pymol-users Mailing List for PyMOL Molecular Graphics System

FYI, that worked for me.  I just copied the binary to /usr/local/lib.

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner <mgl...@gm...> wrote:
> Can you go to the "Program Locations" tab and find out which version of APBS
> you're using? There's a problem with the one in
> /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.
>
> I've added instructions for fixing this problem to
> http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
> top of the page, under "APBS Plugin FAQ". Could you try them out and see if
> they work for you?
>
> Thanks,
>
> -Michael
>
> On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dga...@ni...>
> wrote:
>>
>> I download and install macpymol-1_2r2.tgz.
>>
>> I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
>> up.
>>
>> Load a pdb file after removing HETATM lines.
>>
>> Open APBS Tools and set grid:
>> Log:
>> Maximum number of grid points exceeded.  Old grid dimensions were
>> [129, 97, 129]
>> Fine grid points rounded down from [117, 87, 117]
>> New grid dimensions are [97, 65, 97]
>>  APBS Tools: coarse grid: (76.908,61.259,77.489)
>>  APBS Tools: fine grid: (65.240,56.035,65.582)
>>  APBS Tools: center: (-22.620,-1.106,-3.967)
>>  APBS Tools: fine grid points (97,65,97)
>>
>> Click "Run APBS", see hydrogens appear, see residues being selected
>> and unselected, then the display says:
>>
>> Log:
>> ObjectMapLoadDXFile-Error: Unable to open file!
>> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>>
>>
>> Help?
>> PowerBook, PPC, 10.4.11
>>
>> Dave
>>
>>
>> --
>> David N. Garboczi, PhD
>> Phone: 301-496-4773
>> Head, Structural Biology Section (SBS)
>> Research Technologies Branch (RTB)
>> National Institute of Allergy and Infectious Diseases (NIAID)
>> National Institutes of Health (NIH)
>> Twinbrook 2/Room 110
>> 12441 Parklawn Drive
>> Rockville, Maryland 20852-1742
>> Fax:    301-402-0284
>> Email: dga...@ni...
>>
>>
>> The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be
>> used by anyone who is not the original intended recipient.  If you have
>> received this e-mail in error please inform the sender and delete it
>> from your mailbox or any other storage devices.  The National Institute
>> of Allergy and Infectious Diseases (NIAID) shall not accept liability
>> for any statement made that are the sender's own and not expressly made
>> on behalf of the NIAID by one of its representatives.
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> ------------------------------------------------------------------------------
> Join us December 9, 2009 for the Red Hat Virtual Experience,
> a free event focused on virtualization and cloud computing.
> Attend in-depth sessions from your desk. Your couch. Anywhere.
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Can you go to the "Program Locations" tab and find out which version of APBS
you're using? There's a problem with the one in
/Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.

I've added instructions for fixing this problem to
http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
top of the page, under "APBS Plugin FAQ". Could you try them out and see if
they work for you?

Thanks,

-Michael

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dga...@ni...>wrote:

> I download and install macpymol-1_2r2.tgz.
>
> I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
> up.
>
> Load a pdb file after removing HETATM lines.
>
> Open APBS Tools and set grid:
> Log:
> Maximum number of grid points exceeded.  Old grid dimensions were
> [129, 97, 129]
> Fine grid points rounded down from [117, 87, 117]
> New grid dimensions are [97, 65, 97]
>  APBS Tools: coarse grid: (76.908,61.259,77.489)
>  APBS Tools: fine grid: (65.240,56.035,65.582)
>  APBS Tools: center: (-22.620,-1.106,-3.967)
>  APBS Tools: fine grid points (97,65,97)
>
> Click "Run APBS", see hydrogens appear, see residues being selected
> and unselected, then the display says:
>
> Log:
> ObjectMapLoadDXFile-Error: Unable to open file!
> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>
>
> Help?
> PowerBook, PPC, 10.4.11
>
> Dave
>
>
> --
> David N. Garboczi, PhD
> Phone: 301-496-4773
> Head, Structural Biology Section (SBS)
> Research Technologies Branch (RTB)
> National Institute of Allergy and Infectious Diseases (NIAID)
> National Institutes of Health (NIH)
> Twinbrook 2/Room 110
> 12441 Parklawn Drive
> Rockville, Maryland 20852-1742
> Fax:    301-402-0284
> Email: dga...@ni...
>
>
> The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be
> used by anyone who is not the original intended recipient.  If you have
> received this e-mail in error please inform the sender and delete it
> from your mailbox or any other storage devices.  The National Institute
> of Allergy and Infectious Diseases (NIAID) shall not accept liability
> for any statement made that are the sender's own and not expressly made
> on behalf of the NIAID by one of its representatives.
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

I download and install macpymol-1_2r2.tgz.

I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up.

Load a pdb file after removing HETATM lines.

Open APBS Tools and set grid:
Log:
Maximum number of grid points exceeded.  Old grid dimensions were 
[129, 97, 129]
Fine grid points rounded down from [117, 87, 117]
New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

Click "Run APBS", see hydrogens appear, see residues being selected 
and unselected, then the display says:

Log:
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


Help?
PowerBook, PPC, 10.4.11

Dave


-- 
David N. Garboczi, PhD
Phone: 301-496-4773
Head, Structural Biology Section (SBS)
Research Technologies Branch (RTB)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
Fax:    301-402-0284
Email: dga...@ni...


The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient.  If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices.  The National Institute
of Allergy and Infectious Diseases (NIAID) shall not accept liability
for any statement made that are the sender's own and not expressly made
on behalf of the NIAID by one of its representatives.

Robert,

Great point!  My original script had selections from protein A to a
ligand in any other protein B.  I just left it in there.

I agree that creating a named selection for each object is
unnecessary.  If he really wanted a clean namespace, he could dump all
of those into a group(s) or a multi-state object.

Nice attention to detail,

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Sun, Nov 29, 2009 at 9:50 PM, Robert Campbell
<rob...@qu...> wrote:
> Hi Jason,
>
> On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees <jas...@gm...>
> wrote:
>
>> You can automate the task.  Load your 100 proteins.  Use a wildcard
>> from the command line or a script like loadDir
>> (http://pymolwiki.org/index.php/LoadDir).  Align them.  Then, run:
>>
>> python
>> for n in cmd.get_names("objects"):
>>   selName = "s" + n
>>   cmd.select(selName, n)
>>   cmd.distance("dist"+n, selName, selName + " and (organic and " + n + ")", 3.2, mode=2)
>> python end
>
> I'm just curious, but why do you go to the trouble to create a selection that
> is just the whole object? Especially if Chimed has 100s of objects, he
> doesn't need to add a named selection for each. Why not do the following?
>
> python
> for n in cmd.get_names("objects"):
>  cmd.distance("dist"+n,n,n + " and organic",3.2, mode=2)
> python end
>
> The latter worked for me.  If you wanted to eliminate waters from
> the selection for the protein, you could change it to:
>
> python
> for n in cmd.get_names("objects"):
>  cmd.distance("dist"+n,n + " and not solvent",n + " and organic",3.2,mode=2)
> python end
>
> Or to make it more readable:
>
> python
> for n in cmd.get_names("objects"):
>  protein_sele = n + " and not solvent"
>  organic_sele = n + " and organic"
>  cmd.distance("dist"+n, protein_sele, organic_sele, 3.2, mode=2)
> python end
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821            Fax: 613-533-2497
> <rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Jason,

On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees <jas...@gm...>
wrote:

> You can automate the task.  Load your 100 proteins.  Use a wildcard
> from the command line or a script like loadDir
> (http://pymolwiki.org/index.php/LoadDir).  Align them.  Then, run:
> 
> python
> for n in cmd.get_names("objects"):
>   selName = "s" + n
>   cmd.select(selName, n)
>   cmd.distance("dist"+n, selName, selName + " and (organic and " + n + ")", 3.2, mode=2)
> python end

I'm just curious, but why do you go to the trouble to create a selection that
is just the whole object? Especially if Chimed has 100s of objects, he
doesn't need to add a named selection for each. Why not do the following?

python
for n in cmd.get_names("objects"):
  cmd.distance("dist"+n,n,n + " and organic",3.2, mode=2)
python end

The latter worked for me.  If you wanted to eliminate waters from
the selection for the protein, you could change it to:

python
for n in cmd.get_names("objects"):
  cmd.distance("dist"+n,n + " and not solvent",n + " and organic",3.2,mode=2) 
python end

Or to make it more readable:

python
for n in cmd.get_names("objects"):
  protein_sele = n + " and not solvent"
  organic_sele = n + " and organic"
  cmd.distance("dist"+n, protein_sele, organic_sele, 3.2, mode=2)
python end

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Chimed,

You can automate the task.  Load your 100 proteins.  Use a wildcard
from the command line or a script like loadDir
(http://pymolwiki.org/index.php/LoadDir).  Align them.  Then, run:

python
for n in cmd.get_names("objects"):
  selName = "s" + n
  cmd.select(selName, n)
  cmd.distance("dist"+n, selName, selName + " and (organic and " + n +
")", 3.2, mode=2)
python end

This will create the hbond objects for all your proteins.  If this
clutters up the UI too much, check out the group ('help group' in
PyMOL, or http://pymolwiki.org/index.php/Group) command and modify the
loop accordingly.  If you must have all objects in one object, you can
create a multi-state object.  For that, see the create command ("help
create" in PyMOL, or http://pymolwiki.org/index.php/Create).

Hope this helps,

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Sat, Nov 28, 2009 at 5:51 PM, Chimed Jansen <chi...@gm...> wrote:
> Hi Jason,
>
> Thank you, but I have just over 100 pdbs open, so I was hoping to avoid
> having to perform steps on each of them.
>
> I thought there might be a way to create just one conditional object which
> shows the hydrogen bonds between the ligand and protein for each pdb as I
> view them.
>
> Thanks,
> Chimed
>
> On Sat, Nov 28, 2009 at 6:22 PM, Jason Vertrees <jas...@gm...>
> wrote:
>>
>> Chimed,
>>
>> Define a selection between one protein and one ligand.  Then using the
>> mouse, A->Action->Find->Polar Contacts->Within Selection.
>>
>> Let's say you load 10 proteins and 7 have ligands.  You could simply
>> do something like:
>>    select complex1, pdbName1
>> then using the mouse A->Action->Find->Polar Contacts->Within
>> Selection, for that selection.  Repeat for proteins 2..10.
>>
>> If you want to mix the ligands and proteins, say check the bonds
>> between protein1 and ligand7 you could do:
>>    select curComplex, (pdbName1 and polymer) or (pdbName7 and organic)
>> and repeat the A->Action->Find->Polar Contacts->Within Selection step
>> for the curComplex selection.
>>
>> -- Jason
>>
>> --
>> Jason Vertrees, PhD
>>
>> PyMOLWiki -- http://www.pymolwiki.org
>>
>>
>>
>> On Sat, Nov 28, 2009 at 7:59 AM, Chimed Jansen <chi...@gm...>
>> wrote:
>> > Hello PyMol users,
>> >
>> > I have a lot of pdb files open and I've superposed them to compare the
>> > pockets. Now I would like to see the hydrogen bonds formed by each
>> > ligand to
>> > the protein its been crystalised with. I would ideally like an object
>> > which
>> > shows hydrogen bonds between the ligand(s) present (I use organic to
>> > identify them since the naming is different in each pdb) and the protein
>> > of
>> > the enabled object. So far I keep getting an object showing all the
>> > hydrogen
>> > bonds in all the pdbs at once. Given the number of pdbs I'm comparing
>> > creating hydrogen bond objects for each of them would be cumbersome.
>> >
>> > Thank you,
>> > Chimed
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> > 30-Day
>> > trial. Simplify your report design, integration and deployment - and
>> > focus
>> > on
>> > what you do best, core application coding. Discover what's new with
>> > Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>
>

Cun,

To answer your last outstanding question, I don't think PyMOL saves
anything beside the basic atom info for PDB files.  PSE files--PyMOL
session files--save everything.  If you're using linux or a Mac, you
can always just paste the header back on.  An unideal solution, but it
will work.  For those familiar with Warren, he used to joke that PyMOL
could read nearly everything, but didn't export much.  :-)

Good work on that script.  As an exercise, I created a similar script
that given any selection, it will select atoms of a certain type
within it.  So, you can do something like:
    selInside someSelection, solvent
    selInside someSelection, *
which will create a new selection of all those solvent atoms inside
the bounding box (which can be any selection, box or object) you
declare.  You could also create two pseudoatoms anywhere you in your
pdb and use those to define the bounding box. For example,
   load $TUT/1hpv.pdb
   pseudoatom b1, pos=[0,0,0]
   pseudoatom b2, pos=[10,10,10]
   selInside b1 or b2
and the new selection called (insideBoundingObj) has those atoms
within b1 and b2 selected.

You can access the script at http://pymolwiki.org/index.php/SelInside

Hope this helps,

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Thu, Nov 26, 2009 at 6:00 PM, Cun Zhang <apz...@gm...> wrote:
> hi, Jason.
> Thank you for your advice.  I  attach the pdb file at the end.
>
> Cun Zhang
>
>
> The script which is to delete the water molecules inside CNT (with Radii
> 6.26 A ) is :
>
> #!/usr/bin/python
> import __main__
> __main__.pymol_argv = ['pymol','-qc']#Quiet and no GUI
>
> import sys,os,re,pexpect
> import pymol
> from pymol import cmd
>
> pymol.finish_launching()
>
> def selHOH(R):
>     cmd.delete("CNT")
>     cmd.delete("water")
>     cmd.select("CNT","resn UNK")
>     cmd.center("CNT")
>     CENTER=cmd.get_position()[0:2]
>     cmd.delete("CNT")
>     cmd.select("water","resn SOL")
>     atoms=cmd.get_model("water")
>     cmd.select("Water",None)
>     for at in atoms.atom:
>         if (at.coord[0]-CENTER[0])**2+(at.coord[1]-CENTER[1])**2<R**2:
>             cmd.select("Water","Water or byres index %d"%at.index)
>     cmd.remove("Water")
>     cmd.deselect()
>
> The command I use in pymol is:
>
>>load b4em.pdb
>>run selSOL.py
>>selHOH(6.2)
>>save b4em.pdb
>
> b4em.pdb
>
>
>
> 27/11/09 04:48:54, Jason Vertrees <jas...@gm...>:
>
> Can you send me a copy of the PDB file? I'd like to try it on my computer.
>
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> On Wed, Nov 25, 2009 at 9:28 PM, Cun Zhang <apz...@gm...> wrote:
>> Hi, pymol users.
>> I'm a pymol newbie .I have serval question.
>> I have a pdb file which include the information about box size, like
>> TITLE     God Rules Over Mankind, Animals, Cosmos and Such
>> REMARK    THIS IS A SIMULATION BOX
>> CRYST1   39.000   39.000   56.140  90.00  90.00  90.00 P 1           1
>> MODEL        1
>> HETATM    1  C   UNK     1      25.851  19.500   0.710  1.00  0.00
>>
>> I run pymol, and load it, then delete some molecules and save it. Now the
>> information about box size is losing.
>>
>> 2. Is there any way to get  the information about bonds, angles and
>> dihedrals ?
>>    I found the following command can display the bonds information, but
>> can't be assigned to a variable.
>>       >cmd.select('all')
>>       >atoms=cmd.get_model('sele')
>>       >print atoms.list()
>> 3. Is there any way to learn these python api commands of pymol ?
>>
>> Thank you!
>>
>>
>> Blog: http://blog.4message.net
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>

Hello PyMol users,

I have a lot of pdb files open and I've superposed them to compare the
pockets. Now I would like to see the hydrogen bonds formed by each ligand to
the protein its been crystalised with. I would ideally like an object which
shows hydrogen bonds between the ligand(s) present (I use organic to
identify them since the naming is different in each pdb) and the protein of
the enabled object. So far I keep getting an object showing all the hydrogen
bonds in all the pdbs at once. Given the number of pdbs I'm comparing
creating hydrogen bond objects for each of them would be cumbersome.

Thank you,
Chimed

Cun,

For measuring, also check out the Measurement Wizard.  Select
  Wizard > Measurement
from the Upper Control Window (the Tcl/Tk window).  Then, on the far
right you will see a box with "Distances" in it.  This is a menu
option displaying what PyMOL is measuring.  If you want to measure
distances leave it as is; if you want to measure angles or dihedrals
click on "Distances" and change it to your desired option.  Once
you're done with your measurements, click "Done" to quit the wizard.

As for learning the PyMOL API check out
    http://pymolwiki.org/index.php/Category:Commands
which has over 160 commands documented.  Most PyMOL API commands
directly mirror their UI counterparts.  For example,
  save fileName.pdb, objName, state=0
would simply translate to
  cmd.save( "fileName.pdb", "objName", state=0 );

Finally, welcome to PyMOL.

-- Jason

Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Wed, Nov 25, 2009 at 9:28 PM, Cun Zhang <apz...@gm...> wrote:
> Hi, pymol users.
> I'm a pymol newbie .I have serval question.
> I have a pdb file which include the information about box size, like
> TITLE     God Rules Over Mankind, Animals, Cosmos and Such
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   39.000   39.000   56.140  90.00  90.00  90.00 P 1           1
> MODEL        1
> HETATM    1  C   UNK     1      25.851  19.500   0.710  1.00  0.00
>
> I run pymol, and load it, then delete some molecules and save it. Now the
> information about box size is losing.
>
> 2. Is there any way to get  the information about bonds, angles and
> dihedrals ?
>    I found the following command can display the bonds information, but
> can't be assigned to a variable.
>       >cmd.select('all')
>       >atoms=cmd.get_model('sele')
>       >print atoms.list()
> 3. Is there any way to learn these python api commands of pymol ?
>
> Thank you!
>
>
> Blog: http://blog.4message.net
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

>2. Is there any way to get  the information about bonds, angles and dihedrals ?
>   I found the following command can display the bonds information, but can't 
> be assigned to a variable.
>>      >cmd.select('all')
>      >atoms=cmd.get_model('sele')
>      >print atoms.list()
http://pymolwiki.org/index.php/Get_Distance 
http://pymolwiki.org/index.php/Get_Angle
http://pymolwiki.org/index.php/Get_Dihedral

>3. Is there any way to learn these python api commands of pymol ?
http://pymolwiki.org/index.php/Category:Commands is a good start, looking 
through the script library is good.  using other python techniques to dump the 
contents of cmd is good.

>
>Thank you!
>
> 
>Blog: http://blog.4message.net
>



      

Hi, pymol users.
I'm a pymol newbie .I have serval question.
I have a pdb file which include the information about box size, like
TITLE     God Rules Over Mankind, Animals, Cosmos and Such
REMARK    THIS IS A SIMULATION BOX
CRYST1   39.000   39.000   56.140  90.00  90.00  90.00 P 1           1
MODEL        1
HETATM    1  C   UNK     1      25.851  19.500   0.710  1.00  0.00

I run pymol, and load it, then delete some molecules and save it. Now the
information about box size is losing.

2. Is there any way to get  the information about bonds, angles and
dihedrals ?
   I found the following command can display the bonds information, but
can't be assigned to a variable.
      >cmd.select('all')
      >atoms=cmd.get_model('sele')
      >print atoms.list()
3. Is there any way to learn these python api commands of pymol ?

Thank you!


Blog: http://blog.4message.net

Hi,

I can try to look into this, although I'm not sure what's causing it. Can
you tell me

 - what version of PyMOL you have and how it was installed
 - what version of APBS you have and how it was installed
 - when exactly the segmentation fault happens (are you working with a
particular PDB file, etc.)

Thanks,

-Michael

On Sun, Nov 22, 2009 at 4:00 PM, Mehdi Talebzadeh Farooji <
mah...@ya...> wrote:

> Dear All,
>
> I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try
> to call plugin of pymol for APBS, pymol crashes with segmentation fault
> message.  Every suggestion would be welcomed!
>
> Thanks,
>
> Mehdi
>
> __________________________________________________
> Do You Yahoo!?
> Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz
> gegen Massenmails.
> http://mail.yahoo.com
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Dear All,

I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try to call plugin
of pymol for APBS, pymol crashes with segmentation fault message.  Every suggestion
would be welcomed!

Thanks,

Mehdi    


__________________________________________________
Do You Yahoo!?
Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. 
http://mail.yahoo.com 

Problem solved: it looks like I just had to use javac from openjdk instead of javac from gcj.

-David



----- Original Message ----
> From: David Hall <dwa...@ya...>
> To: pym...@li...
> Sent: Sun, November 22, 2009 2:22:18 PM
> Subject: [PyMOL] Jymol Question
> 
> I wanted to play around with Jymol free evaluation builds ( 
> http://delsci.com/jymol/ ), but I'm having trouble with the instructions given 
> in the README.txt for using javac to compile the examples.  I know almost 
> nothing about Java, so my problem may be something obvious.
> 
> When I run:
> javac -classpath ../lib/jymol-0.7.1.jar -d . ../src/demos/jymol/simple/*.java
> 
> I get:
> ../src/demos/jymol/simple/Simple.java:16: warning: The serializable class Simple 
> does not declare a static final serialVersionUID field of type long
>         public class Simple extends JFrame
>                      ^^^^^^
> ../src/demos/jymol/simple/Simple.java:21: warning: The serializable class 
> QuitAction does not declare a static final serialVersionUID field of type long
>         class QuitAction extends AbstractAction {
>               ^^^^^^^^^^
> ../src/demos/jymol/simple/Simple.java:151: warning: The local variable app is 
> never read
>         Simple app = new Simple(sb.toString());
>                ^^^
> 3 problems (3 warnings)
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../lib64/crt1.o: In function 
> `_start':
> /usr/src/packages/BUILD/glibc-2.10.1/csu/../sysdeps/x86_64/elf/start.S:109: 
> undefined reference to `main'
> /tmp/ccok2T2B.o: In function 
> `demos::jymol::simple::Simple::Simple(java::lang::String*)':
> cce9zTHY.jar:(.text+0x33c): undefined reference to 
> `com::delsci::jymol::JyMol::class$'
> cce9zTHY.jar:(.text+0x34c): undefined reference to 
> `com::delsci::jymol::JyMol::JyMol()'
> /tmp/ccok2T2B.o:(.data+0x1088): undefined reference to 
> `com::delsci::jymol::JyMol::class$'
> collect2: ld returned 1 exit status
> 
> 
> My javac version (in case it matters):
> javac (SUSE Linux) 4.4.1 [gcc-4_4-branch revision 150839]
> 
> Thanks for any help,
> David
> 
> 
> 
>       
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



      

I wanted to play around with Jymol free evaluation builds ( http://delsci.com/jymol/ ), but I'm having trouble with the instructions given in the README.txt for using javac to compile the examples.  I know almost nothing about Java, so my problem may be something obvious.

When I run:
javac -classpath ../lib/jymol-0.7.1.jar -d . ../src/demos/jymol/simple/*.java

I get:
../src/demos/jymol/simple/Simple.java:16: warning: The serializable class Simple does not declare a static final serialVersionUID field of type long
        public class Simple extends JFrame
                     ^^^^^^
../src/demos/jymol/simple/Simple.java:21: warning: The serializable class QuitAction does not declare a static final serialVersionUID field of type long
        class QuitAction extends AbstractAction {
              ^^^^^^^^^^
../src/demos/jymol/simple/Simple.java:151: warning: The local variable app is never read
        Simple app = new Simple(sb.toString());
               ^^^
3 problems (3 warnings)
/usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../lib64/crt1.o: In function `_start':
/usr/src/packages/BUILD/glibc-2.10.1/csu/../sysdeps/x86_64/elf/start.S:109: undefined reference to `main'
/tmp/ccok2T2B.o: In function `demos::jymol::simple::Simple::Simple(java::lang::String*)':
cce9zTHY.jar:(.text+0x33c): undefined reference to `com::delsci::jymol::JyMol::class$'
cce9zTHY.jar:(.text+0x34c): undefined reference to `com::delsci::jymol::JyMol::JyMol()'
/tmp/ccok2T2B.o:(.data+0x1088): undefined reference to `com::delsci::jymol::JyMol::class$'
collect2: ld returned 1 exit status


My javac version (in case it matters):
javac (SUSE Linux) 4.4.1 [gcc-4_4-branch revision 150839]

Thanks for any help,
David



      

On 11/20/2009 07:43 PM, Jason Vertrees wrote:
> Stephen,
>
> openSuse Linux does not come with Pmw installed by default.  Please
> re-download and install Pmw. Let me know if it's something else.
>
> -- Jason
>
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> On Fri, Nov 20, 2009 at 4:54 PM, Justin Lecher <j.l...@fz...> wrote:
>   
>> Stephen P. Molnar wrote:
>>     
>>> Here's teh end of the log file that I recorded.  I really don't have
>>> anyplace to which to upload the entire 125 kb log file.
>>>       
>> Hi Stephen,
>>
>> as Donnie already mentioned, we cannot help if we could not see the
>> _complete_ build.log. From the part you past, it looks succesfull. So
>> please try to provide us the log, in worst case compress it and attach
>> it to your mail.
>> What exactly is the output if you start it in a shell?
>>
>> Justin
>>
>>
>>
>> --
>> Justin Lecher
>> Institute for Neuroscience and Biophysics
>> ISB 3 - Institute for structural biochemistry
>> Research Centre Juelich GmbH,
>> 52425 Juelich,Germany
>> phone: +49 2461 61 5385
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>     
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>   
Many thanks.  That was the missing library.  The compilation was
completly successful.

I still have a bit of a problem, however.  When I attempt toinstall a
new plugin I get an error message:

"Unable to write to the plugin directory.
Perhaps you have insufficient privileges?"

I don't understand this as
/home/computation/Applications/pymol/modules/pmg_tk/startup has rwx
privileges,


-- 
Stephen P. Molnar, Ph.D.       Life is a fuzzy set
Foundation for Chemistry      Stochastic and multivariate
http://www.FoundationForChemistry.com

I realized I made a mistake.  The proper import statement is:

  from epymol import rigimol

This is shipped in the incentive build of 1.1r2.

-- Jaso

Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Fri, Nov 20, 2009 at 2:50 PM, Huang, Xin <hx...@am...> wrote:
> Thanks Jason.  Does the latest version (1.2r2) of pymol comes with rigimol as warren indicates on the website?  I cannot seem to import rigimol.  (I typed "import rigimol" but have this import error "no module named rigimol).  Any suggestions?  Many Thanks.
>
>
>
> -----Original Message-----
> From: Jason Vertrees [mailto:jas...@gm...]
> Sent: Friday, November 20, 2009 2:38 PM
> To: Michael Zimmermann
> Cc: Huang, Xin; pym...@li...
> Subject: Re: [PyMOL] make morph with rigimol
>
> Michael,
>
> Great advice.  Also, I'd like to point out that the incentive build of
> PyMOL ships with the rigimol morphing module built in.  Rigimol is
> only to be used for visualization, not for pathwway determination.  If
> you only need to make a movie and don't necessarily care about a
> perfect pathway it's as easy as:
>
> from pymol import rigimol
> load str1.pdb, str1    # load two structures
> load str2.pdb, str2
> align str1, str2    # align them
> create m_in, str1, 1, 1  # create the input for rigimol
> create m_in, str2, 1, 2
> rigimol.morph( "m_in", "m_out", refinement=5, async=1)
>
> This creates the "m_out" object as a multistate object. Save the
> output to a mutli-state PDB with:
>
>  save myConf.pdb, m_out, 0
>
> then use that in your movies.
>
> HTH,
>
> -- Jason
>
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> On Fri, Nov 20, 2009 at 2:08 PM, Michael Zimmermann
> <mic...@ia...> wrote:
>> one option would be to make intermediates based on linear
>> interpolation and then make a movie of the "morph."  Gerstein's group
>> has done some work at this.
>> http://www2.molmovdb.org/wiki/info/index.php/Morph_Server
>>
>> If you just want to visualize them together my suggestion would be to:
>> show one of the structures without the helix
>> make an object for the helix in each structure and another object with
>> both helices
>> show cartoons of each helix
>> show a transparent surface of the object with both helices
>> color each helix differently so that the cartoons and surfaces
>> represent conformational changes.
>> play with clipping planes applied to the transparent surface.
>>
>> you could do this type of image for the morph too to emphasize the helix.
>>
>> On Fri, Nov 20, 2009 at 12:45 PM, Huang, Xin <hx...@am...> wrote:
>>> I want to make movie showing conformational changes of one helix (including a couple of side chains) between two structures of the same protein.  Could anybody teach me how to make morph using pymol version 1.2r2?
>>>
>>> Many Thanks.
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>>> trial. Simplify your report design, integration and deployment - and focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>

Stephen,

openSuse Linux does not come with Pmw installed by default.  Please
re-download and install Pmw. Let me know if it's something else.

-- Jason

Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Fri, Nov 20, 2009 at 4:54 PM, Justin Lecher <j.l...@fz...> wrote:
> Stephen P. Molnar wrote:
>> Here's teh end of the log file that I recorded.  I really don't have
>> anyplace to which to upload the entire 125 kb log file.
>
> Hi Stephen,
>
> as Donnie already mentioned, we cannot help if we could not see the
> _complete_ build.log. From the part you past, it looks succesfull. So
> please try to provide us the log, in worst case compress it and attach
> it to your mail.
> What exactly is the output if you start it in a shell?
>
> Justin
>
>
>
> --
> Justin Lecher
> Institute for Neuroscience and Biophysics
> ISB 3 - Institute for structural biochemistry
> Research Centre Juelich GmbH,
> 52425 Juelich,Germany
> phone: +49 2461 61 5385
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Stephen P. Molnar wrote:
> Here's teh end of the log file that I recorded.  I really don't have
> anyplace to which to upload the entire 125 kb log file.

Hi Stephen,

as Donnie already mentioned, we cannot help if we could not see the
_complete_ build.log. From the part you past, it looks succesfull. So
please try to provide us the log, in worst case compress it and attach
it to your mail.
What exactly is the output if you start it in a shell?

Justin



-- 
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

On 11/20/2009 02:16 PM, Donnie Berkholz wrote:
> On 13:38 Fri 20 Nov     , Stephen P. Molnar wrote:
>   
>> I had successfully compiled Plymol from the Subversion repository in
>> OpenSuSE v103. Linux.
>>
>> I say successfully, because I have just upgraded my linux computer to
>> OpenSuSE v11.2.  Unfortunaltely, I have a bit of a problem compiling the
>> source code in the new linux OS in that I can compile the PyMol Viewer
>> but notthe Pcl/Tck GUI.  Obviously there is something missing in the new
>> compiler installation, but I don't have the faintest idea as to what it
>> could be.
>>
>> I was wonderig if anyone else has encountered this problem and/or might
>> have a possible solution?
>>     
> Dear Stephen,
>
> Could you supply the complete error message you encountered, along with 
> the final line of compilation? It's very difficult to make any 
> suggestions without seeing exactly what happened.
>
> If it's unclear to you what to send, just upload the whole build log 
> somewhere and post a link to it here.
>
>   
Here's teh end of the log file that I recorded.  I really don't have
anyplace to which to upload the entire 125 kb log file.
running install
running install_lib
copying build/lib.linux-x86_64-2.6/pymol/_cmd.so ->
/usr/local/lib64/python2.6/site-packages/pymol
copying build/lib.linux-x86_64-2.6/pymol/opengl/glu/_glu_num.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/glu
copying build/lib.linux-x86_64-2.6/pymol/opengl/glu/_glu.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/glu
copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/openglutil_num.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/gl
copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/_opengl.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/gl
copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/_opengl_num.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/gl
copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/openglutil.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/gl
copying build/lib.linux-x86_64-2.6/pymol/opengl/glut/_glut.so ->
/usr/local/lib64/python2.6/site-packages/pymol/opengl/glut
copying build/lib.linux-x86_64-2.6/chempy/champ/_champ.so ->
/usr/local/lib64/python2.6/site-packages/chempy/champ
running install_egg_info
Removing /usr/local/lib64/python2.6/site-packages/pymol-1.2.0-py2.6.egg-info
Writing /usr/local/lib64/python2.6/site-packages/pymol-1.2.0-py2.6.egg-info

 After running:

     python setup.py install
    
 Please run, to complete the installation:

     python setup2.py install

 To uninstall PyMOL, run:

     python setup2.py uninstall

abnormal:/sda1/src/pymol # (Bpython setup2.py install

 Installing into /usr/local/lib64/python2.6/site-packages ...

 Created "./pymol" which can be used to launch PyMOL.  You may wish to copy
 this file into a standard location such as /usr/bin or /usr/local/bin.

Michael,

Great advice.  Also, I'd like to point out that the incentive build of
PyMOL ships with the rigimol morphing module built in.  Rigimol is
only to be used for visualization, not for pathwway determination.  If
you only need to make a movie and don't necessarily care about a
perfect pathway it's as easy as:

from pymol import rigimol
load str1.pdb, str1    # load two structures
load str2.pdb, str2
align str1, str2    # align them
create m_in, str1, 1, 1  # create the input for rigimol
create m_in, str2, 1, 2
rigimol.morph( "m_in", "m_out", refinement=5, async=1)

This creates the "m_out" object as a multistate object. Save the
output to a mutli-state PDB with:

  save myConf.pdb, m_out, 0

then use that in your movies.

HTH,

-- Jason

Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Fri, Nov 20, 2009 at 2:08 PM, Michael Zimmermann
<mic...@ia...> wrote:
> one option would be to make intermediates based on linear
> interpolation and then make a movie of the "morph."  Gerstein's group
> has done some work at this.
> http://www2.molmovdb.org/wiki/info/index.php/Morph_Server
>
> If you just want to visualize them together my suggestion would be to:
> show one of the structures without the helix
> make an object for the helix in each structure and another object with
> both helices
> show cartoons of each helix
> show a transparent surface of the object with both helices
> color each helix differently so that the cartoons and surfaces
> represent conformational changes.
> play with clipping planes applied to the transparent surface.
>
> you could do this type of image for the morph too to emphasize the helix.
>
> On Fri, Nov 20, 2009 at 12:45 PM, Huang, Xin <hx...@am...> wrote:
>> I want to make movie showing conformational changes of one helix (including a couple of side chains) between two structures of the same protein.  Could anybody teach me how to make morph using pymol version 1.2r2?
>>
>> Many Thanks.
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

On 11/20/2009 01:57 PM, Andreas Förster wrote:
> Hey Stephen,
>
> make sure you have Tkinter and freeglut-devel installed.  These are
> the dependencies that make trouble in RHEL.
>
>
> Andreas
>
>
>
> Stephen P. Molnar wrote:
>> I had successfully compiled Plymol from the Subversion repository in
>> OpenSuSE v103. Linux.
>>
>> I say successfully, because I have just upgraded my linux computer to
>> OpenSuSE v11.2.  Unfortunaltely, I have a bit of a problem compiling the
>> source code in the new linux OS in that I can compile the PyMol Viewer
>> but notthe Pcl/Tck GUI.  Obviously there is something missing in the new
>> compiler installation, but I don't have the faintest idea as to what it
>> could be.
>>
>> I was wonderig if anyone else has encountered this problem and/or might
>> have a possible solution?
>>
>> Thanks in advance.
>>
>
Thanks for the suggestion, but that isn't the problem, both Tkiner and
freeglyt-devel are installed.

-- 
Stephen P. Molnar, Ph.D.       Life is a fuzzy set
Foundation for Chemistry      Stochastic and multivariate
http://www.FoundationForChemistry.com

On 13:38 Fri 20 Nov     , Stephen P. Molnar wrote:
> I had successfully compiled Plymol from the Subversion repository in
> OpenSuSE v103. Linux.
> 
> I say successfully, because I have just upgraded my linux computer to
> OpenSuSE v11.2.  Unfortunaltely, I have a bit of a problem compiling the
> source code in the new linux OS in that I can compile the PyMol Viewer
> but notthe Pcl/Tck GUI.  Obviously there is something missing in the new
> compiler installation, but I don't have the faintest idea as to what it
> could be.
> 
> I was wonderig if anyone else has encountered this problem and/or might
> have a possible solution?

Dear Stephen,

Could you supply the complete error message you encountered, along with 
the final line of compilation? It's very difficult to make any 
suggestions without seeing exactly what happened.

If it's unclear to you what to send, just upload the whole build log 
somewhere and post a link to it here.

-- 
Thanks,
Donnie

Donald S. Berkholz, Postdoctoral research fellow
James R. Thompson lab, Physiology & Biomedical Engineering
Grazia Isaya lab, Pediatric & Adolescent Medicine
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905

one option would be to make intermediates based on linear
interpolation and then make a movie of the "morph."  Gerstein's group
has done some work at this.
http://www2.molmovdb.org/wiki/info/index.php/Morph_Server

If you just want to visualize them together my suggestion would be to:
show one of the structures without the helix
make an object for the helix in each structure and another object with
both helices
show cartoons of each helix
show a transparent surface of the object with both helices
color each helix differently so that the cartoons and surfaces
represent conformational changes.
play with clipping planes applied to the transparent surface.

you could do this type of image for the morph too to emphasize the helix.

On Fri, Nov 20, 2009 at 12:45 PM, Huang, Xin <hx...@am...> wrote:
> I want to make movie showing conformational changes of one helix (including a couple of side chains) between two structures of the same protein.  Could anybody teach me how to make morph using pymol version 1.2r2?
>
> Many Thanks.
>
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Hey Stephen,

make sure you have Tkinter and freeglut-devel installed.  These are the 
dependencies that make trouble in RHEL.


Andreas



Stephen P. Molnar wrote:
> I had successfully compiled Plymol from the Subversion repository in
> OpenSuSE v103. Linux.
> 
> I say successfully, because I have just upgraded my linux computer to
> OpenSuSE v11.2.  Unfortunaltely, I have a bit of a problem compiling the
> source code in the new linux OS in that I can compile the PyMol Viewer
> but notthe Pcl/Tck GUI.  Obviously there is something missing in the new
> compiler installation, but I don't have the faintest idea as to what it
> could be.
> 
> I was wonderig if anyone else has encountered this problem and/or might
> have a possible solution?
> 
> Thanks in advance.
> 

-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk