pymol-users Mailing List for PyMOL Molecular Graphics System

> Thomas,
>
> The PyMOL UI runs asynchronously. I think you are deleting your PDB
> files before they can be aligned. I made a couple changes in your
> script. Instead of calling cmd.do just call cealign directly.  See
> below,
>
> query_template_chains = {
> "1ebh" : ["1ebg", "1els", "1one", "2one",
> "5enl", "6enl", "7enl"]
> }
>
> for query in query_template_chains.keys():
>         for template in query_template_chains[query]:
>                 cmd.fetch(query, async=0)
>                 cmd.fetch(template, async=0)
>                 print "Superimposing ", query, " onto ", template
>                 cealign( query+" and c. A", template+" and c. A")
>         cmd.delete(query)
>         cmd.delete(template)
>
> Hope this helps,
>
> -- Jason
>
> Jason Vertrees, PhD

Jason,

I can't run cealign() from a script:

NameError: global name 'cealign' is not defined

I installed pymol from Fedora repositories and can't find .pymolrc,  
therefore I load CEalig in my script like this:

cmd.do("run /home/thomas/Documents/cealign-0.9/cealign.py") # load  
CEalign plugin
cmd.do("run /home/thomas/Documents/cealign-0.9/qkabsch.py")

The only way to run CEalign is using cmd.do().

Thomas

And of

Dear Pymol users,



I have to compare 20 different structures of the same protein, all  with the
same origin.
The protein is a homotetramer and I am interested in comparing the catalytic
pocket of each monomer inside a single structure and across the 20
structures.
Also I would like to compare not only the same monomer across all the
structures but also compare  different monomers from different structures.
To be more clear I would like to have the following layout in the pymol
menu:


Mutant1
Catalytic pocket monomer A
Catalytic pocket monomer B
Catalytic pocket monomer C
Catlytic  pocket  monomer  D

Mutant2

 Catalytic pocket monomer A
Catalytic pocket monomer B
Catalytic pocket monomer C
Catlytic  pocket  monomer D

and so on for all of 20, to be able to compare the catalytic pocket of one
monomer of one structure with the monomer of another structure simply
selecting and deselecting from the menu.
In order to do this, I have to find a way to superimpose all the 80 monomers
on the top of each other applying  the same selection and view of the
catalytic pocket to all of them and keeping the link with the original
pdb in a way that there is a distinction for e.g  from monomer A of mutant 1
and monomer A of any other mutant.
Can anyone suggest to me a way to do this without generating 80 objects and
keeping the exact same view of the catalytic pocket for all of them?

Thank you in advance,


Ivan Campeotto

> Message: 6
> Date: Thu, 29 Oct 2009 13:40:56 +0200
> From: Thomas Evangelidis <te...@mb...>
> Subject: Re: [PyMOL] how to get RMSD from CEalign command
> To: Andreas Forster <doc...@gm...>
> Cc: pym...@li...
> Message-ID: <200...@we...>
> Content-Type: text/plain;       charset=ISO-8859-7;     DelSp="Yes";
>        format="flowed"
>
> Thank you Adnreas.
>
> I'm straggling with cealign now. When I run it in batch mode I get
> "Selector-Error: Invalid selection name" for certain structures, which
> in fact are very close homologs, whereas the number of RMSD values I
> get varies (sometimes 3, 5, etc). Here's the code:
>
> query_template_chains = {
>                             "1ebh" : ["1ebg", "1els", "1one", "2one",
> "5enl", "6enl", "7enl"]
> }
>
> for query in query_template_chains.keys():
>         for template in query_template_chains[query]:
>             cmd.fetch(query)
>             cmd.fetch(template)
>             print "Superimposing ", query, " onto ", template
>             cmd.do("cealign "+query+" and c. A, "+template+" and c. A")
>             cmd.delete(query)
>             cmd.delete(template)
>
> Do you know what's wrong?
>
> Thomas

Thomas,

The PyMOL UI runs asynchronously. I think you are deleting your PDB
files before they can be aligned. I made a couple changes in your
script. Instead of calling cmd.do just call cealign directly.  See
below,

query_template_chains = {
"1ebh" : ["1ebg", "1els", "1one", "2one",
"5enl", "6enl", "7enl"]
}

for query in query_template_chains.keys():
        for template in query_template_chains[query]:
                cmd.fetch(query, async=0)
                cmd.fetch(template, async=0)
                print "Superimposing ", query, " onto ", template
                cealign( query+" and c. A", template+" and c. A")
        cmd.delete(query)
        cmd.delete(template)

Hope this helps,

-- Jason

Jason Vertrees, PhD

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

Tom,

Because the number of atoms in the alignment can vary with each pairwise
structure comparison, the RMS number returned by align cannot be
considered valid criterion except perhaps if presented along with the
number of atoms in each comparison.  E.g.:

RMS over X atoms

0.5     1451
0.3     1273
0.4     1343

But remember, each final RMS value will involve a different set of
atoms...and that's the root of the problem...there's no common reference
point.  

Therefore, I must recommand against using 'align' for this purpose --
it's just not the right tool for the job.

Cheers,
Warren

> -----Original Message-----
> From: Thomas Evangelidis [mailto:te...@mb...]
> Sent: Thursday, October 29, 2009 4:56 PM
> To: Warren DeLano
> Cc: Thomas Evangelidis; pym...@li...
> Subject: RE: [PyMOL] how to get RMSD from align command
> 
> Warren,
> 
> before I write something incorrect into Methods section, do you think
> the overall RMSD returned by align command is a valid criterion to
> select which structure of the family is most similar?
> 
> Tom
> 
> > Tom,
> >
> > Apologies for the confusion, but there really isn't any way to
> > measure overall structural similarity in PyMOL other than pair_fit,
> > but you have to do the work of explicitly stating which pairs are to
> > be aligned.
> >
> > The pair_fit selections don't have to be identical, but they do have
> > to correspond in a pairwise fashion.  In other words, you can
> > compare any number of C-alpha positions so long as the same number
> > of atomic positions are specified in each structure.
> >
> > Cheers,
> > Warren
> >
> > -----Original Message-----
> > From: Thomas Evangelidis [mailto:te...@mb...]
> > Sent: Thu 10/29/2009 5:24 AM
> > To: Warren DeLano
> > Cc: pym...@li...
> > Subject: Re: [PyMOL] how to get RMSD from align command
> >
> > Hi Warren,
> >
> > Now I am more confused. I used align command to measure the overall
> > RMSD between homologous structures. Apparently align is not
> > appropriate if not sufficient sequence similarity is present. I
later
> > came across CEalign plugin, which does structure-based
> > superimposition. This command also returns an RMSD value, which
> > happens to be higher for the set of homologous structures I
analysed.
> > Based on this I concluded that align command is more appropriate to
> > measure measure structural similarity, but I'm not sure now.
> >
> > My objective is to select between a small set of homologous
structures
> > (co-crystallized with ligands), the one with the highest structural
> > similarity and use it to place a dummy ligand into one where it's
> > missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg",
> > "1els", "1one", "2one", "5enl", "6enl", "7enl" which have
> > co-crystallized ligands. According to both align and cealign, 5ENL
is
> > the most similar with overall RMSD 0.246 and 0.420907 respectively.
> > The question is which command produces the best superimposition
> > provided that these proteins belong to the enolase family and thus
> > have high sequence and structural similarity? Based on the RMSD
> > values, align does, but as you said this value pertains to only a
> > subset of atoms after refinement.
> >
> > Apparently pair_fit command cannot be used for my purpose as it
> > requires identical selections.
> >
> > Tom
> >
> >
> >> Tom,
> >>
> >> The complication with cmd.align() is that it is doing a whole lot
> >> more than a simple alignment.  The first number is in fact the RMS,
> >> but it covers only the subset of the input atoms remaining after
> >> refinement is completed. The count of aligned atoms is the second
> >> field.
> >>
> >> If you're looking for exact RMS fit values over a well-defined set
> >> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for
example:
> >>
> >> load $TUT/1hpv.pdb
> >>
> >> create loopA, A/46-55/
> >>
> >> create loopB, B/46-55/
> >>
> >> show sticks, loop*
> >>
> >> print cmd.pair_fit("loopA////CA", "loopB////CA")
> >>
> >> Cheers,
> >> Warren
> >>
> >> -----Original Message-----
> >> From: Thomas Evangelidis [mailto:te...@mb...]
> >> Sent: Wed 10/28/2009 8:09 PM
> >> To: pym...@li...
> >> Subject: [PyMOL] how to get RMSD from align command
> >>
> >> Simple question, it must have been answered before but couldn't
find
> >> it so far:
> >>
> >> how can I get the RMSD value from the align command in a python
> >> script? cmd.align() returnes a tuple of 8 numbers and none of them
is
> >> the actual RMSD value I get when I align these 2 structures
manually.
> >>
> >> thanks,Tom
> >>
> >>
> >>
-----------------------------------------------------------------------
> -------
> >> Come build with us! The BlackBerry(R) Developer Conference in SF,
CA
> >> is the only developer event you need to attend this year. Jumpstart
> your
> >> developing skills, take BlackBerry mobile applications to market
and
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> >> ahead of the curve. Join us from November 9 - 12, 2009. Register
now!
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> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives:
http://www.mail-archive.com/pym...@li...
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> > ----- End message from wa...@de... -----
> >
> >
> >
> >
------------------------------------------------------------------------
> ------
> > Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> > is the only developer event you need to attend this year. Jumpstart
your
> > developing skills, take BlackBerry mobile applications to market and
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http://www.mail-archive.com/pym...@li...
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> 
> 
> ----- End message from wa...@de... -----
> 
> 
> 
> 
> 

Dear PyMOL-Users:

Today's questions regarding alignment RMS values suggest to me that I
should re-emphasize what PyMOL is and is not good for:

Please everyone keep in mind that PyMOL is intended to be just a
"molecular graphics" program, to be used for displaying, comparing, and
manipulating molecular structure in various visual and interactive ways.
PyMOL is a figure maker, a movie maker, a presentation tool -- a
molecular communications platform, if you will.

PyMOL is not intended to be, nor should it be used as, a molecular
analysis  tool.  It wasn't built with that goal in mind, and most of the
algorithms inside the program have not been rigorously validated.  As a
general rule, if the "numbers" matter, then you should be using other
more rigorous software for those tasks, and then loading only the final
output into PyMOL (for rendering, etc.).
 
Thank you all for keeping this in mind as you continue to apply PyMOL in
your work.  

Cheers,
Warren

Warren,

before I write something incorrect into Methods section, do you think  
the overall RMSD returned by align command is a valid criterion to  
select which structure of the family is most similar?

Tom

> Tom,
>
> Apologies for the confusion, but there really isn't any way to  
> measure overall structural similarity in PyMOL other than pair_fit,  
> but you have to do the work of explicitly stating which pairs are to  
> be aligned.
>
> The pair_fit selections don't have to be identical, but they do have  
> to correspond in a pairwise fashion.  In other words, you can  
> compare any number of C-alpha positions so long as the same number  
> of atomic positions are specified in each structure.
>
> Cheers,
> Warren
>
> -----Original Message-----
> From: Thomas Evangelidis [mailto:te...@mb...]
> Sent: Thu 10/29/2009 5:24 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] how to get RMSD from align command
>
> Hi Warren,
>
> Now I am more confused. I used align command to measure the overall
> RMSD between homologous structures. Apparently align is not
> appropriate if not sufficient sequence similarity is present. I later
> came across CEalign plugin, which does structure-based
> superimposition. This command also returns an RMSD value, which
> happens to be higher for the set of homologous structures I analysed.
> Based on this I concluded that align command is more appropriate to
> measure measure structural similarity, but I'm not sure now.
>
> My objective is to select between a small set of homologous structures
> (co-crystallized with ligands), the one with the highest structural
> similarity and use it to place a dummy ligand into one where it's
> missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg",
> "1els", "1one", "2one", "5enl", "6enl", "7enl" which have
> co-crystallized ligands. According to both align and cealign, 5ENL is
> the most similar with overall RMSD 0.246 and 0.420907 respectively.
> The question is which command produces the best superimposition
> provided that these proteins belong to the enolase family and thus
> have high sequence and structural similarity? Based on the RMSD
> values, align does, but as you said this value pertains to only a
> subset of atoms after refinement.
>
> Apparently pair_fit command cannot be used for my purpose as it
> requires identical selections.
>
> Tom
>
>
>> Tom,
>>
>> The complication with cmd.align() is that it is doing a whole lot
>> more than a simple alignment.  The first number is in fact the RMS,
>> but it covers only the subset of the input atoms remaining after
>> refinement is completed. The count of aligned atoms is the second
>> field.
>>
>> If you're looking for exact RMS fit values over a well-defined set
>> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:
>>
>> load $TUT/1hpv.pdb
>>
>> create loopA, A/46-55/
>>
>> create loopB, B/46-55/
>>
>> show sticks, loop*
>>
>> print cmd.pair_fit("loopA////CA", "loopB////CA")
>>
>> Cheers,
>> Warren
>>
>> -----Original Message-----
>> From: Thomas Evangelidis [mailto:te...@mb...]
>> Sent: Wed 10/28/2009 8:09 PM
>> To: pym...@li...
>> Subject: [PyMOL] how to get RMSD from align command
>>
>> Simple question, it must have been answered before but couldn't find
>> it so far:
>>
>> how can I get the RMSD value from the align command in a python
>> script? cmd.align() returnes a tuple of 8 numbers and none of them is
>> the actual RMSD value I get when I align these 2 structures manually.
>>
>> thanks,Tom
>>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>>
>>
>>
>>
>
>
> ----- End message from wa...@de... -----
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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>
>
>
>
>
>


----- End message from wa...@de... -----

Tom,

Apologies for the confusion, but there really isn't any way to measure overall structural similarity in PyMOL other than pair_fit, but you have to do the work of explicitly stating which pairs are to be aligned.   

The pair_fit selections don't have to be identical, but they do have to correspond in a pairwise fashion.  In other words, you can compare any number of C-alpha positions so long as the same number of atomic positions are specified in each structure.

Cheers,
Warren

-----Original Message-----
From: Thomas Evangelidis [mailto:te...@mb...]
Sent: Thu 10/29/2009 5:24 AM
To: Warren DeLano
Cc: pym...@li...
Subject: Re: [PyMOL] how to get RMSD from align command
 
Hi Warren,

Now I am more confused. I used align command to measure the overall  
RMSD between homologous structures. Apparently align is not  
appropriate if not sufficient sequence similarity is present. I later  
came across CEalign plugin, which does structure-based  
superimposition. This command also returns an RMSD value, which  
happens to be higher for the set of homologous structures I analysed.  
Based on this I concluded that align command is more appropriate to  
measure measure structural similarity, but I'm not sure now.

My objective is to select between a small set of homologous structures  
(co-crystallized with ligands), the one with the highest structural  
similarity and use it to place a dummy ligand into one where it's  
missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg",  
"1els", "1one", "2one", "5enl", "6enl", "7enl" which have  
co-crystallized ligands. According to both align and cealign, 5ENL is  
the most similar with overall RMSD 0.246 and 0.420907 respectively.  
The question is which command produces the best superimposition  
provided that these proteins belong to the enolase family and thus  
have high sequence and structural similarity? Based on the RMSD  
values, align does, but as you said this value pertains to only a  
subset of atoms after refinement.

Apparently pair_fit command cannot be used for my purpose as it  
requires identical selections.

Tom


> Tom,
>
> The complication with cmd.align() is that it is doing a whole lot  
> more than a simple alignment.  The first number is in fact the RMS,  
> but it covers only the subset of the input atoms remaining after  
> refinement is completed. The count of aligned atoms is the second  
> field.
>
> If you're looking for exact RMS fit values over a well-defined set  
> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:
>
> load $TUT/1hpv.pdb
>
> create loopA, A/46-55/
>
> create loopB, B/46-55/
>
> show sticks, loop*
>
> print cmd.pair_fit("loopA////CA", "loopB////CA")
>
> Cheers,
> Warren
>
> -----Original Message-----
> From: Thomas Evangelidis [mailto:te...@mb...]
> Sent: Wed 10/28/2009 8:09 PM
> To: pym...@li...
> Subject: [PyMOL] how to get RMSD from align command
>
> Simple question, it must have been answered before but couldn't find
> it so far:
>
> how can I get the RMSD value from the align command in a python
> script? cmd.align() returnes a tuple of 8 numbers and none of them is
> the actual RMSD value I get when I align these 2 structures manually.
>
> thanks,Tom
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>
>
>
>


----- End message from wa...@de... -----



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Archives: http://www.mail-archive.com/pym...@li...

Hi Warren,

Now I am more confused. I used align command to measure the overall  
RMSD between homologous structures. Apparently align is not  
appropriate if not sufficient sequence similarity is present. I later  
came across CEalign plugin, which does structure-based  
superimposition. This command also returns an RMSD value, which  
happens to be higher for the set of homologous structures I analysed.  
Based on this I concluded that align command is more appropriate to  
measure measure structural similarity, but I'm not sure now.

My objective is to select between a small set of homologous structures  
(co-crystallized with ligands), the one with the highest structural  
similarity and use it to place a dummy ligand into one where it's  
missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg",  
"1els", "1one", "2one", "5enl", "6enl", "7enl" which have  
co-crystallized ligands. According to both align and cealign, 5ENL is  
the most similar with overall RMSD 0.246 and 0.420907 respectively.  
The question is which command produces the best superimposition  
provided that these proteins belong to the enolase family and thus  
have high sequence and structural similarity? Based on the RMSD  
values, align does, but as you said this value pertains to only a  
subset of atoms after refinement.

Apparently pair_fit command cannot be used for my purpose as it  
requires identical selections.

Tom


> Tom,
>
> The complication with cmd.align() is that it is doing a whole lot  
> more than a simple alignment.  The first number is in fact the RMS,  
> but it covers only the subset of the input atoms remaining after  
> refinement is completed. The count of aligned atoms is the second  
> field.
>
> If you're looking for exact RMS fit values over a well-defined set  
> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:
>
> load $TUT/1hpv.pdb
>
> create loopA, A/46-55/
>
> create loopB, B/46-55/
>
> show sticks, loop*
>
> print cmd.pair_fit("loopA////CA", "loopB////CA")
>
> Cheers,
> Warren
>
> -----Original Message-----
> From: Thomas Evangelidis [mailto:te...@mb...]
> Sent: Wed 10/28/2009 8:09 PM
> To: pym...@li...
> Subject: [PyMOL] how to get RMSD from align command
>
> Simple question, it must have been answered before but couldn't find
> it so far:
>
> how can I get the RMSD value from the align command in a python
> script? cmd.align() returnes a tuple of 8 numbers and none of them is
> the actual RMSD value I get when I align these 2 structures manually.
>
> thanks,Tom
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>
>
>
>


----- End message from wa...@de... -----

Thank you Adnreas.

I'm straggling with cealign now. When I run it in batch mode I get  
"Selector-Error: Invalid selection name" for certain structures, which  
in fact are very close homologs, whereas the number of RMSD values I  
get varies (sometimes 3, 5, etc). Here's the code:

query_template_chains = {
                             "1ebh" : ["1ebg", "1els", "1one", "2one",  
"5enl", "6enl", "7enl"]
}

for query in query_template_chains.keys():
         for template in query_template_chains[query]:
             cmd.fetch(query)
             cmd.fetch(template)
             print "Superimposing ", query, " onto ", template
             cmd.do("cealign "+query+" and c. A, "+template+" and c. A")
             cmd.delete(query)
             cmd.delete(template)

Do you know what's wrong?

Thomas



> Hey Thomas,
>
> if you want to use align anyway, make sure to use the quite=0 option.
> The "quiet" option (if present) is set to zero by default for parsed
> PyMOL commands, but is not set for Python API calls.
>
> align
> is nearly equal to
> cmd.align(quiet=0)
>
> Thus, if you want to get rmsd output, include quiet=0 and run your
> script with output redirection.
>
>
> Andreas
>
>
>
> On Thu, Oct 29, 2009 at 2:48 AM, Thomas Evangelidis  
> <te...@mb...> wrote:
>> Simple question, it must have been answered before but couldn't find
>> it so far:
>>
>> how can I get the RMSD value from the align command in a python
>> script? cmd.align() returnes a tuple of 8 numbers and none of them is
>> the actual RMSD value I get when I align these 2 structures manually.
>>
>> thanks,Tom
>>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>


----- End message from doc...@gm... -----

Hey Thomas,

if you want to use align anyway, make sure to use the quite=0 option.
The "quiet" option (if present) is set to zero by default for parsed
PyMOL commands, but is not set for Python API calls.

align
is nearly equal to
cmd.align(quiet=0)

Thus, if you want to get rmsd output, include quiet=0 and run your
script with output redirection.


Andreas



On Thu, Oct 29, 2009 at 2:48 AM, Thomas Evangelidis <te...@mb...> wrote:
> Simple question, it must have been answered before but couldn't find
> it so far:
>
> how can I get the RMSD value from the align command in a python
> script? cmd.align() returnes a tuple of 8 numbers and none of them is
> the actual RMSD value I get when I align these 2 structures manually.
>
> thanks,Tom
>
>
> ------------------------------------------------------------------------------
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Tom,

The complication with cmd.align() is that it is doing a whole lot more than a simple alignment.  The first number is in fact the RMS, but it covers only the subset of the input atoms remaining after refinement is completed. The count of aligned atoms is the second field.

If you're looking for exact RMS fit values over a well-defined set of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:

load $TUT/1hpv.pdb

create loopA, A/46-55/

create loopB, B/46-55/

show sticks, loop*

print cmd.pair_fit("loopA////CA", "loopB////CA")

Cheers,
Warren

-----Original Message-----
From: Thomas Evangelidis [mailto:te...@mb...]
Sent: Wed 10/28/2009 8:09 PM
To: pym...@li...
Subject: [PyMOL] how to get RMSD from align command
 
Simple question, it must have been answered before but couldn't find  
it so far:

how can I get the RMSD value from the align command in a python  
script? cmd.align() returnes a tuple of 8 numbers and none of them is  
the actual RMSD value I get when I align these 2 structures manually.

thanks,Tom


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Simple question, it must have been answered before but couldn't find  
it so far:

how can I get the RMSD value from the align command in a python  
script? cmd.align() returnes a tuple of 8 numbers and none of them is  
the actual RMSD value I get when I align these 2 structures manually.

thanks,Tom

Hello Michael,

Unfortunately, there is no programmatic way to get this information out of PyMOL -- my apologies!

Cheers,
Warren

-----Original Message-----
From: Michael Zimmermann [mailto:mic...@ia...]
Sent: Mon 10/26/2009 9:04 PM
To: pymol-users
Subject: [PyMOL] number of h-bonds
 
Dear PyMOL users,

I was using Action -> find -> polar interactions within selection
to get an idea about the hydrogen bonds and other polar interactions
in some molecules.  I would like to compare different conformations of
a certain molecule and one metric could be the number of pair returned
by one of these distance evaluations.  Could someone help me figure
out how to get routines like this to return the number of pairs that
they define? Alternatively, for the object that is returned, is there
a way to loop through the line objects or labels and count them?

Thank you.

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Dear PyMOL users,

I was using Action -> find -> polar interactions within selection
to get an idea about the hydrogen bonds and other polar interactions
in some molecules.  I would like to compare different conformations of
a certain molecule and one metric could be the number of pair returned
by one of these distance evaluations.  Could someone help me figure
out how to get routines like this to return the number of pairs that
they define? Alternatively, for the object that is returned, is there
a way to loop through the line objects or labels and count them?

Thank you.

Eep -- I go away for a few days & look what happens!  :)

Seth: you got my original point exactly -- thank you for the well worded explication!

Tsjerk & Warren: thank you for the explanation of the "under-the-hood" workings of the render engine....  It may very well be more effort than it's worth, but if this were to be approached as a future feature for PyMOL, it sounds to me like it would also be best implemented with shadows "off" so that one needn't account for the off-screen contributions to the on-screen objects.  PyMOL doesn't do radiosity (correct?), so there is no need to worry about bouncing photons coming off adjacent objects that are not visible....

I personally have never become a fan of rendering in POVray (despite its power) since it has been prohibitively difficult for me to sort getting the same "look and feel" as PyMOL offers so easily.... especially the depth cuing.

Cheers,
Tom



-----Original Message-----
From: Tsjerk Wassenaar [mailto:ts...@gm...] 
Sent: Saturday, October 24, 2009 11:46 AM
To: Seth Harris
Cc: pym...@li...
Subject: Re: [PyMOL] Rendering in parts

Hi Seth,

Well, you're partly right that you wouldn't need to load all of the scene in to memory. But, don't forget that shadows can be cast from one end of the scene to another. These long range effects would be even more pronounced when reflections were present, like they may be with POV Ray. In that case you certainly wouldn't be able to make an a priori assessment of the part of the scene that could contribute to a certain ray from that part of the viewport.
Then again, if you feel that you can cut the scene in parts, you can achieve the same effect by turning off parts of the scene, making them black. Cutting on the number of objects would definitely cut on the complexity of the scene and hence on the memory demand. Subsequently you could stitch the parts of the image together by mere addition (since black pixels count as rgb 0 0 0). But I'd go for hash_max...
Well, actually I'd probably go for POV Ray... :p

Cheers,

Tsjerk

> Hi Tsjerk,
> Ok, yes, I see your point now. I was unaware of the memory aspects not 
> being helped by the rendering in parts, so I did not catch the 
> deliberate redirection you had done! However, Tom's method would be 
> able to avoid the too large memory issue since if the viewport only 
> 'saw' one little piece at a time and worked on that independently of 
> the rest of the scene (essentially unaware if there is one more tile 
> or a hundred more...) But there are the multiple perspective limitations, etc.
> Thanks for clarifying the 'under the hood' part for me and sorry to 
> have then added my own assumptions to the mix!! (as I worried about in 
> my last
> paragraph!)
> -Seth
>
> On Sat, Oct 24, 2009 at 2:41 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
>>
>> Hi Seth,
>>
>> Rendering in parts does not avoid taking the whole scene in memory.
>> That is a more important obstacle than the size of the image. That is 
>> why Warren suggested using the hash_max setting, which will alleviate 
>> the memory dependence of the ray tracing, avoiding crashing. The 
>> raytracing in parts that POV ray offers is not about saving memory; a 
>> scene that is too complex to load will still break. It's about CPU
>> efficiency: you can distribute the calculation over multiple CPUs.
>> This was particularly important for POV Ray versions <= 3.6 (3.7 will 
>> be able to use multiple CPUs). Also, there's nothing mathematically 
>> tricky about what POV Ray does for partial ray tracing: it only 
>> traces the rays that belong to pixels you want to have rendered. E.g. 
>> it will write a 9000x6000 pixel image (according to the header), but 
>> only have part of the image filled in.
>>
>> Maybe you can see that I wasn't so much missing the point, or maybe 
>> was deliberately trying to miss it, since it builds on misconception 
>> of what is under the hood. If you want to connect withe the 
>> capabilities that POV ray offers in that regard, which may have some 
>> merits, you may want to suggest Warren to implement partial 
>> renderings, adding startrow, endrow, startcolumn and endcolumn to the 
>> ray command. That might be handy when using pymol for raytracing 
>> scriptwise on a cluster. But you'll be disappointed if you expect it 
>> will keep your scene from crashing Pymol (but then there's the 
>> hash_setting...).
>>
>> I hope this clarifies things a bit.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Sat, Oct 24, 2009 at 8:21 AM, Seth Harris <se...@gm...> wrote:
>> > Tsjerk,
>> > I think you are missing the point of Tom's post, which was a 
>> > suggestion to aid someone who's computer could NOT deliver the 
>> > image in "as high a rsolution as you want', so Tom was proposing a 
>> > way to break the image down into bite-size chunks that the computer 
>> > COULD then handle. So the suggestion was to take one scene desired 
>> > at 9000x6000 which would make the computer crash and instead 
>> > mathematically figure the necessary transpositions to render it in 
>> > tiles such as upper left quadrant, upper right, etc. each at 
>> > 4500x3000 or whatever the computer could handle (and then you could 
>> > put them all back together in photoshop, e.g.). So for someone with 
>> > deep coding skills they could likely teach pymol to ray just the 
>> > segments they wanted and deal with the overall perspective of the 
>> > whole scene, but for a hack like myself I'd likely start the work 
>> > around of trying to figure out the camera position and where I'd 
>> > have to put it to get just a quarter of the scene at a time in the 
>> > viewport (or an eighth, or whatever). As Warren said, you'd likely 
>> > have to set orthoscopic to get rid of the perspective for starters 
>> > (at least in the hack approach, but there would be more direct 
>> > better ways for the skilled).
>> >
>> > As a side point, Povray (if I remember correctly)  in fact allows 
>> > you to break a large rendering job up into tiles pretty much just 
>> > like Tom suggests, so not so crazy of an idea! I think in that case 
>> > you can specify starting and ending x,y pixel coordinates from your 
>> > large scene. But not in Pymol as far as I know.
>> >
>> > Sorry if I've now gone stepping in and misinterpreting someone's 
>> > points myself, but it seemed like there was a lot of cross-purpose 
>> > talk either from assumptions or extra politeness!
>> >
>> > -Seth
>> >>
>> >> > The requested size is 20" by 30". I calculated that it would 
>> >> > correspond to a 6000 x 9000 pixel image.
>> >> > How can I create such a large ray traced image without crashing 
>> >> > the computer?
>> >>
>> >>
>> >> Message: 2
>> >> Date: Fri, 23 Oct 2009 11:27:47 +0200
>> >> From: Tsjerk Wassenaar <ts...@gm...>
>> >> Subject: Re: [PyMOL] Saving high resolution images
>> >> To: Thomas Stout <ts...@ex...>
>> >> Cc: pym...@li...
>> >> Message-ID:
>> >>        <8ff...@ma...>
>> >> Content-Type: text/plain; charset=ISO-8859-1
>> >>
>> >> Hi Thomas,
>> >>
>> >> You can also zoom out to get everything in view. You can also change
>> >> the field of view. And then you can ray just the way you want, based
>> >> on what you have in sight, in as high a resolution you want.
>> >>
>> >> Cheers,
>> >>
>> >> Tsjerk
>> >>
>> >> On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout <ts...@ex...>
>> >> wrote:
>> >> >
>> >> > But isn't it true that only the objects that are visible in the
>> >> > viewport
>> >> > are what are written to the rendered image file? ?I was proposing
>> >> > rendering
>> >> > a poster-sized image in "tiles" and stitching them back together post
>> >> > facto
>> >> > to create a very large, high resolution image.
>> >> >
>> >> > something like:
>> >> > -----------------------
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | render 1 | render 2 |
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > |----------------------
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | render 3 | render 4 |
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > -----------------------
>> >> >
>> >> > I feel like I'm missing something important here!
>> >> > -Tom
>> >> >
>> >> > -----Original Message-----
>> >> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
>> >> > Sent: Thursday, October 22, 2009 11:45 AM
>> >> > To: Thomas Stout
>> >> > Cc: pym...@li...
>> >> > Subject: Re: [PyMOL] Saving high resolution images
>> >> >
>> >> > Hi Thomas,
>> >> >
>> >> > The viewport is not important for rendering. You can render at
>> >> > whatever
>> >> > resolution/dimensions you want with whatever viewport. You can even
>> >> > make a
>> >> > panorama using a wide angle lens if you want to have something for on
>> >> > your
>> >> > wall ;)
>> >> >
>> >> > Cheers,
>> >> >
>> >> > Tsjerk
>> >> >
>> >> > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout <ts...@ex...>
>> >> > wrote:
>> >> >>
>> >> >>
>> >> >> Here's a crazy idea: ?if someone out there were clever at both
>> >> >> python
>> >> >> and manipulating orientation matrices, I would bet that a "scene"
>> >> >> could be quartered or cut into eighths and "translated" such that
>> >> >> each
>> >> >> portion filled the viewport for rendering; then the individual
>> >> >> images
>> >> >> could be spliced back together in one's favorite image handling
>> >> >> program a la panoramas in photography.... ?Is this way too complex
>> >> >> to
>> >> >> be bothered with? ?I suspect parallax may be a problem...
>> >> >>
>> >> >> -Tom
>> >> >>
>> >> >>
>> >> >>
>> >> >> -----Original Message-----
>> >> >> From: Eva Vanamee [mailto:Eva...@ms...]
>> >> >> Sent: Monday, October 19, 2009 1:51 PM
>> >> >> To: pym...@li...
>> >> >> Subject: [PyMOL] Saving high resolution images
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> I'd like to save an image in high resolution for a poster.
>> >> >> The requested size is 20" by 30". I calculated that it would
>> >> >> correspond to a 6000 x 9000 pixel image.
>> >> >> How can I create such a large ray traced image without crashing the
>> >> >> computer?
>> >> >> Many thanks in advance for the help.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> - Eva
>> >> >>
>> >> >>
>> >> >>
>> >> >> ----------------------------------------------------------------------
>> >>
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> > is the only developer event you need to attend this year. Jumpstart your
>> > developing skills, take BlackBerry mobile applications to market and
>> > stay
>> > ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> > http://p.sf.net/sfu/devconference
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>>
>>
>>
>> --
>> 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
>
>



-- 
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

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Warren,

I was trying to write a script that would read in CHARMM trajectory files (DCD) specifically for users who do not have access to the most current version of PyMOL.  I have written a Python script that will interpret a DCD file and load it into the corresponding object but this process is definitely not as fast as the C implementation already available in version 1.2.  I can see where it would be difficult to access the coordinates in the C array via Python.  This is not a pressing need of mine by any means as it was something that I am revisiting (if you recall, I had tried this in the past) as I definitely made some mistakes earlier that made the script very slow and inefficient.  Now, I have an "optimized" version of the Python script with the limitation being the replacement of the coordinates.  

Sean

Subject: RE: [PyMOL] Replace Coordinates in State
Date: Mon, 26 Oct 2009 10:54:39 -0700
From: wa...@de...
To: mag...@ho...; pym...@li...

























Sean,

 

Unfortunately, there isn’t any way
at present to directly expose PyMOL’s internal C coordinate array to
Python in an accessible form.  Yes, iterate_state and alter_state are highly
inefficient – it would make more sense to provide a means of exporting and
re-importing coordinate sets via either native Python lists or, even better,
NumPy arrays.  In what form do you have the current coordinate data?

 

Cheers,

Warren

 











From: Sean Law
[mailto:mag...@ho...] 

Sent: Friday, October 23, 2009
4:54 PM

To:
pym...@li...

Subject: [PyMOL] Replace
Coordinates in State



 

Hi All,



I was wondering if there was a faster way to replace all coordinates. 
I've used commands such as iterate_state and alter_state before but they are
far too slow since they have to iterate over each atom.  Instead, I want
to replace one set of coordinates that correspond to a specific state with a
different set.  Here's what I have to work with:



I have a list that contains x, y, z coordinates.  Of course, this list can
be manipulated and/or separated if necessary.  I'm assuming that the
coordinates for a specific state are stored somewhere in memory and I would
basically like to replace one set of coordinates with the other.  I would
think that something like "pointers or references" would work a lot
faster than having to copy the coordinates over (which is typically slow and is
likely what alter_state is doing?). In addition, I am dealing with 100+ states
using alter_state for each state would be far too slow.



Any suggestions would be greatly appreciated.



Thanks in advance!



Sean







Save up to 84% on Windows 7 until Jan 3-eligible CDN College
or University students only. Hurry-buy it now for $39.99!



 		 	   		  
_________________________________________________________________
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http://go.microsoft.com/?linkid=9691635

Sean,

 

Unfortunately, there isn't any way at present to directly expose PyMOL's
internal C coordinate array to Python in an accessible form.  Yes,
iterate_state and alter_state are highly inefficient - it would make
more sense to provide a means of exporting and re-importing coordinate
sets via either native Python lists or, even better, NumPy arrays.  In
what form do you have the current coordinate data?

 

Cheers,

Warren

 

________________________________

From: Sean Law [mailto:mag...@ho...] 
Sent: Friday, October 23, 2009 4:54 PM
To: pym...@li...
Subject: [PyMOL] Replace Coordinates in State

 

Hi All,

I was wondering if there was a faster way to replace all coordinates.
I've used commands such as iterate_state and alter_state before but they
are far too slow since they have to iterate over each atom.  Instead, I
want to replace one set of coordinates that correspond to a specific
state with a different set.  Here's what I have to work with:

I have a list that contains x, y, z coordinates.  Of course, this list
can be manipulated and/or separated if necessary.  I'm assuming that the
coordinates for a specific state are stored somewhere in memory and I
would basically like to replace one set of coordinates with the other.
I would think that something like "pointers or references" would work a
lot faster than having to copy the coordinates over (which is typically
slow and is likely what alter_state is doing?). In addition, I am
dealing with 100+ states using alter_state for each state would be far
too slow.

Any suggestions would be greatly appreciated.

Thanks in advance!

Sean

________________________________

Save up to 84% on Windows 7 until Jan 3-eligible CDN College or
University students only. Hurry-buy it now for $39.99!
<" rel="nofollow">http://go.microsoft.com/?linkid=9691631> 

Dear Suneel Kumar,



2009/10/26 Suneel Kumar Bommisetty <sun...@gv...>:
> Dear All,
>
>
>
> I am looking for script for “object find” In pymol. I have a sd file
> contains 20 molecules. I have loaded into pymol. If I want visualize next
> molecule, I need to press Play or forward or disply – sequence function. Is
> there any script to/load/select/highlight specific molecule from one object?
>
>
>
> Please reply back
>


I don't think you need a script to do this.
Look into this link
http://pymolwiki.org/index.php/States
and I think you will understand.

Best regards,
Folmer Fredslund

Dear All,

 

I am looking for script for "object find" In pymol. I have a sd file
contains 20 molecules. I have loaded into pymol. If I want visualize
next molecule, I need to press Play or forward or disply - sequence
function. Is there any script to/load/select/highlight specific molecule
from one object?

 

Please reply back

 

Thanks & Regards,

Suneel Kumar BVS

 


 





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> 1. What type of RMSD is calculated with align comman i.e All Atoms or
only Backbone?
 
It depends on the input selections.  If you don't restrict it to backbone atoms, PyMOL will perform the fit for all matched atoms.  Also, it is important to understand that "align" is a combined sequence and 3D refined structure alignment which, by default, iteratively discards outliers in order to achieve a well-matched core structure.  "super" is similar except that it doesn't use sequence.
 
> 2. If I have few models/PDB stuructures of the same protein how I can
clauclate the total atoms and backbone only RMSD between these.
Actually I am confused with usuage of these commands i.e align ,
super, rms, rms_cur  etc.
 
If you're trying to calculate RMS between specific pairs of atoms :
 
If the proteins have matched identifiers (identical segment, chain, and residue identifier), then the command you want is "fit":
 
# all atom
 
fit obj1, obj2 
 
# C-calpha only
 
fit obj1////CA, obj2////CA
 
If the protein do not have matched identifiers, then you must manually select exactly N atom pairs in each structure, and then use pair_fit:
 
# C-alpha fit for residues 10 through 80  and 100 through 120
 
pair_fit obj1///10-80+100-120/CA,  obj2///10-80+100-120/CA
 
Cheers,
Warren
 

________________________________

From: Bio Brain [mailto:bio...@gm...]
Sent: Sat 10/24/2009 1:11 PM
To: pym...@li...
Subject: [PyMOL] Pymol Align Command and RMSD Calculation ?



Dear Pymol Users,

I am looking for some very basic information about the PyMol commands.

1. What type of RMSD is calculated with align comman i.e All Atoms or
only Backbone?

2. If I have few models/PDB stuructures of the same protein how I can
clauclate the total atoms and backbone only RMSD between these.
Actually I am confused with usuage of these commands i.e align ,
super, rms, rms_cur  etc.

Regards

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Dear Pymol Users,

I am looking for some very basic information about the PyMol commands.

1. What type of RMSD is calculated with align comman i.e All Atoms or
only Backbone?

2. If I have few models/PDB stuructures of the same protein how I can
clauclate the total atoms and backbone only RMSD between these.
Actually I am confused with usuage of these commands i.e align ,
super, rms, rms_cur  etc.

Regards

Hi Seth,

Well, you're partly right that you wouldn't need to load all of the
scene in to memory. But, don't forget that shadows can be cast from
one end of the scene to another. These long range effects would be
even more pronounced when reflections were present, like they may be
with POV Ray. In that case you certainly wouldn't be able to make an a
priori assessment of the part of the scene that could contribute to a
certain ray from that part of the viewport.
Then again, if you feel that you can cut the scene in parts, you can
achieve the same effect by turning off parts of the scene, making them
black. Cutting on the number of objects would definitely cut on the
complexity of the scene and hence on the memory demand. Subsequently
you could stitch the parts of the image together by mere addition
(since black pixels count as rgb 0 0 0). But I'd go for hash_max...
Well, actually I'd probably go for POV Ray... :p

Cheers,

Tsjerk

> Hi Tsjerk,
> Ok, yes, I see your point now. I was unaware of the memory aspects not being
> helped by the rendering in parts, so I did not catch the deliberate
> redirection you had done! However, Tom's method would be able to avoid the
> too large memory issue since if the viewport only 'saw' one little piece at
> a time and worked on that independently of the rest of the scene
> (essentially unaware if there is one more tile or a hundred more...) But
> there are the multiple perspective limitations, etc.
> Thanks for clarifying the 'under the hood' part for me and sorry to have
> then added my own assumptions to the mix!! (as I worried about in my last
> paragraph!)
> -Seth
>
> On Sat, Oct 24, 2009 at 2:41 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
>>
>> Hi Seth,
>>
>> Rendering in parts does not avoid taking the whole scene in memory.
>> That is a more important obstacle than the size of the image. That is
>> why Warren suggested using the hash_max setting, which will alleviate
>> the memory dependence of the ray tracing, avoiding crashing. The
>> raytracing in parts that POV ray offers is not about saving memory; a
>> scene that is too complex to load will still break. It's about CPU
>> efficiency: you can distribute the calculation over multiple CPUs.
>> This was particularly important for POV Ray versions <= 3.6 (3.7 will
>> be able to use multiple CPUs). Also, there's nothing mathematically
>> tricky about what POV Ray does for partial ray tracing: it only traces
>> the rays that belong to pixels you want to have rendered. E.g. it will
>> write a 9000x6000 pixel image (according to the header), but only have
>> part of the image filled in.
>>
>> Maybe you can see that I wasn't so much missing the point, or maybe
>> was deliberately trying to miss it, since it builds on misconception
>> of what is under the hood. If you want to connect withe the
>> capabilities that POV ray offers in that regard, which may have some
>> merits, you may want to suggest Warren to implement partial
>> renderings, adding startrow, endrow, startcolumn and endcolumn to the
>> ray command. That might be handy when using pymol for raytracing
>> scriptwise on a cluster. But you'll be disappointed if you expect it
>> will keep your scene from crashing Pymol (but then there's the
>> hash_setting...).
>>
>> I hope this clarifies things a bit.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Sat, Oct 24, 2009 at 8:21 AM, Seth Harris <se...@gm...> wrote:
>> > Tsjerk,
>> > I think you are missing the point of Tom's post, which was a suggestion
>> > to
>> > aid someone who's computer could NOT deliver the image in "as high a
>> > rsolution as you want', so Tom was proposing a way to break the image
>> > down
>> > into bite-size chunks that the computer COULD then handle. So the
>> > suggestion
>> > was to take one scene desired at 9000x6000 which would make the computer
>> > crash and instead mathematically figure the necessary transpositions to
>> > render it in tiles such as upper left quadrant, upper right, etc. each
>> > at
>> > 4500x3000 or whatever the computer could handle (and then you could put
>> > them
>> > all back together in photoshop, e.g.). So for someone with deep coding
>> > skills they could likely teach pymol to ray just the segments they
>> > wanted
>> > and deal with the overall perspective of the whole scene, but for a hack
>> > like myself I'd likely start the work around of trying to figure out the
>> > camera position and where I'd have to put it to get just a quarter of
>> > the
>> > scene at a time in the viewport (or an eighth, or whatever). As Warren
>> > said,
>> > you'd likely have to set orthoscopic to get rid of the perspective for
>> > starters (at least in the hack approach, but there would be more direct
>> > better ways for the skilled).
>> >
>> > As a side point, Povray (if I remember correctly)  in fact allows you to
>> > break a large rendering job up into tiles pretty much just like Tom
>> > suggests, so not so crazy of an idea! I think in that case you can
>> > specify
>> > starting and ending x,y pixel coordinates from your large scene. But not
>> > in
>> > Pymol as far as I know.
>> >
>> > Sorry if I've now gone stepping in and misinterpreting someone's points
>> > myself, but it seemed like there was a lot of cross-purpose talk either
>> > from
>> > assumptions or extra politeness!
>> >
>> > -Seth
>> >>
>> >> > The requested size is 20" by 30". I calculated that it would
>> >> > correspond
>> >> > to a 6000 x 9000 pixel image.
>> >> > How can I create such a large ray traced image without crashing the
>> >> > computer?
>> >>
>> >>
>> >> Message: 2
>> >> Date: Fri, 23 Oct 2009 11:27:47 +0200
>> >> From: Tsjerk Wassenaar <ts...@gm...>
>> >> Subject: Re: [PyMOL] Saving high resolution images
>> >> To: Thomas Stout <ts...@ex...>
>> >> Cc: pym...@li...
>> >> Message-ID:
>> >>        <8ff...@ma...>
>> >> Content-Type: text/plain; charset=ISO-8859-1
>> >>
>> >> Hi Thomas,
>> >>
>> >> You can also zoom out to get everything in view. You can also change
>> >> the field of view. And then you can ray just the way you want, based
>> >> on what you have in sight, in as high a resolution you want.
>> >>
>> >> Cheers,
>> >>
>> >> Tsjerk
>> >>
>> >> On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout <ts...@ex...>
>> >> wrote:
>> >> >
>> >> > But isn't it true that only the objects that are visible in the
>> >> > viewport
>> >> > are what are written to the rendered image file? ?I was proposing
>> >> > rendering
>> >> > a poster-sized image in "tiles" and stitching them back together post
>> >> > facto
>> >> > to create a very large, high resolution image.
>> >> >
>> >> > something like:
>> >> > -----------------------
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | render 1 | render 2 |
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > |----------------------
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | render 3 | render 4 |
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > | ? ? ? ? ?| ? ? ? ? ?|
>> >> > -----------------------
>> >> >
>> >> > I feel like I'm missing something important here!
>> >> > -Tom
>> >> >
>> >> > -----Original Message-----
>> >> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
>> >> > Sent: Thursday, October 22, 2009 11:45 AM
>> >> > To: Thomas Stout
>> >> > Cc: pym...@li...
>> >> > Subject: Re: [PyMOL] Saving high resolution images
>> >> >
>> >> > Hi Thomas,
>> >> >
>> >> > The viewport is not important for rendering. You can render at
>> >> > whatever
>> >> > resolution/dimensions you want with whatever viewport. You can even
>> >> > make a
>> >> > panorama using a wide angle lens if you want to have something for on
>> >> > your
>> >> > wall ;)
>> >> >
>> >> > Cheers,
>> >> >
>> >> > Tsjerk
>> >> >
>> >> > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout <ts...@ex...>
>> >> > wrote:
>> >> >>
>> >> >>
>> >> >> Here's a crazy idea: ?if someone out there were clever at both
>> >> >> python
>> >> >> and manipulating orientation matrices, I would bet that a "scene"
>> >> >> could be quartered or cut into eighths and "translated" such that
>> >> >> each
>> >> >> portion filled the viewport for rendering; then the individual
>> >> >> images
>> >> >> could be spliced back together in one's favorite image handling
>> >> >> program a la panoramas in photography.... ?Is this way too complex
>> >> >> to
>> >> >> be bothered with? ?I suspect parallax may be a problem...
>> >> >>
>> >> >> -Tom
>> >> >>
>> >> >>
>> >> >>
>> >> >> -----Original Message-----
>> >> >> From: Eva Vanamee [mailto:Eva...@ms...]
>> >> >> Sent: Monday, October 19, 2009 1:51 PM
>> >> >> To: pym...@li...
>> >> >> Subject: [PyMOL] Saving high resolution images
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> I'd like to save an image in high resolution for a poster.
>> >> >> The requested size is 20" by 30". I calculated that it would
>> >> >> correspond to a 6000 x 9000 pixel image.
>> >> >> How can I create such a large ray traced image without crashing the
>> >> >> computer?
>> >> >> Many thanks in advance for the help.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> - Eva
>> >> >>
>> >> >>
>> >> >>
>> >> >> ----------------------------------------------------------------------
>> >>
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> > is the only developer event you need to attend this year. Jumpstart your
>> > developing skills, take BlackBerry mobile applications to market and
>> > stay
>> > ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> > http://p.sf.net/sfu/devconference
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>>
>>
>>
>> --
>> 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
>
>



-- 
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 Tsjerk,
Ok, yes, I see your point now. I was unaware of the memory aspects not being
helped by the rendering in parts, so I did not catch the deliberate
redirection you had done! However, Tom's method would be able to avoid the
too large memory issue since if the viewport only 'saw' one little piece at
a time and worked on that independently of the rest of the scene
(essentially unaware if there is one more tile or a hundred more...) But
there are the multiple perspective limitations, etc.
Thanks for clarifying the 'under the hood' part for me and sorry to have
then added my own assumptions to the mix!! (as I worried about in my last
paragraph!)
-Seth

On Sat, Oct 24, 2009 at 2:41 AM, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi Seth,
>
> Rendering in parts does not avoid taking the whole scene in memory.
> That is a more important obstacle than the size of the image. That is
> why Warren suggested using the hash_max setting, which will alleviate
> the memory dependence of the ray tracing, avoiding crashing. The
> raytracing in parts that POV ray offers is not about saving memory; a
> scene that is too complex to load will still break. It's about CPU
> efficiency: you can distribute the calculation over multiple CPUs.
> This was particularly important for POV Ray versions <= 3.6 (3.7 will
> be able to use multiple CPUs). Also, there's nothing mathematically
> tricky about what POV Ray does for partial ray tracing: it only traces
> the rays that belong to pixels you want to have rendered. E.g. it will
> write a 9000x6000 pixel image (according to the header), but only have
> part of the image filled in.
>
> Maybe you can see that I wasn't so much missing the point, or maybe
> was deliberately trying to miss it, since it builds on misconception
> of what is under the hood. If you want to connect withe the
> capabilities that POV ray offers in that regard, which may have some
> merits, you may want to suggest Warren to implement partial
> renderings, adding startrow, endrow, startcolumn and endcolumn to the
> ray command. That might be handy when using pymol for raytracing
> scriptwise on a cluster. But you'll be disappointed if you expect it
> will keep your scene from crashing Pymol (but then there's the
> hash_setting...).
>
> I hope this clarifies things a bit.
>
> Cheers,
>
> Tsjerk
>
> On Sat, Oct 24, 2009 at 8:21 AM, Seth Harris <se...@gm...> wrote:
> > Tsjerk,
> > I think you are missing the point of Tom's post, which was a suggestion
> to
> > aid someone who's computer could NOT deliver the image in "as high a
> > rsolution as you want', so Tom was proposing a way to break the image
> down
> > into bite-size chunks that the computer COULD then handle. So the
> suggestion
> > was to take one scene desired at 9000x6000 which would make the computer
> > crash and instead mathematically figure the necessary transpositions to
> > render it in tiles such as upper left quadrant, upper right, etc. each at
> > 4500x3000 or whatever the computer could handle (and then you could put
> them
> > all back together in photoshop, e.g.). So for someone with deep coding
> > skills they could likely teach pymol to ray just the segments they wanted
> > and deal with the overall perspective of the whole scene, but for a hack
> > like myself I'd likely start the work around of trying to figure out the
> > camera position and where I'd have to put it to get just a quarter of the
> > scene at a time in the viewport (or an eighth, or whatever). As Warren
> said,
> > you'd likely have to set orthoscopic to get rid of the perspective for
> > starters (at least in the hack approach, but there would be more direct
> > better ways for the skilled).
> >
> > As a side point, Povray (if I remember correctly)  in fact allows you to
> > break a large rendering job up into tiles pretty much just like Tom
> > suggests, so not so crazy of an idea! I think in that case you can
> specify
> > starting and ending x,y pixel coordinates from your large scene. But not
> in
> > Pymol as far as I know.
> >
> > Sorry if I've now gone stepping in and misinterpreting someone's points
> > myself, but it seemed like there was a lot of cross-purpose talk either
> from
> > assumptions or extra politeness!
> >
> > -Seth
> >>
> >> > The requested size is 20" by 30". I calculated that it would
> >> > correspond
> >> > to a 6000 x 9000 pixel image.
> >> > How can I create such a large ray traced image without crashing the
> >> > computer?
> >>
> >>
> >> Message: 2
> >> Date: Fri, 23 Oct 2009 11:27:47 +0200
> >> From: Tsjerk Wassenaar <ts...@gm...>
> >> Subject: Re: [PyMOL] Saving high resolution images
> >> To: Thomas Stout <ts...@ex...>
> >> Cc: pym...@li...
> >> Message-ID:
> >>        <8ff...@ma...>
> >> Content-Type: text/plain; charset=ISO-8859-1
> >>
> >> Hi Thomas,
> >>
> >> You can also zoom out to get everything in view. You can also change
> >> the field of view. And then you can ray just the way you want, based
> >> on what you have in sight, in as high a resolution you want.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout <ts...@ex...>
> wrote:
> >> >
> >> > But isn't it true that only the objects that are visible in the
> viewport
> >> > are what are written to the rendered image file? ?I was proposing
> rendering
> >> > a poster-sized image in "tiles" and stitching them back together post
> facto
> >> > to create a very large, high resolution image.
> >> >
> >> > something like:
> >> > -----------------------
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > | render 1 | render 2 |
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > |----------------------
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > | render 3 | render 4 |
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > | ? ? ? ? ?| ? ? ? ? ?|
> >> > -----------------------
> >> >
> >> > I feel like I'm missing something important here!
> >> > -Tom
> >> >
> >> > -----Original Message-----
> >> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
> >> > Sent: Thursday, October 22, 2009 11:45 AM
> >> > To: Thomas Stout
> >> > Cc: pym...@li...
> >> > Subject: Re: [PyMOL] Saving high resolution images
> >> >
> >> > Hi Thomas,
> >> >
> >> > The viewport is not important for rendering. You can render at
> whatever
> >> > resolution/dimensions you want with whatever viewport. You can even
> make a
> >> > panorama using a wide angle lens if you want to have something for on
> your
> >> > wall ;)
> >> >
> >> > Cheers,
> >> >
> >> > Tsjerk
> >> >
> >> > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout <ts...@ex...>
> >> > wrote:
> >> >>
> >> >>
> >> >> Here's a crazy idea: ?if someone out there were clever at both python
> >> >> and manipulating orientation matrices, I would bet that a "scene"
> >> >> could be quartered or cut into eighths and "translated" such that
> each
> >> >> portion filled the viewport for rendering; then the individual images
> >> >> could be spliced back together in one's favorite image handling
> >> >> program a la panoramas in photography.... ?Is this way too complex to
> >> >> be bothered with? ?I suspect parallax may be a problem...
> >> >>
> >> >> -Tom
> >> >>
> >> >>
> >> >>
> >> >> -----Original Message-----
> >> >> From: Eva Vanamee [mailto:Eva...@ms...]
> >> >> Sent: Monday, October 19, 2009 1:51 PM
> >> >> To: pym...@li...
> >> >> Subject: [PyMOL] Saving high resolution images
> >> >>
> >> >> Hi,
> >> >>
> >> >> I'd like to save an image in high resolution for a poster.
> >> >> The requested size is 20" by 30". I calculated that it would
> >> >> correspond to a 6000 x 9000 pixel image.
> >> >> How can I create such a large ray traced image without crashing the
> >> >> computer?
> >> >> Many thanks in advance for the help.
> >> >>
> >> >> Best,
> >> >>
> >> >> - Eva
> >> >>
> >> >>
> >> >>
> ----------------------------------------------------------------------
> >>
> >
> >
> ------------------------------------------------------------------------------
> > Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> > is the only developer event you need to attend this year. Jumpstart your
> > developing skills, take BlackBerry mobile applications to market and stay
> > ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> > http://p.sf.net/sfu/devconference
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> 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 Seth,

Rendering in parts does not avoid taking the whole scene in memory.
That is a more important obstacle than the size of the image. That is
why Warren suggested using the hash_max setting, which will alleviate
the memory dependence of the ray tracing, avoiding crashing. The
raytracing in parts that POV ray offers is not about saving memory; a
scene that is too complex to load will still break. It's about CPU
efficiency: you can distribute the calculation over multiple CPUs.
This was particularly important for POV Ray versions <= 3.6 (3.7 will
be able to use multiple CPUs). Also, there's nothing mathematically
tricky about what POV Ray does for partial ray tracing: it only traces
the rays that belong to pixels you want to have rendered. E.g. it will
write a 9000x6000 pixel image (according to the header), but only have
part of the image filled in.

Maybe you can see that I wasn't so much missing the point, or maybe
was deliberately trying to miss it, since it builds on misconception
of what is under the hood. If you want to connect withe the
capabilities that POV ray offers in that regard, which may have some
merits, you may want to suggest Warren to implement partial
renderings, adding startrow, endrow, startcolumn and endcolumn to the
ray command. That might be handy when using pymol for raytracing
scriptwise on a cluster. But you'll be disappointed if you expect it
will keep your scene from crashing Pymol (but then there's the
hash_setting...).

I hope this clarifies things a bit.

Cheers,

Tsjerk

On Sat, Oct 24, 2009 at 8:21 AM, Seth Harris <se...@gm...> wrote:
> Tsjerk,
> I think you are missing the point of Tom's post, which was a suggestion to
> aid someone who's computer could NOT deliver the image in "as high a
> rsolution as you want', so Tom was proposing a way to break the image down
> into bite-size chunks that the computer COULD then handle. So the suggestion
> was to take one scene desired at 9000x6000 which would make the computer
> crash and instead mathematically figure the necessary transpositions to
> render it in tiles such as upper left quadrant, upper right, etc. each at
> 4500x3000 or whatever the computer could handle (and then you could put them
> all back together in photoshop, e.g.). So for someone with deep coding
> skills they could likely teach pymol to ray just the segments they wanted
> and deal with the overall perspective of the whole scene, but for a hack
> like myself I'd likely start the work around of trying to figure out the
> camera position and where I'd have to put it to get just a quarter of the
> scene at a time in the viewport (or an eighth, or whatever). As Warren said,
> you'd likely have to set orthoscopic to get rid of the perspective for
> starters (at least in the hack approach, but there would be more direct
> better ways for the skilled).
>
> As a side point, Povray (if I remember correctly)  in fact allows you to
> break a large rendering job up into tiles pretty much just like Tom
> suggests, so not so crazy of an idea! I think in that case you can specify
> starting and ending x,y pixel coordinates from your large scene. But not in
> Pymol as far as I know.
>
> Sorry if I've now gone stepping in and misinterpreting someone's points
> myself, but it seemed like there was a lot of cross-purpose talk either from
> assumptions or extra politeness!
>
> -Seth
>>
>> > The requested size is 20" by 30". I calculated that it would
>> > correspond
>> > to a 6000 x 9000 pixel image.
>> > How can I create such a large ray traced image without crashing the
>> > computer?
>>
>>
>> Message: 2
>> Date: Fri, 23 Oct 2009 11:27:47 +0200
>> From: Tsjerk Wassenaar <ts...@gm...>
>> Subject: Re: [PyMOL] Saving high resolution images
>> To: Thomas Stout <ts...@ex...>
>> Cc: pym...@li...
>> Message-ID:
>>        <8ff...@ma...>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi Thomas,
>>
>> You can also zoom out to get everything in view. You can also change
>> the field of view. And then you can ray just the way you want, based
>> on what you have in sight, in as high a resolution you want.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout <ts...@ex...> wrote:
>> >
>> > But isn't it true that only the objects that are visible in the viewport
>> > are what are written to the rendered image file? ?I was proposing rendering
>> > a poster-sized image in "tiles" and stitching them back together post facto
>> > to create a very large, high resolution image.
>> >
>> > something like:
>> > -----------------------
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > | render 1 | render 2 |
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > |----------------------
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > | render 3 | render 4 |
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > | ? ? ? ? ?| ? ? ? ? ?|
>> > -----------------------
>> >
>> > I feel like I'm missing something important here!
>> > -Tom
>> >
>> > -----Original Message-----
>> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
>> > Sent: Thursday, October 22, 2009 11:45 AM
>> > To: Thomas Stout
>> > Cc: pym...@li...
>> > Subject: Re: [PyMOL] Saving high resolution images
>> >
>> > Hi Thomas,
>> >
>> > The viewport is not important for rendering. You can render at whatever
>> > resolution/dimensions you want with whatever viewport. You can even make a
>> > panorama using a wide angle lens if you want to have something for on your
>> > wall ;)
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout <ts...@ex...>
>> > wrote:
>> >>
>> >>
>> >> Here's a crazy idea: ?if someone out there were clever at both python
>> >> and manipulating orientation matrices, I would bet that a "scene"
>> >> could be quartered or cut into eighths and "translated" such that each
>> >> portion filled the viewport for rendering; then the individual images
>> >> could be spliced back together in one's favorite image handling
>> >> program a la panoramas in photography.... ?Is this way too complex to
>> >> be bothered with? ?I suspect parallax may be a problem...
>> >>
>> >> -Tom
>> >>
>> >>
>> >>
>> >> -----Original Message-----
>> >> From: Eva Vanamee [mailto:Eva...@ms...]
>> >> Sent: Monday, October 19, 2009 1:51 PM
>> >> To: pym...@li...
>> >> Subject: [PyMOL] Saving high resolution images
>> >>
>> >> Hi,
>> >>
>> >> I'd like to save an image in high resolution for a poster.
>> >> The requested size is 20" by 30". I calculated that it would
>> >> correspond to a 6000 x 9000 pixel image.
>> >> How can I create such a large ray traced image without crashing the
>> >> computer?
>> >> Many thanks in advance for the help.
>> >>
>> >> Best,
>> >>
>> >> - Eva
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
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

Tsjerk,
I think you are missing the point of Tom's post, which was a suggestion to
aid someone who's computer could NOT deliver the image in "as high a
rsolution as you want', so Tom was proposing a way to break the image down
into bite-size chunks that the computer COULD then handle. So the suggestion
was to take one scene desired at 9000x6000 which would make the computer
crash and instead mathematically figure the necessary transpositions to
render it in tiles such as upper left quadrant, upper right, etc. each at
4500x3000 or whatever the computer could handle (and then you could put them
all back together in photoshop, e.g.). So for someone with deep coding
skills they could likely teach pymol to ray just the segments they wanted
and deal with the overall perspective of the whole scene, but for a hack
like myself I'd likely start the work around of trying to figure out the
camera position and where I'd have to put it to get just a quarter of the
scene at a time in the viewport (or an eighth, or whatever). As Warren said,
you'd likely have to set orthoscopic to get rid of the perspective for
starters (at least in the hack approach, but there would be more direct
better ways for the skilled).

As a side point, Povray (if I remember correctly)  in fact allows you to
break a large rendering job up into tiles pretty much just like Tom
suggests, so not so crazy of an idea! I think in that case you can specify
starting and ending x,y pixel coordinates from your large scene. But not in
Pymol as far as I know.

Sorry if I've now gone stepping in and misinterpreting someone's points
myself, but it seemed like there was a lot of cross-purpose talk either from
assumptions or extra politeness!

-Seth

> > The requested size is 20" by 30". I calculated that it would
> > correspond
> > to a 6000 x 9000 pixel image.
> > How can I create such a large ray traced image without crashing the
> > computer?
>
>
> Message: 2
> Date: Fri, 23 Oct 2009 11:27:47 +0200
> From: Tsjerk Wassenaar <ts...@gm...>
> Subject: Re: [PyMOL] Saving high resolution images
> To: Thomas Stout <ts...@ex...>
> Cc: pym...@li...
> Message-ID:
>        <8ff...@ma...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Thomas,
>
> You can also zoom out to get everything in view. You can also change
> the field of view. And then you can ray just the way you want, based
> on what you have in sight, in as high a resolution you want.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Oct 22, 2009 at 9:35 PM, Thomas Stout <ts...@ex...> wrote:
> >
> > But isn't it true that only the objects that are visible in the viewport
> are what are written to the rendered image file? ?I was proposing rendering
> a poster-sized image in "tiles" and stitching them back together post facto
> to create a very large, high resolution image.
> >
> > something like:
> > -----------------------
> > | ? ? ? ? ?| ? ? ? ? ?|
> > | ? ? ? ? ?| ? ? ? ? ?|
> > | render 1 | render 2 |
> > | ? ? ? ? ?| ? ? ? ? ?|
> > | ? ? ? ? ?| ? ? ? ? ?|
> > |----------------------
> > | ? ? ? ? ?| ? ? ? ? ?|
> > | ? ? ? ? ?| ? ? ? ? ?|
> > | render 3 | render 4 |
> > | ? ? ? ? ?| ? ? ? ? ?|
> > | ? ? ? ? ?| ? ? ? ? ?|
> > -----------------------
> >
> > I feel like I'm missing something important here!
> > -Tom
> >
> > -----Original Message-----
> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
> > Sent: Thursday, October 22, 2009 11:45 AM
> > To: Thomas Stout
> > Cc: pym...@li...
> > Subject: Re: [PyMOL] Saving high resolution images
> >
> > Hi Thomas,
> >
> > The viewport is not important for rendering. You can render at whatever
> resolution/dimensions you want with whatever viewport. You can even make a
> panorama using a wide angle lens if you want to have something for on your
> wall ;)
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout <ts...@ex...>
> wrote:
> >>
> >>
> >> Here's a crazy idea: ?if someone out there were clever at both python
> >> and manipulating orientation matrices, I would bet that a "scene"
> >> could be quartered or cut into eighths and "translated" such that each
> >> portion filled the viewport for rendering; then the individual images
> >> could be spliced back together in one's favorite image handling
> >> program a la panoramas in photography.... ?Is this way too complex to
> >> be bothered with? ?I suspect parallax may be a problem...
> >>
> >> -Tom
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: Eva Vanamee [mailto:Eva...@ms...]
> >> Sent: Monday, October 19, 2009 1:51 PM
> >> To: pym...@li...
> >> Subject: [PyMOL] Saving high resolution images
> >>
> >> Hi,
> >>
> >> I'd like to save an image in high resolution for a poster.
> >> The requested size is 20" by 30". I calculated that it would
> >> correspond to a 6000 x 9000 pixel image.
> >> How can I create such a large ray traced image without crashing the
> >> computer?
> >> Many thanks in advance for the help.
> >>
> >> Best,
> >>
> >> - Eva
> >>
> >>
> >> ----------------------------------------------------------------------
>
>