pymol-users Mailing List for PyMOL Molecular Graphics System

Andreas,

Try removing -D_FORTIFY_SOURCE=2 as a compiler option... 

PyMOL's macros sometimes choke on that.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Andreas Henschel
> Sent: Friday, April 27, 2007 2:28 PM
> To: Michael Kluge
> Cc: pym...@li...
> Subject: Re: [PyMOL] PyMOL compilation from source
> 
> Hi,
> 
> Michael Kluge wrote:
> 
> >Hi Andreas,
> >
> >gcc is not the best compiler on an IA64 machine. We always recommend 
> >using the Intel compilers. Would it be possible to try those?
> >
> >  
> >
> I have to figure out, where to modify in the setup script/distutils.
> Thanks.
> 
> Andreas
> 
> PS. @Michael
>  From Martin Hoefling:
> 
> >i have no idea about your error but i can provide you RPMs 
> for Opensuse 
> >10.2
> >i586 and x86_64, if you need them for other SuSE 
> distributions, I can 
> >try to add them to my repository.
> >
> Would that be feasable?
> 
> >Regards, Michael
> >
> >Andreas Henschel wrote:
> >  
> >
> >>Hi all,
> >>
> >>did anyone of you come across the mysterious "internal 
> compiler error:
> >>Segmentation fault"
> >>while compiling pymol from source?
> >>
> >>The offending lines are in contrib/champ/champ.c:2787
> >>
> >> PRINTFD(FB_smiles_parsing)
> >>   " ChampParseBlockAtom: called.\n"
> >>   ENDFD;
> >>
> >>Can I get around it somehow? Is it a 64-bit/gcc issue?
> >>Any help would be greatly appreciated.
> >>
> >>Some more error/system details:
> >>
> >>    
> >>
> >>>python setup.py install
> >>>      
> >>>
> >>...
> >>building 'chempy.champ._champ' extension gcc -pthread 
> >>-fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall
> >>-D_FORTIFY_SOURCE=2 -g -fPIC -Icontrib/champ 
> -I/usr/include/python2.4 
> >>-c contrib/champ/champ.c -o 
> >>build/temp.linux-ia64-2.4/contrib/champ/champ.o
> >>contrib/champ/champ.c: In function 'ChampParseBlockAtom':
> >>contrib/champ/champ.c:2787: internal compiler error: Segmentation 
> >>fault Please submit a full bug report, with preprocessed source if 
> >>appropriate.
> >>See <URL:" rel="nofollow">http://www.suse.de/feedback> for instructions.
> >>error: command 'gcc' failed with exit status 1
> >>
> >>    
> >>
> >>>uname -a
> >>>      
> >>>
> >>Linux mars 2.6.16.27-0.6-default #1 SMP Wed Dec 13 09:34:50 UTC 2006
> >>ia64 ia64 ia64 GNU/Linux
> >>
> >>    
> >>
> >>>gcc -v
> >>>      
> >>>
> >>Using built-in specs.
> >>Target: ia64-suse-linux
> >>Configured with: ../configure --enable-threads=posix --prefix=/usr 
> >>--with-local-prefix=/usr/local --infodir=/usr/share/info 
> >>--mandir=/usr/share/man --libdir=/usr/lib --libexecdir=/usr/lib 
> >>--enable-languages=c,c++,objc,fortran,java,ada 
> >>--enable-checking=release 
> >>--with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp 
> >>--disable-libssp --enable-java-awt=gtk --enable-gtk-cairo 
> >>--disable-libjava-multilib --with-slibdir=/lib --with-system-zlib 
> >>--enable-shared --enable-__cxa_atexit 
> --enable-libstdcxx-allocator=new 
> >>--with-system-libunwind --host=ia64-suse-linux Thread 
> model: posix gcc 
> >>version 4.1.0 (SUSE Linux)
> >>ia64 GNU/Linux
> >>
> >>Cheers,
> >>Andreas
> >>
> >>    
> >>
> >
> >
> >  
> >
> 
> --
> Andreas Henschel
> Bioinformatics Group
> TU Dresden
> Tatzberg 47-51
> 01307 Dresden, Germany
> 
> Phone: +49 351 463 40063
> EMail: ah...@bi...
> 
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
> of your XML. No limits. Just data. Click to get it now.
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Stuart,

Empty PDB files can result from writing a file while PyMOL's global state
number is set to a numerical state that does not actually contain the
coordinates.  Note that by default, single state objects are displayed in
all states (unless static_singletons is disabled), which can cause some
confusion.

If this is the cause of your problem, then make sure that [  1/ ... is
displayed in the lower-right hand corner before saving.  

Cheers,
Warren


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Stuart Endo-Streeter
> Sent: Wednesday, April 25, 2007 5:57 AM
> To: PYMOLBB
> Subject: [PyMOL] failure to save coordinates adjusted with edit tool
> 
> Hi all,
> 
> I am trying to fit part of my search model into my 
> experimental density using pymol.  I got initial model 
> fitting to the experimental map using molrep, but want to 
> make some changes to certain helices and strands before I pop 
> the model into a rigid body and simulated annealing run, 
> since they're obviously off by eye and a correction here 
> would make the subsequent runs that much better.  I've done 
> the following:
> 
> Loaded molrep fit model
> Loaded experimental maps
> Created selection of residues to move
> Turned selection into an object
> Moved object using "3-button Editing" mode Save object.pdb, 
> object name
> 
> However, when I look at the saved file that should contain 
> the coordinates of the adjusted model, it is empty except for 
> an END statement.  As a control I loaded another model, 
> rotated it in editing mode, then saved it as a new pdb file 
> (so no selection creation or change from selection to 
> object).  It also wrote an empty but for END file.  I googled 
> around and look through some of the mailing list, but have 
> not found any clues.
> 
> I also used File-> Save molecule from the pull-down menu, same result.
> 
> Does anyone have an idea what is going on or how to correct?
> Pymol version 0.99rc6 running on Linux (CentOS 4.4)
> 
> 
> Stuart Endo-Streeter
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ______________________________________
> Stuart T. Endo-Streeter
> Structural Biology and Biophysics
> Dept. Biochemistry
> LSRC C266
> Duke University
> 919-681-1668
> stu...@du...
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
> of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Evan,

By default, the slice tracks with the 3D center of the camera view.

If you turn off tracking, then you can rotate the camera independently of
the slice.  Then, with the mouse in 3-button-editing mode you can manipulate
it with shift-click-and-drag actions.

Height map is self-explanatory (once tracking is off...).

Dynamic grid can improve performance by reducing sampling to only what is
needed onscreen.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of J. Evan Sadler
> Sent: Tuesday, April 24, 2007 2:14 PM
> To: PyM...@li...
> Subject: [PyMOL] Using "slice" on a map
> 
> Hi,
> 
> I'm trying to use the "slice" function on the map of an EM 
> reconstruction, but can't find any documentation or list comments.
> 
> "Slice" makes a thin section of the map and colors it red 
> (empty) to blue (high density). I've figured out how to move 
> the map through the slice with the mouse (Shift, Wheel) but 
> can't see how to do this with commands.
> 
> Also, is there a way to rotate the slice, so I can see it 
> from an angle?
> 
> Finally, what is the meaning or use of "tracking on/off", 
> "height map on/off", and "dynamic grid on/off"?
> 
> Thanks,
> Evan Sadler
> 
> --
> J. Evan Sadler, M.D., Ph.D.
> Howard Hughes Medical Institute
> Washington University
> 660 S. Euclid Ave., Box 8022
> St. Louis, MO   63110
> Tel: 314-362-9067
> FAX: 314-454-3012
> email: es...@im...
> 
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Am Samstag, 28. April 2007 schrieb Michael Kluge:

> > Would that be feasable?

Oh sorry, i overlooked the ia64 in your gcc line. I have no idea how much I=
A64=20
SuSE,  differs from the others. OpenSuSE is only provided for i586 and=20
x86_64, not Itanium. But if you want, you can either use my spec file and=20
compile yourself or I can also ask the guys here at the LRZ if they can che=
ck=20
this.
I am using opensuse build service to build for  Opensuse 10.2
http://build.opensuse.org/project/monitor?project=3Dhome%3Amartoss

> You could try the IA32 stuff in the Itanium. But that runs through an
> IA32 emulation layer. Thats like running with ball and chains. For a GUI

The emulation layer is really...
=2E.. slow :-). Newer Itaniums don't even have hardware support for=20
this "feature" but do it entirely in SW.=20

> is this probably OK as processor utilization is not the key, but for HPC
> it is just slow. We have 2584 Core AMD Athlon PC Farm. Maybe you want to
> try deimos?

Hmm, still did not get the point? Do you wanna run pymol on a cluster and n=
ot=20
on a workstation? Most workstations are intel core or opteron/athlon64 base=
d.

Cheers
	Martin
=2D-=20
Echt frustrierend, wenn man so vor seiner Hardware
sitzt und den min=FCtlichen Preisverfall verfolgt...
(John Gawe in de.comp misc)

Hi Andreas,

> PS. @Michael
>  From Martin Hoefling:
>=20
>> i have no idea about your error but i can provide you RPMs for=20
>> Opensuse 10.2 i586 and x86_64, if you need them for other SuSE=20
>> distributions, I can try to add them to my repository.
>>
> Would that be feasable?

You could try the IA32 stuff in the Itanium. But that runs through an=20
IA32 emulation layer. Thats like running with ball and chains. For a GUI=20
is this probably OK as processor utilization is not the key, but for HPC=20
it is just slow. We have 2584 Core AMD Athlon PC Farm. Maybe you want to=20
try deimos?


Michael

____________________________________________
Michael Kluge, M.Sc.

Technische Universit=E4t Dresden
Center for Information Services and
High Performance Computing (ZIH)
D-01062 Dresden
Germany

Contact:
Room : HRSK 151
Phone:  (+49) 351 463 32424
Fax  :  (+49) 351 463 37773
email: mic...@tu...

Hi,

Michael Kluge wrote:

>Hi Andreas,
>
>gcc is not the best compiler on an IA64 machine. We always recommend
>using the Intel compilers. Would it be possible to try those?
>
>  
>
I have to figure out, where to modify in the setup script/distutils.
Thanks.

Andreas

PS. @Michael
 From Martin Hoefling:

>i have no idea about your error but i can provide you RPMs for Opensuse 10.2 
>i586 and x86_64, if you need them for other SuSE distributions, I can try to 
>add them to my repository.
>
Would that be feasable?

>Regards, Michael
>
>Andreas Henschel wrote:
>  
>
>>Hi all,
>>
>>did anyone of you come across the mysterious "internal compiler error:
>>Segmentation fault"
>>while compiling pymol from source?
>>
>>The offending lines are in contrib/champ/champ.c:2787
>>
>> PRINTFD(FB_smiles_parsing)
>>   " ChampParseBlockAtom: called.\n"
>>   ENDFD;
>>
>>Can I get around it somehow? Is it a 64-bit/gcc issue?
>>Any help would be greatly appreciated.
>>
>>Some more error/system details:
>>
>>    
>>
>>>python setup.py install
>>>      
>>>
>>...
>>building 'chempy.champ._champ' extension
>>gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall
>>-D_FORTIFY_SOURCE=2 -g -fPIC -Icontrib/champ -I/usr/include/python2.4 -c
>>contrib/champ/champ.c -o build/temp.linux-ia64-2.4/contrib/champ/champ.o
>>contrib/champ/champ.c: In function 'ChampParseBlockAtom':
>>contrib/champ/champ.c:2787: internal compiler error: Segmentation fault
>>Please submit a full bug report,
>>with preprocessed source if appropriate.
>>See <URL:" rel="nofollow">http://www.suse.de/feedback> for instructions.
>>error: command 'gcc' failed with exit status 1
>>
>>    
>>
>>>uname -a
>>>      
>>>
>>Linux mars 2.6.16.27-0.6-default #1 SMP Wed Dec 13 09:34:50 UTC 2006
>>ia64 ia64 ia64 GNU/Linux
>>
>>    
>>
>>>gcc -v
>>>      
>>>
>>Using built-in specs.
>>Target: ia64-suse-linux
>>Configured with: ../configure --enable-threads=posix --prefix=/usr
>>--with-local-prefix=/usr/local --infodir=/usr/share/info
>>--mandir=/usr/share/man --libdir=/usr/lib --libexecdir=/usr/lib
>>--enable-languages=c,c++,objc,fortran,java,ada --enable-checking=release
>>--with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp
>>--disable-libssp --enable-java-awt=gtk --enable-gtk-cairo
>>--disable-libjava-multilib --with-slibdir=/lib --with-system-zlib
>>--enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new
>>--with-system-libunwind --host=ia64-suse-linux
>>Thread model: posix
>>gcc version 4.1.0 (SUSE Linux)
>>ia64 GNU/Linux
>>
>>Cheers,
>>Andreas
>>
>>    
>>
>
>
>  
>

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi Andreas,

gcc is not the best compiler on an IA64 machine. We always recommend
using the Intel compilers. Would it be possible to try those?


Regards, Michael

Andreas Henschel wrote:
> Hi all,
>=20
> did anyone of you come across the mysterious "internal compiler error:
> Segmentation fault"
> while compiling pymol from source?
>=20
> The offending lines are in contrib/champ/champ.c:2787
>=20
>  PRINTFD(FB_smiles_parsing)
>    " ChampParseBlockAtom: called.\n"
>    ENDFD;
>=20
> Can I get around it somehow? Is it a 64-bit/gcc issue?
> Any help would be greatly appreciated.
>=20
> Some more error/system details:
>=20
>> python setup.py install
> ...
> building 'chempy.champ._champ' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=3D0 -Wa=
ll
> -D_FORTIFY_SOURCE=3D2 -g -fPIC -Icontrib/champ -I/usr/include/python2.4=
 -c
> contrib/champ/champ.c -o build/temp.linux-ia64-2.4/contrib/champ/champ.=
o
> contrib/champ/champ.c: In function 'ChampParseBlockAtom':
> contrib/champ/champ.c:2787: internal compiler error: Segmentation fault
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <URL:" rel="nofollow">http://www.suse.de/feedback> for instructions.
> error: command 'gcc' failed with exit status 1
>=20
>> uname -a
> Linux mars 2.6.16.27-0.6-default #1 SMP Wed Dec 13 09:34:50 UTC 2006
> ia64 ia64 ia64 GNU/Linux
>=20
>> gcc -v
> Using built-in specs.
> Target: ia64-suse-linux
> Configured with: ../configure --enable-threads=3Dposix --prefix=3D/usr
> --with-local-prefix=3D/usr/local --infodir=3D/usr/share/info
> --mandir=3D/usr/share/man --libdir=3D/usr/lib --libexecdir=3D/usr/lib
> --enable-languages=3Dc,c++,objc,fortran,java,ada --enable-checking=3Dre=
lease
> --with-gxx-include-dir=3D/usr/include/c++/4.1.0 --enable-ssp
> --disable-libssp --enable-java-awt=3Dgtk --enable-gtk-cairo
> --disable-libjava-multilib --with-slibdir=3D/lib --with-system-zlib
> --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=3Dne=
w
> --with-system-libunwind --host=3Dia64-suse-linux
> Thread model: posix
> gcc version 4.1.0 (SUSE Linux)
> ia64 GNU/Linux
>=20
> Cheers,
> Andreas
>=20


--=20
____________________________________________
Michael Kluge, M.Sc.

Technische Universit=E4t Dresden
Center for Information Services and
High Performance Computing (ZIH)
D-01062 Dresden
Germany

Contact:
Willersbau, Room HRSK 151
Phone:  (+49) 351 463-32424
Fax:    (+49) 351 463-37773
e-mail: mic...@tu...
WWW:    http://www.tu-dresden.de/zih

Hi all,

did anyone of you come across the mysterious "internal compiler error: 
Segmentation fault"
while compiling pymol from source?

The offending lines are in contrib/champ/champ.c:2787

  PRINTFD(FB_smiles_parsing)
    " ChampParseBlockAtom: called.\n"
    ENDFD;

Can I get around it somehow? Is it a 64-bit/gcc issue?
Any help would be greatly appreciated.

Some more error/system details:

 > python setup.py install
...
building 'chempy.champ._champ' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall 
-D_FORTIFY_SOURCE=2 -g -fPIC -Icontrib/champ -I/usr/include/python2.4 -c 
contrib/champ/champ.c -o build/temp.linux-ia64-2.4/contrib/champ/champ.o
contrib/champ/champ.c: In function 'ChampParseBlockAtom':
contrib/champ/champ.c:2787: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:" rel="nofollow">http://www.suse.de/feedback> for instructions.
error: command 'gcc' failed with exit status 1

 > uname -a
Linux mars 2.6.16.27-0.6-default #1 SMP Wed Dec 13 09:34:50 UTC 2006 
ia64 ia64 ia64 GNU/Linux

 > gcc -v
Using built-in specs.
Target: ia64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr 
--with-local-prefix=/usr/local --infodir=/usr/share/info 
--mandir=/usr/share/man --libdir=/usr/lib --libexecdir=/usr/lib 
--enable-languages=c,c++,objc,fortran,java,ada --enable-checking=release 
--with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp 
--disable-libssp --enable-java-awt=gtk --enable-gtk-cairo 
--disable-libjava-multilib --with-slibdir=/lib --with-system-zlib 
--enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new 
--with-system-libunwind --host=ia64-suse-linux
Thread model: posix
gcc version 4.1.0 (SUSE Linux)
ia64 GNU/Linux

Cheers,
Andreas

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi, 

I was wondering if it's possible to redefine the x, y and z axis using
coordinates of your own choice. I would like to not only set origin for a
coordinates system, but also where the x, y and z axes go. I know how to get
coordinates and unit vectors for the new coordinate system, but I don't know
where to input them to get the effect that I want in PYMOL :) 

Btw, thanks very much for the help with the spheres, that worked out just great
:) 

Cheers, 
Siv

-- 
Siv Midtun Hollup 
PhD Student
Dept. of Informatics
University of Bergen, Norway
si...@ii... (NOTE: new email adress)
- Blessed are the flexible, for they can be tied into knots. -

Hi all,

I am trying to fit part of my search model into my experimental density using 
pymol.  I got initial model fitting to the experimental map using molrep, but 
want to make some changes to certain helices and strands before I pop the 
model into a rigid body and simulated annealing run, since they're obviously 
off by eye and a correction here would make the subsequent runs that much 
better.  I've done the following:

Loaded molrep fit model
Loaded experimental maps
Created selection of residues to move
Turned selection into an object
Moved object using "3-button Editing" mode
Save object.pdb, object name

However, when I look at the saved file that should contain the coordinates of 
the adjusted model, it is empty except for an END statement.  As a control I 
loaded another model, rotated it in editing mode, then saved it as a new pdb 
file (so no selection creation or change from selection to object).  It also 
wrote an empty but for END file.  I googled around and look through some of 
the mailing list, but have not found any clues.

I also used File-> Save molecule from the pull-down menu, same result.

Does anyone have an idea what is going on or how to correct?
Pymol version 0.99rc6 running on Linux (CentOS 4.4)


Stuart Endo-Streeter









______________________________________
Stuart T. Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
stu...@du...

Hi,

I'm trying to use the "slice" function on the map of an EM reconstruction,
but can't find any documentation or list comments.

"Slice" makes a thin section of the map and colors it red (empty) to blue
(high density). I've figured out how to move the map through the slice with
the mouse (Shift, Wheel) but can't see how to do this with commands.

Also, is there a way to rotate the slice, so I can see it from an angle?

Finally, what is the meaning or use of "tracking on/off", "height map
on/off", and "dynamic grid on/off"?

Thanks,
Evan Sadler

-- 
J. Evan Sadler, M.D., Ph.D.
Howard Hughes Medical Institute
Washington University
660 S. Euclid Ave., Box 8022
St. Louis, MO   63110
Tel: 314-362-9067
FAX: 314-454-3012
email: es...@im...

Hi,

I'd like to add user defined colors to the "color by element" list.
How is this done? Also, I'd like to order them by my preference.
Thanks in advance for the help.

- Eva

Dear all,
I don't know how to iterate over the whole number of states of a trajectory=
 in=20
order to perform some actions, which are usually performed only on a single=
=20
state.

=46or example, how can I alter the coordinates of all the states like in th=
e=20
command
cmd.alter_state(all,selection,"(x,y,z)=3D(x+1,y+1,z+1)"
?

Thanks,
gianluca
=2D-=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Gianluca Santarossa
Institute for Chemical and Bioengineering
Department of Chemistry and Applied Biosciences
ETH Zurich, H=F6nggerberg, HCI, 8093 Zurich

Phone: +41 44 633 4232
E-Mail: gia...@ch...
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Hi Justin,

If you have a pdb file of your coumarin derivative (which you can
obtain e.g. with the PRODRG server), you can use 'fuse' to attach it
to some amino acid side chain.

By the way, it may be a good idea to try and polish your english a
bit. A question clearly phrased will help people on the list to
understand what you need and to provide an answer.

Tschuss,

Tsjerk

On 4/22/07, Justin Schmitz <Jus...@un...> wrote:
> Good morning everyone!
>
> I want to build a modell with an unnatural aminoacid inside. I'm using a
> system wich allows me to incooperate a Coummarinderivatet aminoacid at
> speziel positions in my protein. For my talks I want to create some nice
> pictures. so how can mutate the sequence in my structure file or how can
> I do this in pymol.
>
> THX 4 help
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Good morning everyone!

I want to build a modell with an unnatural aminoacid inside. I'm using a 
system wich allows me to incooperate a Coummarinderivatet aminoacid at 
speziel positions in my protein. For my talks I want to create some nice 
pictures. so how can mutate the sequence in my structure file or how can 
I do this in pymol.

THX 4 help

Andreas,

Thank you for posting that script.

One of the new features in the PyMOL 1.0 betas is the pseudoatom command
which has a similar behavior.

pseudoatom object-name, selection
show spheres, object-name

In terms of finding the center of mass, try:

center selection
print cmd.get_position()

Cheers,
Warren


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Andreas Henschel
> Sent: Friday, April 20, 2007 10:51 AM
> To: Siv Midtun Hollup
> Cc: pym...@li...
> Subject: Re: [PyMOL] building centroids for residues
> 
> Hi Siv,
> 
> below is a python script (I sent earlier to the mailing list) 
> that calculates the Center of mass for a given selection and 
> creates a CGO sphere there. It is is not 100% exact as it 
> only weighs C-Alpha atoms.
> This is exactly how pymol centers selections: when you run 
> the script, the domain is centered and if you rotate the 
> structure with the mouse, the CGO will remain centered.
> For side chains you could make a selection of the sidechain 
> carbon atoms of that residue, or all of the side chain atoms:
> 
> centerOfmass("/1n8o//E/41 and not (name c+n+o)").
> 
> Also see the ellipsoid script in the wiki.
> CGOs and self defined atoms perfectly rotate along (infact 
> you are changing the camera view, the coordinates remain - 
> unless you explictely use cmd.rotate or cmd.translate).
> See e.g.
> http://yggdrasil.biotec.tu-dresden.de/abac/b.47.1.2___b.16.1.1
> ___g.4.1.1.html
> 
> I hope that helps.
> 
> ha det bra,
> Andreas
> 
> 
> from pymol import cmd
> from pymol.cgo import *
> 
> def centerOfMass(selection):
>    ## assumes equal weights (best called with "and name ca" suffix)
>    model = cmd.get_model(selection)
>    x,y,z=0,0,0
>    for a in model.atom:
>        x+= a.coord[0]
>        y+= a.coord[1]
>        z+= a.coord[2]
>    return (x/len(model.atom), y/len(model.atom), z/len(model.atom))
> 
> cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")
> cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## 
> selecting a domain
> 
> domainCenter=centerOfMass("domain")
> 
> print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter 
> cmd.as("cartoon", "all") cmd.show("spheres", "domain")
> 
> ## Creating a sphere CGO
> com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + 
> [3.0] ## white sphere with 3A radius cmd.load_cgo(com, "CoM")
> 
> cmd.zoom("1c7c", 1.0)
> cmd.center("domain")
> 
> #ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py 
> #Center of mass: (-1.0,24.5,48.2) #ah@bioinfws19:~/Projects/PyMOL$
> 
> Siv Midtun Hollup wrote:
> 
> >Hi,
> >
> >I would like to examine the approximate volume of different 
> residues in 
> >a protein. To do this, I would like to add a centroid for 
> each residue, 
> >and visualise the volume by using different sphere-sizes.
> >
> >Is there a built-in function to find center of mass for a 
> selection of atoms?
> >The center command looks promising, can I get the coordinates of the 
> >center of mass using that?  (feks using get_view() or similar?)
> >
> >Can I add a centroid "atom" to a residue in PYMOL? Would it be 
> >translated and rotated along with the residue if I move the 
> structure around afterwards?
> >
> >Any pointers much appriciated :)
> >
> >Cheers,
> >Siv
> >
> >  
> >
> 
> --
> Andreas Henschel
> Bioinformatics Group
> TU Dresden
> Tatzberg 47-51
> 01307 Dresden, Germany
> 
> Phone: +49 351 463 40063
> EMail: ah...@bi...
> 
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
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Dear Felix,

One of the easiest ways to determine whether a point is inside a
triclinic box is by matrix multiplying the coordinates with the
inverse of the box matrix. Then, every point which has coordinates
within [0,1] will be inside the box. Furthermore, every point can be
mapped to the triclinic box of the unit cell by subtracting the
integer portions (keeping the fractions only, which indicate the
fractional coordinates in a box). The only difficult part in what you
desire seems to be determining the centers of mass of each molecule,
where you need to know what are the molecules in a selection given.
This must be in Pymol somewhere, but that one I pass to Warren (or
anyone else who knows it). With that it would be rather trivial and
maybe it's worth 15 minutes to make somebody's life perfect :) It is
to say that I already have some routines in python which will
transform coordinates to box coordinates and back, so it'll be putting
a few parts together.

Best,

Tsjerk

On 4/21/07, Felix Frolow <mbf...@po...> wrote:
> Hi Tsjerk
> To make our life perfect we need a script (we do it on this stage
> manually)
> to select molecules with the center of gravity inside the cell
> Then, applying script you suggest it will be possible to show packing
> arrangement
> inside any box of multiple cell. Very much needed...
> FF
> Dr  Felix Frolow
> Professor of Structural Biology and Biotechnology
> Department of Molecular Microbiology
> and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica D, co-editor
>
> e-mail: mbf...@po...
> Tel:  ++972-3640-8723
> Fax: ++972-3640-9407
>
>
> On Apr 20, 2007, at 9:30 AM, Tsjerk Wassenaar wrote:
>
> > Hi Gianluca,
> >
> > Unfortunately, Pymol offers no such functionality intrinsically. But
> > this is where python comes in handy. Attached you find a script I
> > wrote for the purpose. It allows you to shift objects or selections
> > over the periodic lattice:
> >
> > run lattice.py
> > create ObjectCopy,MyObject
> > shift 1,0,0,ObjectCopy # make one shift over the first vector of
> > the lattice
> > shift 0,1,0,ObjectCopy # make one shift over the second vector of
> > the lattice
> > shift 2,2,2,ObjectCopy # make two shifts over each of the vectors of
> > the lattice
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On 4/19/07, Gianluca Santarossa <gia...@ch...>
> > wrote:
> >> Dear all,
> >> is there a way to show the periodic images from a slab in PyMOL?
> >>
> >> Thanks,
> >> Gianluca
> >> --
> >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> >> Gianluca Santarossa
> >> Institute for Chemical and Bioengineering
> >> Department of Chemistry and Applied Biosciences
> >> ETH Zurich, H=F6nggerberg, HCI, 8093 Zurich
> >>
> >> Phone: +41 44 633 4232
> >> E-Mail: gia...@ch...
> >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> >>
> >> ---------------------------------------------------------------------
> >> ----
> >> This SF.net email is sponsored by DB2 Express
> >> Download DB2 Express C - the FREE version of DB2 express and take
> >> control of your XML. No limits. Just data. Click to get it now.
> >> http://sourceforge.net/powerbar/db2/
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> > <lattice.py>
> > ----------------------------------------------------------------------
> > ---
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>


--=20
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Siv,

below is a python script (I sent earlier to the mailing list) that 
calculates the Center of mass for a given selection
and creates a CGO sphere there. It is is not 100% exact as it only 
weighs C-Alpha atoms.
This is exactly how pymol centers selections: when you run the script, 
the domain is centered and if you rotate the structure with the mouse, 
the CGO will remain centered.
For side chains you could make a selection of the sidechain carbon atoms 
of that residue, or all of the side chain atoms:

centerOfmass("/1n8o//E/41 and not (name c+n+o)").

Also see the ellipsoid script in the wiki.
CGOs and self defined atoms perfectly rotate along (infact you are 
changing the camera view, the coordinates remain - unless you explictely 
use cmd.rotate or cmd.translate).
See e.g.
http://yggdrasil.biotec.tu-dresden.de/abac/b.47.1.2___b.16.1.1___g.4.1.1.html

I hope that helps.

ha det bra,
Andreas


from pymol import cmd
from pymol.cgo import *

def centerOfMass(selection):
   ## assumes equal weights (best called with "and name ca" suffix)
   model = cmd.get_model(selection)
   x,y,z=0,0,0
   for a in model.atom:
       x+= a.coord[0]
       y+= a.coord[1]
       z+= a.coord[2]
   return (x/len(model.atom), y/len(model.atom), z/len(model.atom))

cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")
cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain

domainCenter=centerOfMass("domain")

print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter
cmd.as("cartoon", "all")
cmd.show("spheres", "domain")

## Creating a sphere CGO
com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + [3.0] ## white 
sphere with 3A radius
cmd.load_cgo(com, "CoM")

cmd.zoom("1c7c", 1.0)
cmd.center("domain")

#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
#Center of mass: (-1.0,24.5,48.2)
#ah@bioinfws19:~/Projects/PyMOL$

Siv Midtun Hollup wrote:

>Hi, 
>
>I would like to examine the approximate volume of different residues in a
>protein. To do this, I would like to add a centroid for each residue, and
>visualise the volume by using different sphere-sizes. 
>
>Is there a built-in function to find center of mass for a selection of atoms?
>The center command looks promising, can I get the coordinates of the center of
>mass using that?  (feks using get_view() or similar?)
>
>Can I add a centroid "atom" to a residue in PYMOL? Would it be translated and
>rotated along with the residue if I move the structure around afterwards?
>
>Any pointers much appriciated :) 
>
>Cheers,
>Siv
>
>  
>

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi, 

I would like to examine the approximate volume of different residues in a
protein. To do this, I would like to add a centroid for each residue, and
visualise the volume by using different sphere-sizes. 

Is there a built-in function to find center of mass for a selection of atoms?
The center command looks promising, can I get the coordinates of the center of
mass using that?  (feks using get_view() or similar?)

Can I add a centroid "atom" to a residue in PYMOL? Would it be translated and
rotated along with the residue if I move the structure around afterwards?

Any pointers much appriciated :) 

Cheers,
Siv

-- 
Siv Midtun Hollup 
PhD Student
Dept. of Informatics
University of Bergen, Norway
si...@ii... (NOTE: new email adress)
- Blessed are the flexible, for they can be tied into knots. -

Hi Jim,

Hmmm. I think your best option is to color the surface according to
the atoms and write the surface in povray format. This will give you
all the vertices. Just another thought springing to mind, you could
cycle over the atoms using a script, writing away only the part of the
surface belonging to the active atom.
I don't think the vertices are available otherwise, and you would need
to dive into the source code to get them out otherwise.

Best,

Tsjerk

On 4/17/07, jjv5 <jj...@jj...> wrote:
> Hello,
>
> Is there a way to access the individual vertices of a surface abd there
> association with atoms? I know it's done under the hood, but can I write
> some code that say returns a list of surface vertices associated with a
> particular atom?
>
> In the end, I'd like to know if two atoms share a surface vertex to
> determine if they are "surface neighbors".
>
> Thanks,
> Jim
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Gianluca,

Unfortunately, Pymol offers no such functionality intrinsically. But
this is where python comes in handy. Attached you find a script I
wrote for the purpose. It allows you to shift objects or selections
over the periodic lattice:

run lattice.py
create ObjectCopy,MyObject
shift 1,0,0,ObjectCopy # make one shift over the first vector of the lattic=
e
shift 0,1,0,ObjectCopy # make one shift over the second vector of the latti=
ce
shift 2,2,2,ObjectCopy # make two shifts over each of the vectors of
the lattice

Hope it helps,

Tsjerk

On 4/19/07, Gianluca Santarossa <gia...@ch...> wrote:
> Dear all,
> is there a way to show the periodic images from a slab in PyMOL?
>
> Thanks,
> Gianluca
> --
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> Gianluca Santarossa
> Institute for Chemical and Bioengineering
> Department of Chemistry and Applied Biosciences
> ETH Zurich, H=F6nggerberg, HCI, 8093 Zurich
>
> Phone: +41 44 633 4232
> E-Mail: gia...@ch...
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--=20
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Dear all,
is there a way to show the periodic images from a slab in PyMOL?

Thanks,
Gianluca
=2D-=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Gianluca Santarossa
Institute for Chemical and Bioengineering
Department of Chemistry and Applied Biosciences
ETH Zurich, H=F6nggerberg, HCI, 8093 Zurich

Phone: +41 44 633 4232
E-Mail: gia...@ch...
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Martin,

No, sorry, you will need an external tool to do this.

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Martin Sztacho
> Sent: Monday, April 16, 2007 3:51 AM
> To: pym...@li...
> Subject: [PyMOL] (no subject)
> 
> Hello,
>  I would like to ask about building phosphate group at Tyr 
> residue. Is there any posibility to do it at PyMOL programe?
> Thank you for answer
> Martin Sztacho
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
> of your XML. No limits. Just data. Click to get it now.
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> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Just FYI -- use the latest open-source code or recent beta builds for
current VRML export, since older versions export faulty VRML.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of aaron bryden
> Sent: Wednesday, April 18, 2007 12:15 PM
> To: pym...@li...
> Subject: [PyMOL] vrml export normals
> 
> Has anyone had good luck with the VRML export. It seems that 
> there is a problem with the normals that are exported in some 
> cases.  Can anyone recommend a VRML viewer that works well 
> with the exported files.
> 
> aaron
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
> of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Tom,
 
This isn't currently possible without "hacking" the session files, and doing
so is not something I can encourage as a "supportable" activity.
 
Use a script!
 
Cheers,
Warren


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Thomas Stout
Sent: Wednesday, April 18, 2007 10:24 AM
To: pym...@li...
Subject: [PyMOL] "report" or "clone" settings?


 
Does anyone know if there is a way of reporting all of the display settings
for an object, or - conversely - "cloning" the display settings from one
object onto another?  Specifically, I am thinking about the situation where
I have one elaborately displayed object that is protein A in complex with
ligand 1.  Now I am in a position where I want to apply those same settings
to many more objects that are also protein A, although each in complex with
a different ligand (2 through N).  All objects are named identically in
terms of chains, residue numbers, et cetera.
 
Thanks!
-Tom
 
PS - Yes, I know that the "right" way to have done this was via  a script
that defined all settings, a la molscript, but that's not the situation I am
in now!



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