesm.mx (David)
Date: Fri, 30 May 2008 01:53:41 -0500
Subject: [Chimera-users] Installing Chimera in Ubunty Hardy
Message-ID: <1212130421.9096.6.camel@david-radiosun>

Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for
6 gb of ram that couldn't be used in XP 32 bits. I need help installing
Linux version of Chimera, I have read and goggled web for instructions,
and none of them seems to work, I run .exe in terminal (knowing linux
doesn't use .exe i find this confusing) and nothing happens, I try that
Chmod command and running again and nothing too... Im a really beginner
here in linux, also browsed Ubuntu forums for help and at least till
today have got no answer. All help would be greatly appreciated.

sincerely,
David Bulnes Abundis