Re: [PyMOL] how to convert .pse to html?

[Robert Hanson]

Albert, I just note that JSmol reads PyMOL PSE files directly - fully
JavaScript/HTML5 - and allows interactive viewing of them in JavaScript as
well as all the functionality of Jmol; nothing to change in terms of the
PyMOL file. Just load it.

Of course, not every capability of PyMOL is reproduced. It's a moving
target.
​
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Re: [PyMOL] 3D printing

[Robert Hanson]

On Tue, Oct 4, 2016 at 11:28 AM, Spencer Bliven 
wrote:

> I've done a bit of 3D printing of proteins. I found links in the previous
> thread VRML2 export and edu pymol
> helpful.
>
> STL is the best supported format for the printers, but since it's not
> supported by pymol I've used VRML2 (.wrl). Fortunately free tools to
> convert are readily available. A bigger problem is ensuring that the
> exported geometry is manifold. I've always had to do some cleanup in a 3D
> modeling program (e.g. blender, sketchup, etc) to get 3D printing software
> like Slic3r to accept it. Algorithms to automatically merge all geometry
> would be really nice if you're improving Jmol's export functionality.
>

Yes, the "hole" problem is important. The thing that happens with Jmol is
that when a cylinder penetrates a sphere, that causes a crossing that has
to be fixed. I was hoping someone has an easy fix for that, but now I see
that the printer-related software is used to this and can take care of it.
So perhaps it is not something that we need to worry about in PyMOL or
Jmol.

It seems to me PyMOL could easily implement STL. It is an extremely simple
format. I added this last week to Jmol in an afternoon. The problem I had
was that a lot of 3D printing software does not recognize the higher-level
objects such as Cylinder, Cone, and Sphere that are in VRML. So although
they may say they are "VRML 2.0" that's not really the case. They are "VRML
2.0 basic". But once that was done, it was a snap. Just a few extra lines
of code once the WRL is working. The files are big, though!



>
> You don't need to worry about support material. That should be handled by
> the slicing software, since it needs to know about the printer hardware to
> be generated efficiently.
>
>
It's not "support material" as much as "support". Jmol (and I think Pymol)
has automatic strut construction for proteins. This is critical for some
modeling materials that are brittle, such as colored silica like they use
at the Center for Biomolecular Modeling.


> -Spencer
>
>
> On Mon, Oct 3, 2016 at 9:50 PM, Sampson, Jared M. <
> jms2...@cumc.columbia.edu> wrote:
>
>> Hi Bob -
>>
>> I also haven't done much of anything with 3D printing myself, but having
>> worked on the COLLADA exporter as one of my POSF fellowship projects, I can
>> share some info about the formats themselves and what data is being
>> included in the output files.
>>
>> > Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary],
>> other)
>>
>> The list on the Save wiki page is fairly complete.  It reads:
>>
>> "The file format is autodetected if the extension is .pdb, .pqr, .mol,
>> .sdf, .pkl, .pkla, .mmd, .out, .dat, .mmod, .pmo, .pov, .png, .pse, .psw,
>> .aln, .fasta, .obj, .mtl, .wrl, .idtf, .dae, or .mol2."
>>
>> The 3D formats among these (that I recognize, anyway) are .obj (Wavefront
>> Object), .mtl (Wavefront Material), .wrl (VRML2), .idtf (Intermediate Data
>> Text Format), and .dae (COLLADA).
>>
>>
>> > Q: Does the generation of these include algorithms for ensuring closure
>> or for stitching together objects in order to not have ragged overlap?
>>
>> I'm not sure what you mean by "stitching together objects," but in
>> general, as long as you have fully closed surfaces, it shouldn't be an
>> issue.  The only situation I can think of that would be problematic is if
>> you had clipping panes that cut through the object's representation and end
>> up with a hollow, infinitesimally thin shell.  That would be pretty
>> difficult to print.  :)
>>
>> > Q: What is needed to add support struts so that the model is connected
>> and strong enough?
>>
>> No, this is related to what Paul was asking about recently.  My guess is
>> some 3D printing software or sites might have more appropriate tools to put
>> these in, although you could do it manually (and probably quite tediously)
>> with CGO cylinders or distance dashes with dash_gap = 0 if you know the
>> orientation you want to use.
>>
>> > Q: If features are not amenable to printing (labels,  perhaps?), are
>> they automatically ignored? Need to be manually removed?
>>
>> As far as I know, none of the supported 3D formats include labels in
>> their exported data.  Each one has its own implementation, but in general,
>> representations stored within PyMOL as triangle meshes (surfaces and
>> cartoons, primarily, although you can get everything as triangles with `set
>> use_shaders, 0`) are supported by all of them.  The COLLADA exporter also
>> handles spheres, cylinders, sausages (i.e. rounded cylinders, such as ) and
>> cones.  VRML2 includes spheres, cylinders and sausages.  The .obj exporter
>> has a bug in sphere export that I looked at about a year ago but got busy
>> and didn't actually follow through on.  The others I don't know enough
>> about to comment, but hopefully this gets you on the right track.
>>
>> If you want to look further 

[PyMOL] 3D printing

[Robert Hanson]

Can someone give me a summary of capabilities and limitations in PyMOL re
3D printing?

For example:

Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary],
other)

Q: Does the generation of these include algorithms for ensuring closure or
for stitching together objects in order to not have ragged overlap?

Q: What is needed to add support struts so that the model is connected and
strong enough?

Q: If features are not amenable to printing (labels,  perhaps?), are they
automatically ignored? Need to be manually removed?

Thanks,

Bob Hanson
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Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

[Robert Hanson]

To finish this thread -- Jmol and JSmol can now read (basic) PyMOL 1.8 PSE
files that have

set dump_binary, 1

for faster loading and smaller file sizes. Jmol only implements a small,
basic range of PyMOL functionality, of course.

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.6/Version%2014.6.1/Jmol-14.6.1_2016.08.09-binary.zip/download

Thank you, Thomas, for pointing me in the right direction on this.

Bob Hanson





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Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

[Robert Hanson]

Almost have it. Having trouble fitting all that into 120 bytes, though. I'm
good through bytes 96-99, visrep. Somehow, though I count 124 bytes total,
not 120 (which is clearly the case in the PSE file). What is
sizeof(AtomInfo_1_8_1) ? I calculate:

...
100-105 (six booleans)
106-111 (six characters)
112-116 (5 char for ElemName)
117-118 (2 char for SSType)
119-120 (2 char for Chain)
121 stereo
123 chemFlag
123 protekted

I need this to end at 119, not 123, to be consistent with the pickle data.


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Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

[Robert Hanson]

Ah, that is what I needed. For some reason that file is not in the download
I unzipped. Much more sensible!

Bob

On Mon, Aug 8, 2016 at 3:18 PM, Thomas Holder <thomas.hol...@schrodinger.com
> wrote:

> On 08 Aug 2016, at 16:01, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > I see this in 1.8.2.1:
> >
> > #define _PyMOL_VERSION "1.8.2.1"
> >
> > and in AtomInfo.h:
> >
> > #if _PyMOL_VERSION_int < 1770
> > #define AtomInfoVERSION  176
> > #define BondInfoVERSION  176
> > #elif _PyMOL_VERSION_int < 1810
> > #define AtomInfoVERSION  177
> > #define BondInfoVERSION  177
> > #else
> > #define AtomInfoVERSION  181
> > #define BondInfoVERSION  181
> > #endif
> >
> > So that must be where that 181 version indicator is coming from in a PSE
> file saved by 1.8.2.3, right?
>
> Correct.
>
> > But when you look at AtomInfoType in that same file, we see:
> >
> > typedef struct AtomInfoType {
> >   union {
> > float * anisou;   // only allocate with get_anisou
> > int64_t dummyanisou;
> >   };
> >
> >   lexidx_t segi;
> >   lexidx_t chain;
> >   lexidx_t resn;
> >   lexidx_t name;
> >   lexidx_t textType;
> >   lexidx_t custom;
> >   lexidx_t label;
> > ...
> >
> > What am I missing?
>
> You're looking at the wrong struct. When doing the binary dump, structs
> from layer2/AtomInfoHistory.h are used. See https://sourceforge.net/p/
> pymol/code/HEAD/tree/trunk/pymol/layer2/AtomInfoHistory.h#l187
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

[Robert Hanson]

I see this in 1.8.2.1:

#define _PyMOL_VERSION "1.8.2.1"

and in AtomInfo.h:

#if _PyMOL_VERSION_int < 1770
#define AtomInfoVERSION  176
#define BondInfoVERSION  176
#elif _PyMOL_VERSION_int < 1810
#define AtomInfoVERSION  177
#define BondInfoVERSION  177
#else
#define AtomInfoVERSION  181
#define BondInfoVERSION  181
#endif

So that must be where that 181 version indicator is coming from in a PSE
file saved by 1.8.2.3, right?

But when you look at AtomInfoType in that same file, we see:

typedef struct AtomInfoType {
  union {
float * anisou;   // only allocate with get_anisou
int64_t dummyanisou;
  };

  lexidx_t segi;
  lexidx_t chain;
  lexidx_t resn;
  lexidx_t name;
  lexidx_t textType;
  lexidx_t custom;
  lexidx_t label;
...

What am I missing?

Bob





On Mon, Aug 8, 2016 at 10:51 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> look here:
> https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/
> pymol/layer2/AtomInfoHistory.h
>
> The AtomInfoType_1_8_1 version (used in 1.8.2) stores ANISOU as shorts
> (PDB precision). The AtomInfoType_1_7_7 version (used in 1.8.0) doesn't
> support ANISOU (will indeed write an unused NULL pointer), at the time it
> was work in progress for a specific use case which didn't require ANISOU.
>
> Cheers,
>   Thomas
>
> On 08 Aug 2016, at 11:32, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > I do like the compactness of that and the quicker loading, but I do see
> how this could be a nightmare. I'm looking  at a file that lists the dump
> version as 1.8.1, but I don't even see how that would ever work, since in
> that AtomInfo structure the ANISOU data is just a 64-bit pointer. That
> would end up just a useless reference, wouldn't it?
> >
> > On Mon, Aug 8, 2016 at 10:05 AM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
> > Hi Bob,
> >
> > I assume those are PSE files with setting "pse_binary_dump=on". This is
> not the default. You can load such files into PyMOL, set
> pse_binary_dump=off and save it as a regular serialized PSE. I definitely
> recommend the conversion step over reimplementing the "pse_binary_dump"
> decoding. Right now there are 3 binary atom layouts (for 1.7.6, 1.8.0 and
> 1.8.2). Grep the PyMOL code for "AtomInfoTypeConverter" if you're
> interested in the details.
> >
> > The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and
> with the "pse_export_version" setting you can also export for older PyMOL
> versions.
> >
> > Cheers,
> >   Thomas
> >
> > On 08 Aug 2016, at 07:57, Robert Hanson <hans...@stolaf.edu> wrote:
> >
> > > Thomas,
> > >
> > > In reading PyMOL PSE files into Jmol I have recently run into the
> problem with some of these files (version 1.8.2.3). Jmol has no problem
> reading the standard Pickle format, but there seems to be an option in
> PyMOL to serialize binary data structures as BINSTRING or SHORT_BINSTRING
> format along with other standard strings. This sounds like a great idea; I
> have no doubt that this will lead to considerably smaller PSE files and
> also faster loading. However, I'm struggling with atom information
> deserialization.
> > >
> > > Q: Is this the default format now for saving PyMOL PSE files?
> > >
> > > Q: Is there a way to turn that off?
> > >
> > > Q: In order to do this properly, how many versions of the atom info
> data structure do I need to be able to process?
> > >
> > > Bob
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

[Robert Hanson]

I do like the compactness of that and the quicker loading, but I do see how
this could be a nightmare. I'm looking  at a file that lists the dump
version as 1.8.1, but I don't even see how that would ever work, since in
that AtomInfo structure the ANISOU data is just a 64-bit pointer. That
would end up just a useless reference, wouldn't it?

On Mon, Aug 8, 2016 at 10:05 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Bob,
>
> I assume those are PSE files with setting "pse_binary_dump=on". This is
> not the default. You can load such files into PyMOL, set
> pse_binary_dump=off and save it as a regular serialized PSE. I definitely
> recommend the conversion step over reimplementing the "pse_binary_dump"
> decoding. Right now there are 3 binary atom layouts (for 1.7.6, 1.8.0 and
> 1.8.2). Grep the PyMOL code for "AtomInfoTypeConverter" if you're
> interested in the details.
>
> The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and
> with the "pse_export_version" setting you can also export for older PyMOL
> versions.
>
> Cheers,
>   Thomas
>
> On 08 Aug 2016, at 07:57, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > Thomas,
> >
> > In reading PyMOL PSE files into Jmol I have recently run into the
> problem with some of these files (version 1.8.2.3). Jmol has no problem
> reading the standard Pickle format, but there seems to be an option in
> PyMOL to serialize binary data structures as BINSTRING or SHORT_BINSTRING
> format along with other standard strings. This sounds like a great idea; I
> have no doubt that this will lead to considerably smaller PSE files and
> also faster loading. However, I'm struggling with atom information
> deserialization.
> >
> > Q: Is this the default format now for saving PyMOL PSE files?
> >
> > Q: Is there a way to turn that off?
> >
> > Q: In order to do this properly, how many versions of the atom info data
> structure do I need to be able to process?
> >
> > Bob
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
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[PyMOL] dump_binary and PyMOL 1.8 PSE files

[Robert Hanson]

Thomas,

In reading PyMOL PSE files into Jmol I have recently run into the problem
with some of these files (version 1.8.2.3). Jmol has no problem reading the
standard Pickle format, but there seems to be an option in PyMOL to
serialize binary data structures as BINSTRING or SHORT_BINSTRING format
along with other standard strings. This sounds like a great idea; I have no
doubt that this will lead to considerably smaller PSE files and also faster
loading. However, I'm struggling with atom information deserialization.

Q: Is this the default format now for saving PyMOL PSE files?

Q: Is there a way to turn that off?

Q: In order to do this properly, how many versions of the atom info data
structure do I need to be able to process?



Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [PyMOL] The Wiki appears outdated or in error

[Robert Hanson]

In case you are interested, Jim, Jmol will read (most/some) PyMOL session
files, and Jmol can then create both an idtf for generating a u3d file, and
a small sample TeX file also that can be used to create a PDF containing
it.

I had some interest in u3d back in 2009, when I wrote this exporter. You
might be interested in my notes at the top of
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/export/_IdtfExporter.java

Here are a few examples created using Jmol:
http://chemapps.stolaf.edu/jmol/u3d/
As I recall, the TeX file is necessary in order to properly reproduce the
viewport state.

My conclusion was that u3d is an absolutely unmanageable file format. Its
construction is totally obtuse, and the idtf->u3d converter has bugs that
will probably never be fixed. I could be wrong, and in the intervening
years it has improved, but my impression at the time was that it was an
experimental format out of Adobe's research labs that never really made it
and hasn't been developed much since then.

Its inclusion in PDF file quite frankly takes the "P" out of "PDF."

Bob Hanson
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Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

[Robert Hanson]

Ioannis,

I suggest using the CIF file from EBI instead:

http://www.ebi.ac.uk/pdbe/static/entry/download/1hho-assembly-1.cif.gz

It looks good to me -- just one model.

For reference, the RCSB site is using Jmol and is simply loading 1HHO
itself and constructing the assembly *in situ *using the symmetry operators
in that file, not reading the assembly file.  PyMOL must have a simple way
to do that as well. Right? Or do you have to load the assembly file?

There is no mistake in the PDB assembly file. Jmol also reads that just
fine, but as you point out, it is in the form of two models, for reasons I
do not understand. It looks to me like when the PDB assembly file is
created, each BIOMT transformation is put into a separate model. This is
NOT what EBI does when they create the analogous mmCIF assembly file.

A totally different multi-model (NMR solution) issue has been noticed with
CIF assembly files from EBI. [e.g.
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz] In
that case, there are 20 models, and the atom ordering ens up by chain, not
be model, so that the coordinates for each "model" are scattered
throughout  the file, which seems quite odd to me. And I notice that RCSB
also creates a PDB assembly file for 2lev, but in that case only one model
is produced, and it is just the first NMR model. So this is still an
imperfect design all around. In both cases, I my opinion, there are design
flaws. Don't know that you can call that a bug

Bob Hanson
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[PyMOL] status of Uppsala EDS server?

[Robert Hanson]

Does anyone know the status of http://eds.bmc.uu.se? Is it gone forever?
Does anyone know the replacement URL for getting electron density maps and
difference maps?  (Which I think is at EBI, right?)

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
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Re: [PyMOL] Version question -- PSE session file format

[Robert Hanson]

Ah, I see. I just use files that others send me. Yes, this was from
MacPyMOL. The "main" dictionary item does seem supremely useful. Is there a
way of deriving that information from the PSE file? Otherwise, how does one
reproduce an image created by PyMOL from a session file?

On Wed, Dec 23, 2015 at 8:53 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Bob,
>
> Nothing has changed here in 1.8. I assume you used MacPyMOL recently? As
> far as I know, MacPyMOL never stored the "main" dictionary item. Or if you
> export a session with partial=1, it will also not store the viewport.
>
> Cheers,
>   Thomas
>
> On 23 Dec 2015, at 19:12, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > I have a question about the PSE file format.
> >
> > Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no
> indication of the desired viewport width and height. These were in the
> "main" dictionary item. Is there any way in these new files to find out the
> original viewport size?
> >
> > Bob
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > Chair, Department of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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[PyMOL] Version question -- PSE session file format

[Robert Hanson]

I have a question about the PSE file format.

Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no
indication of the desired viewport width and height. These were in the
"main" dictionary item. Is there any way in these new files to find out the
original viewport size?

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [PyMOL] JyMOL vs JSMol

[Robert Hanson]

I guess I should chime in here. JSmol does read (some fraction of) PyMOL
session files. To be sure it has not been a priority to keep up to date
with all the amazing PyMOL capabilities, but certainly as a proof of
concept it has worked well, and it would be great to collaborate on this to
improve it more. See, for example:  http://noys3.weizmann.ac.il/a2jb/browse

I certainly don't claim to know anything about JyMOL, except I guess it
uses JNLP. Does Chrome support JNLP anymore?

Bob Hanson
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Re: [PyMOL] JyMOL vs JSMol

[Robert Hanson]

Don't worry. No apology necessary. It's a closely held secret that JSmol
can do this. In any case, trust me, you will find plenty that JSmol cannot
handle. There are many mysteries of the PSE format that I could only guess
at.

Enjoy!
​
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Re: [PyMOL] Problems loading new mrc-format electron density files into pymol

[Robert Hanson]

>From Steven Ludtke (EMAN2):

We'll get it fixed in today's daily release.

On Tue, Oct 6, 2015 at 7:37 AM, Michael F. Summers  wrote:

> Colleagues:
>
> In the past, I was able to load MRC format electron density maps into
> pymol without problems.  However, files I’ve received from collaborators,
> saved
> with a new version of EMAN2, don’t load properly into pymol.  The data are
> loaded, but the unit cell information is not read, so the dimensions of the
> density map are incorrect. The maps DO load properly into Chimera … but I’d
> prefer to continue using pymol.  Any help would be appreciated.  From my
> limited ability to look a the content of the files, it appears that the
> header information of the new files is stored differently.
>
> Alternatively, in the short term, would it be possible to load the .mrc
> files and then manually adjust the unit cell dimensions in pymol?
>
> I can provide the .mrc files if someone would like to take a look at them.
> They are too large to attach to this email (they bounced back from the
> pymol mail server).
>
>
> Thanks in advance for any help,
>
>
> Mike
>
> Michael F. Summers
> HHMI, UMBC
>
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Re: [PyMOL] sulfated tyrosine's losing connection

[Robert Hanson]

This unusual file has all the backbone bonds indicated with CONECT records
-- except the missing links you note. I'm guessing that PyMOL is respecting
that, and that it could be an RCSB file error.

CONECT 9606 9593
9607
CONECT 9607
9606
CONECT 9608
9609
...
CONECT 1674 1661
1675
CONECT 1675
1674
CONECT 1676
1677


What are missing there are

CONECT 9606 9608
CONECT 9608 9606
CONECT 1674 1676
CONECT 1676 1674

Jmol has the same missing links.
​
(forwarding to Andreas Prlic at RCSB)
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Re: [PyMOL] sulfated tyrosine's losing connection

[Robert Hanson]

actually -- I see there are just CONECT records for all the HETATMs, as
usual. Nothing odd about that. But, nonetheless, in this case those CONECT
records are not there. The point is that it has nothing to do with PyMOL.
​
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Re: [PyMOL] CGOs

[Robert Hanson]

OK. I will look at the PyMOL code if I need to. For instance:

LINE  has eight parameters. I don't know what the first two are.

LINE ? ? x1 y1 z1  x2 y2 z2




On Sun, Dec 21, 2014 at 3:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Bob,

 Unfortunately, there is little documentation on CGO objects. You can have
 a look in modules/cgo.py and in the example scripts in examples/devel/ in
 the pymol directory to get some more information. If there is something
 specific you want to do, please let us know.

 Cheers,

 Tsjerk


 On Sun, Dec 21, 2014 at 9:57 PM, Robert Hanson hans...@stolaf.edu wrote:

 I'm looking for something that is relatively comprehensive. There are far
 more commands than VERTEX, CYLINDER, CONE, and SPHERE, I think.



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Re: [PyMOL] CGOs

[Robert Hanson]

OK, that explains it. I think I made that one up. It was a while ago that I
worked on this. :)
I see the list at
https://github.com/speleo3/pymol/blob/master/modules/pymol/cgo.py

Thanks​, David.

Bob
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Re: [PyMOL] CGOs

[Robert Hanson]

Great. Thanks very much. The ones perhaps missing there are:

#define CGO_INDENT   0x18
#define CGO_RESET_NORMAL 0x1E
#define CGO_PICK_COLOR   0x1F

And I think

#define CGO_LIGHTING 0x0B50

may be an internal flag, not a CGO command.
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[PyMOL] CGOs

[Robert Hanson]

Happy holidays!

Q: Is there a resource that describes the syntax for compiled graphical
objects in PyMOL?

I see http://pymol.sourceforge.net/newman/user/S0500cgo.html, but that is
pretty minimal.

Bob



-- 
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Larson-Anderson Professor of Chemistry
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Northfield, MN
http://www.stolaf.edu/people/hansonr


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Re: [PyMOL] CGOs

[Robert Hanson]

I'm looking for something that is relatively comprehensive. There are far
more commands than VERTEX, CYLINDER, CONE, and SPHERE, I think.
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Re: [PyMOL] View Matrix operation

[Robert Hanson]

I don't think this is possible. Those 9 numbers simply tell you the
orientation. There is much more to it than that. Perspective, camera
position, x-y translation, screen dimensions, for example. Some of these
are in other PyMOL settings.

On Wed, Nov 19, 2014 at 6:14 AM, Feitsma, L.J. l.j.feit...@uu.nl wrote:

  Hi all,



 I have a small question about transformations with the view matrix in
 pymol, since I’m not very familiar with the architecture of the matrix.



 E.g. I take some coordinates [x1,y1,z1], and using cgo objects, I want to
 draw a line/triangle/square to a point distance 4 to the right on the
 screen (so not 4 in object x-coördinates!).

 How can I use the information in [0:8] of the view matrix to calculate
 object coordinates [x2, y2, z2] needed to draw the line between [x1, y1,
 z1] and [x2, y2, z2]?



 Does anyone has an example script, or link about which matrix operation I
 need for this?



 Kind regards,



 Louris Feitsma



 Crystal and Structural Chemistry

 Utrecht University

  Padualaan 8

 3584 CH Utrecht

 The Netherlands

 P: +31-30-2539182




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[PyMOL] mmCIF -- multicharacter chain labels

[Robert Hanson]

What's the trick to loading mmCIF files with multi-character chain IDS?
Maybe I just need to upgrade? (Using PyMOL 1.6.0.0) What I see now is just
the first character of _atom_site.auth_asym_id

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

[Robert Hanson]

My only real objection is that WebGL is not supported on iOS in browsers.
Beyond that, I probably just don't know enough about it to do it right.


On Wed, Feb 12, 2014 at 1:50 PM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Hi Bob,

 On 10 Feb 2014, at 20:43, Robert Hanson hans...@stolaf.edu wrote:
  I haven't explored JyMOL, but I guess it has the potential to do that,
 and like Jmol could probably be converted to JavaScript. I don't know. But
 I'm guessing it uses WebGL which isn't an adequate solution in my opinion.
 Thomas...?

 JyMOL actually runs native PyMOL graphics (without the Python) using
 Java and JOGL. It can't just be converted to JavaScript, but provides a
 JavaScript API similar to our Python API.

 WebGL is a different, but very interesting story. Why do you think it's
 not adequate?

 Cheers,
   Thomas

 --
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 PyMOL Developer
 Schrödinger, Inc.




-- 
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Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

[Robert Hanson]

So in the mean time, Riccardo, I guess what you are already using:

xxx.pse -- JmolData.jar -- idtf

is your best bet.

Q: What sort of size of PDF file are you seeing in the end?
Q: Do you see this a practical and useful in some way?  If so, in what way?

Bob Hanson
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Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

[Robert Hanson]

Riccardo, like me, I think you forgot to reply all. (I gather that from
your  addressing two of us and not just me.)

Yes, Jmol does that. It's not perfect, but it's a respectable amount of
PyMOL functionality. This is actually something that Warren and I talked
about not too long before his untimely death, and it took a trip last
January for me to the Weizmann Institute to get my head around.  See
http://ispcsrv.weizmann.ac.il/a2jmolb/browse  It's actually pretty fun to
see PyMOL sessions appear in pure JavaScript!

There will always be aspects of biomolecular visualization that only PyMOL
can reproduce, and that I have no hope of implementing in Jmol, still it's
a good challenge to try, and we feel it fills a need in the area of
interactive web content, at least until Schrodinger comes out with their
own web viewer, which I'm guessing is not far off... (Sorry, that was a
looong sentence!)

I haven't explored JyMOL, but I guess it has the potential to do that, and
like Jmol could probably be converted to JavaScript. I don't know. But I'm
guessing it uses WebGL which isn't an adequate solution in my opinion.
Thomas...?

Bob Hanson



On Mon, Feb 10, 2014 at 6:49 PM, Riccardo mitm...@gmail.com wrote:

 @Jared: Hello! Thanks for you reply! I supposed it... So, must be
 implemented yet; is that the only interested file for that exporting
 function? Thanks a lot.

 @Bob: Hello! Nice to hear you here! Thanks.
 Yes. So JmolData.jar can read a .pse file as is (with lights,
 transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good.

 Thanks a lot to you.

 Regards,
 Riccardo Volpe


  *ChemBioScripting | X3D PyMOL Molecule Viewer
 http://chembioscripting.hol.es *|* Gioacchino Riccardo Volpe*


 2014-02-10 23:25 GMT+01:00 Robert Hanson hans...@stolaf.edu:

 So in the mean time, Riccardo, I guess what you are already using:

 xxx.pse -- JmolData.jar -- idtf

 is your best bet.

 Q: What sort of size of PDF file are you seeing in the end?
 Q: Do you see this a practical and useful in some way?  If so, in what
 way?

 Bob Hanson







-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [PyMOL] minimum rotation between views

[Robert Hanson]

Jonathan, this is called the quaternion difference, but I don't know how
you get access to quaternions in PyMOL. If you could, you would just take
the difference between the two quaternion representations of the views and
get it's angle for the corresponding axis-angle.

Jason, are there standard Python utilities that one can use to get the
quaternion equivalents of PyMOL matrices?

Bob



On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes
jonat...@strubi.ox.ac.ukwrote:


is there a script available to calculate the min rotation about a vector
that describes the relationship between 2 views……

i am happy to ignore any translational component but i have 2 views
of a molecule and want to say that theres a *** deg rotation between the
 2 views ?

thanks
 jon


 Dr. Jonathan M. Grimes,
 NDM Senior Reseach Fellow
 University Research Lecturer
 DIAMOND Research Fellow

 Division of Structural Biology
 Wellcome Trust Centre for Human Genetics
 University of Oxford
 Roosevelt Drive,
 Oxford OX3 7BN, UK

 Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
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Re: [PyMOL] new metals keyword

[Robert Hanson]

see http://chemapps.stolaf.edu/jmol/docs/#atomproperties for several
suggestions.


On Tue, Aug 13, 2013 at 10:56 AM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Greetings,

 this is a quick announcement that we added the metals keyword to the
 selection language (SVN code revision 4039).

 Since PyMOL's selection language is one of the powerful core features
 that make so many complex tasks so easy, we plan to add more useful
 keywords and operators. For example selecting by x,y,z coordinates, or
 selecting by secondary structure element. If you have a good idea for a
 new keyword or operator, please file a feature request on sourceforge.

 Cheers,
   Thomas

 --
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Re: [PyMOL] Reducing the surface rendering load for JSmol export

[Robert Hanson]

Nick, if these are just molecular surfaces, there is nothing to do in
PyMOL. The PSE files have only an indication of which atoms to create the
surface for, not the surface itself.  Jmol/JSmol reads the PSE files
directly, determines what molecular surface to create, and uses its own
algorithms. Right now the import doesn't give an option for a default
resolution, but we could adapt that if needed. You are right that the
generation of surfaces is the bottleneck in a JavaScript-only solution.
I'll be documenting the doCache load option for PSE files soon, which
allows you to convert surfaces to a JVXL format and include them in PNGJ
files for better delivery over the web. It's a work in progress...

Bob Hanson



On Wed, Jul 17, 2013 at 2:29 AM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Hi Nick,

 did you try the surface_quality setting? The default value is 0.
 That's for molecular surfaces.

 PyMOL set surface_quality, -1

 The resolution of isosurfaces is determined by the resolution of the map
 as far as I know. You can reduce the map resolution with the map_halve
 command.

 Cheers,
   Thomas

 Greeves, Nick wrote, On 07/16/13 07:56:
  I am interested in displaying PyMOL session files using JSmol
  http://sourceforge.net/projects/jsmol/  Basically this works but some
  of the session files have high resolution surfaces which put a
  tremendous strain on JSmol/browser when they are displayed.
 
  I am new to PyMOL and cannot see how to adjust the settings to produce
  a lower resolution surface in PyMOL that should work better in JSmol.
  I have tried all the menus and looked at all the settings without
 success.
 
  Any advice would be most welcome.
  Best regards
  Nick

 --
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

[Robert Hanson]

(yes, I meant forward compatibility there)

Jason, in our 100+ PyMOL session files that we can now read into Jmol we
have a few files that don't seem to have backward compatibility to PyMOL
1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and
measurements. Should I just send them to you and/or Thomas?

Bob



On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees 
jason.vertr...@schrodinger.com wrote:

 Hi David,

 If you save a session file in the latest version of PyMOL there is never
 the expectation that prior versions can read that file. Such forward
 compatibility (of the older versions) is not supported. We do support,
 however, backward compatibility which is when newer versions of PyMOL
 read older session files.

 Cheers,

 -- Jason


 On Wed, Jun 19, 2013 at 4:18 PM, David Hall li...@cowsandmilk.net wrote:

 I still have this problem:
 session saved in 1.6 with a black background; opens in 1.5 (and earlier)
 with a red background

 Many of my collaborators use old versions of pymol, frequently installed
 onto their machines when they were bought X years ago, and this essentially
 makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
 least not without getting weird e-mails asking why I have a sudden affinity
 for the color red).

 -David




 On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder 
 thomas.hol...@schrodinger.com wrote:

 This is fixed in SVN rev 4032.

 Cheers,
   Thomas

 Thomas Holder wrote, On 06/15/13 10:45:
  Hi Rob,
 
  this has not been fixed yet, I'm really sorry. We'll look into this
  ASAP. It only affects the open-source code, apparently we missed
  something when syncing with the incentive codebase.
 
  Cheers,
Thomas
 
  On Jun 14, 2013, at 9:23 PM, Robert Campbell 
 robert.campb...@queensu.ca wrote:
  Hello Thomas and David,
 
  Was there any resolution of this?  I've just compiled the latest
 version
  from SVN and I have the same problem opening files created under
 version
  1.5.0.  This is on Debian testing (32-bit).
 
  Cheers,
  Rob
 
  On Fri, 2013-04-26 19:15  EDT,  David Hall li...@cowsandmilk.net
  wrote:
 
  Hi Thomas,
 
  I'm running into issues with color compatibility between 1.6 and
  earlier versions when opening pses
  (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
  Setting-Error: type read mismatch (color) 6
  Setting-Error: type read mismatch (color) 663
  Setting-Error: type read mismatch (color) 664
  (b) background color disparity:
  saved in 1.5 with black background; opens in 1.6 with a white
 background
  saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a
 red
  background
 
  These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
  others who would like to beta test can use devel:languages:python
 repo
  in openSUSE:
 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 
  -David

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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Re: [PyMOL] PyMOL 1.6 pre-release announcement

[Robert Hanson]

That would be a problem with all programs -- unless there is a SAVE mode
that is compatible with version   (as, for example, MS Word has). One
cannot expect backward compatibility, I think.

Bob Hanson


On Wed, Jun 19, 2013 at 4:18 PM, David Hall li...@cowsandmilk.net wrote:

 I still have this problem:
 session saved in 1.6 with a black background; opens in 1.5 (and earlier)
 with a red background

 Many of my collaborators use old versions of pymol, frequently installed
 onto their machines when they were bought X years ago, and this essentially
 makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
 least not without getting weird e-mails asking why I have a sudden affinity
 for the color red).

 -David




 On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder 
 thomas.hol...@schrodinger.com wrote:

 This is fixed in SVN rev 4032.

 Cheers,
   Thomas

 Thomas Holder wrote, On 06/15/13 10:45:
  Hi Rob,
 
  this has not been fixed yet, I'm really sorry. We'll look into this
  ASAP. It only affects the open-source code, apparently we missed
  something when syncing with the incentive codebase.
 
  Cheers,
Thomas
 
  On Jun 14, 2013, at 9:23 PM, Robert Campbell 
 robert.campb...@queensu.ca wrote:
  Hello Thomas and David,
 
  Was there any resolution of this?  I've just compiled the latest
 version
  from SVN and I have the same problem opening files created under
 version
  1.5.0.  This is on Debian testing (32-bit).
 
  Cheers,
  Rob
 
  On Fri, 2013-04-26 19:15  EDT,  David Hall li...@cowsandmilk.net
  wrote:
 
  Hi Thomas,
 
  I'm running into issues with color compatibility between 1.6 and
  earlier versions when opening pses
  (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
  Setting-Error: type read mismatch (color) 6
  Setting-Error: type read mismatch (color) 663
  Setting-Error: type read mismatch (color) 664
  (b) background color disparity:
  saved in 1.5 with black background; opens in 1.6 with a white
 background
  saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
  background
 
  These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
  others who would like to beta test can use devel:languages:python repo
  in openSUSE:
 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 
  -David

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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Re: [PyMOL] Possible hydrogen addition bug

[Robert Hanson]

Just adding that N1, C2, and N3 in that ring are all sp2 hybridized. So the
H on the adjacent N is also in the wrong place.

Q: How is PyMOL determining ligand atom hybridization, by the way? Not
using the ligand CIF file at PDB, I guess?

Bob Hanson



On Fri, Jun 7, 2013 at 10:51 AM, Matthew Baumgartner mp...@pitt.edu wrote:

 Hi,
 I may have found a bug in the way pymol interprets connectivity of
 atoms. I noticed this in one pdb structure that I am working with 1RV1.

 Steps to reproduce:
 fetch 1RV1

 #extract one of the ligands to it's own object
 extract 'lig', /1RV1//A/110

 #add hydrogens
 h_add lig

 Now look at atom C2 on the ligand and notice that pymol added a hydrogen
 almost along an existing bond to another ring.

 I am running pymol 1.5.0.1 on Ubuntu 13.04.

 I'm not sure if this has been reported before and has been fixed already
 in 1.6. I haven't gotten around to upgrading yet, but I am willing to.

 Thanks,
 Matt

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Re: [PyMOL] Cartoon transparency

[Robert Hanson]

I must say, 'cartoon skip' does not do what I thought it would do.

fetch 1RV1
cartoon skip, i. 55
# now a helix section is turned into a loop
cartoon skip, i. 56
# now there is a break, but two non-helix ends
cartoon skip, i. 57
# now there is a break, with two non-helix ends


I guess I understand the idea that in PyMOL a cartoon is like a bond --
between two elements rather than being associated with one (perhaps?) --
but why change the helix to a loop before it ends? Is there a way around
that?

Bob




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Re: [PyMOL] Cartoon transparency

[Robert Hanson]

That would not work if you were trying to show selected individual ribbon
segments translucent, I think. Right?

From what I can tell, here is the list of settings that you can assign a
selection. Notably missing is cartoon_transparency and ribbon_transparency.
Perhaps because a cartoon object can't be broken down into individual
segments that way in PyMOL.  Are there more?

cartoon_color
dot_color
ellipsoid_color
ellipsoid_scale
ellipsoid_transparency
label_color
label_position
ladder_color
ladder_mode
ladder_radius
mesh_color
nonbonded_transparency
ribbon_color
ring_color
ring_mode
ring_radius
ring_width
sphere_color
sphere_scale
sphere_transparency
surface_color
transparency






On Thu, Jun 6, 2013 at 6:50 AM, Gianluigi Caltabiano chimic...@yahoo.itwrote:

 You need to create a new object of the part you want transparent and then
 set that cartoon as transparent (and hide the original cartoon for the
 selection).

 G.

   --
  *Da:* James Starlight jmsstarli...@gmail.com
 *A:* pymol-users pymol-users@lists.sourceforge.net
 *Inviato:* Giovedì 6 Giugno 2013 12:36
 *Oggetto:* [PyMOL] Cartoon transparency

 Dear PyMol users!


 I want to set transparency on the selected carton region of my protein ( I
 have closed GFP barell with the chromophore inside it so I'd like set
 transparency of some beta-shits to make chromophore easily visible ).


 In PyMol I've selected region corresponded to that Beta-sheets and than
 used

 set cartoon_transparency, 0.5, sele



 unfortunatelly there were no any changes after this :(

 How I could solve it ?



 Thanks for help,


 James


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[PyMOL] settings

[Robert Hanson]

I'm trying to understand settings. I see that there are at least these
levels of settings:

- global
- object
- state
- unique atom/bond

Are there more?

I'm unclear on when one overrides another. It looks to me that the general
getSetting methods have the option of up to three levels of settings, but
there are four here.

Thus, for example:

If I have unique settings for a bond and then apply the sort of script that
Sid recently was interested in, that might change stick_color, would that
unique bond setting be overridden?

If a state's color is set using Spectrum_states.py, does that override
already-set scene colors? Or is it incorporated into defined scenes then?
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[PyMOL] scenes and states

[Robert Hanson]

Questions:

Can two objects be in two different states -- object1 in state 3 and
object2 in state 10, for instance, at the same time? If so, how is that set
up? How is that then incorporated into a scene?

Do CGO, measurements, mesh, and volume objects have states as well?

Bob

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Re: [PyMOL] scenes and states

[Robert Hanson]

[[sorry -- not  used to a list that requires reply-all to go back to the
list]]

What you describe there is a way to load a specific file into a specific
state, I think. I meant, once you have a set of multi-state objects, can I
select to compare two different states, one from one and one from the other?

1cdr2/10
1sq35/30

and then could I make a scene that does that? -- without viewing all
states

Bob


On Mon, Jun 3, 2013 at 9:07 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Bob,

 The answer is yes to all.

 fetch 1ubq, state=3
 fetch 6lzm, state=10
 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2)

 The representations (e.g. surface) do have states in the sense that the
 each state gives a different surface. But whether the surface is shown or
 not is controlled globally. It is not possible to have the surface
 representation only in one state, such that looping over the states, the
 surface would suddenly pop up for one.

 Hope it helps,

 Tsjerk


 On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote:

 Questions:

 Can two objects be in two different states -- object1 in state 3 and
 object2 in state 10, for instance, at the same time? If so, how is that set
 up? How is that then incorporated into a scene?

 Do CGO, measurements, mesh, and volume objects have states as well?

 Bob

 --
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 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [PyMOL] settings

[Robert Hanson]

Thanks, Thomas


On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder thomas.hol...@schrodinger.com
 wrote:

 Hi Robert,

 you got the levels right.

 The cmd.get method actually doesn't support querying atom level settings,
 even though you can set them with cmd.set.


I see. That's helpful.



 Atom settings are not state specific, unless you have a discrete object.


I see, because then every atom in a multi-model file has is own record, and
thus its own unique ID. Sure. For now, Jmol is loading all PSE files as
though discrete=1. The Jmol equivalent of discrete=0 would be  (in Jmol) *load
TRAJECTORY xxx.pse*, but I don't have that right now able to load some
models as trajectories and some not, as would generally be needed in PSE
file loading. So that will have to wait.





 Scenes do not store settings, so using spectrum_states overrides scene
 colors.


But a scene does store settings in the sense that there are, at least for
colors, for example, _!c_scene_xxx_sticks settings. How does that fit in,
then? I'll look into that.




 Hope that helps.


definitely!



 Cheers,
   Thomas

 On Jun 3, 2013, at 8:34 AM, Robert Hanson hans...@stolaf.edu wrote:
  I'm trying to understand settings. I see that there are at least these
 levels of settings:
 
  - global
  - object
  - state
  - unique atom/bond
 
  Are there more?
 
  I'm unclear on when one overrides another. It looks to me that the
 general getSetting methods have the option of up to three levels of
 settings, but there are four here.
 
  Thus, for example:
 
  If I have unique settings for a bond and then apply the sort of script
 that Sid recently was interested in, that might change stick_color, would
 that unique bond setting be overridden?
 
  If a state's color is set using Spectrum_states.py, does that override
 already-set scene colors? Or is it incorporated into defined scenes then?

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor




-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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[PyMOL] PyMOL session file reader for Jmol

[Robert Hanson]

Hello, PyMOL users,

The driving force behind these last four months of Jmol/JSmol development
has been e-publication. The goal has been to produce a means of
e-publishing working interactive biomolecular models that are ubiquitously
accessible (i.e. no Java, no  WebGL). We achieved that goal for Jmol late
last year, with the introduction of JSmol -- a fully HTML5-based
identical renderer for Jmol. See
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm

Today, I'm letting you all know that we have that for PyMOL as well,
basically. Authors can produce all the beautiful PyMOL images they want for
regular publication purposes and then have them available for general
viewing on a publisher's web site (if that site is so equipped) or on their
own institutional site.

This works because Jmol now has a pretty decent PyMOL session file reader.
It's a work in progress, but we are reproducing our complete set of test
files (104 to date) fully now, with quite a wide variety of features. It's
a work in progress, of course, and we are handling issues as they arise.
But I think one look at http://ispcsrv3.weizmann.ac.il/a2jmolb/browse will
convince you that we have made some pretty significant progress along these
lines.

[That server is having significant issues just this week, so pardon the
Failed signs. Those aren't real problems; just some sort of unidentified
server issue at the Weizmann Institute.]

There are some differences in that test set, but they are only cosmetic --
a few sightly different renderings of cartoons, for instance. Jmol, though
it has a PovRAY interface, doesn't interactively do shadows. Translucency
is handled differently. (PyMOL's translucency is object-based; Jmol's
translucency is pixel-based.) The perspective is exact, though, because
both programs use the same perspective model. Morph-type (not scripted)
movies are no problem. Electron density maps are read. Scenes are
cataloged, reproducible, and easily discovered by web page based
JavaScript.

Of course, the JavaScript-only non-WebGL version is slower than Java, which
itself is (sometimes perceptively) slower than C++. That's a given. Don't
expect prime performance on your smart phone.

Surface generation, particularly the PyMOL default solvent-excluded
surface, is considerably slower in JavaScript, but we have a way around
that. There's a way of caching the session files in Jmol that allows them
to be displayed essentially instantly, even in JavaScript.

This will be released as Jmol 13.2.0 sometime next week. In the mean time,
if you want to experiment --- realizing that most of you do not do anything
with Jmol right now, right? -- that's understandable --- the link to the
compiled Java and HTML5 versions are:

http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.30c.zip
(Java, including stand-alone Jmol.jar and JmolData.jar and applet files)

http://chemapps.stolaf.edu/jmol/jsmol.zip
(HTML5/JavaScript and also applet files, with demo pages)

I'm hoping this will interest some of you, and you might get involved in
future efforts as we develop this connection further.

Bob Hanson

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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[PyMOL] surfaces involving more than one object

[Robert Hanson]

PyMOL questions about surfaces:

Simple enough to create a surface for one object. What about for only a
portion of the object? How to do each of these?

  -- closed surface ignoring a selected set of atoms
  -- open surface not ignoring any atoms, but also not displaying their part

Is the rule, One surface, one object? That is, all atoms involved in a
surface must originate from a single object?

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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[PyMOL] PyMOL measurements

[Robert Hanson]

Is there a way to tie measurement ends to specific atoms, so that when the
structure is tweaked, those measurements update automatically?

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [PyMOL] PyMOL measurements

[Robert Hanson]

But as far as I can tell, in the session file, the coordinates are just
numbers -- no reference to atoms. What am I missing?


On Fri, May 31, 2013 at 8:57 AM, Jason Vertrees 
jason.vertr...@schrodinger.com wrote:

 Hi Bob,

 We added this a year or two ago:

 set dynamic_measures, 1

 In newer versions of PyMOL this is enabled by default.

 Cheers,

 -- Jason


 On Fri, May 31, 2013 at 8:27 AM, Robert Hanson hans...@stolaf.edu wrote:

 Is there a way to tie measurement ends to specific atoms, so that when
 the structure is tweaked, those measurements update automatically?

 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we want,
 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900



 --
 Get 100% visibility into Java/.NET code with AppDynamics Lite
 It's a free troubleshooting tool designed for production
 Get down to code-level detail for bottlenecks, with 2% overhead.
 Download for free and get started troubleshooting in minutes.
 http://p.sf.net/sfu/appdyn_d2d_ap2
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 --
 Jason Vertrees, PhD
 Director of Core Modeling Products
 Schrödinger, Inc.

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120




-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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It's a free troubleshooting tool designed for production
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http://p.sf.net/sfu/appdyn_d2d_ap2___
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[PyMOL] new to list -- simple questions

[Robert Hanson]

Hello, PyMOL users!

I'm new to this list. Some may recognize me as the current principal
developer of Jmol. Until recently I hadn't explored PyMOL much, mostly
because I'm not myself a biochemist. For about three months now, though,
Jaime Prilusky (Weizmann Institute) and I have been working on a PSE file
reader for Jmol, and I think we're just about ready to roll that out, at
least in a preliminary version.

A few questions:

Q: Does the availability of a way to manipulate PyMOL models on the web
using Java or just HTML5 interest this crowd? Or are people more focused
specifically on journal image production or stand-alone PyMOL application
use?

Q: Are there people on this list who can answer fundamental PyMOL
programming issues, or is that another list? I'm pretty much a autodidact,
but there are some nuances that I don't understand. I don't want to waste
this list's bytes if questions like Is the second array in a scene color
definition list always just a list of 1s? are inappropriate.

Q: I also have lots of questions relating to how you go about doing things
in PyMOL. (Getting a list of all defined scenes, for example.) OK to ask
those here?

Q: Now that we have a pretty good handle on how PyMOL is organized and most
of the basic data structures, and with all the *basic* modeling options
reproducible in Jmol, we need more examples. More interesting CGOs than
Hello, World, examples of various specific objects such as Surface
object, that sort of thing. I think I'm just about done with our current
sample set of about 100 PSE files. Anyone interested in contributing PSE
files to the Jmol project? Is there a repository somewhere of those?


Thanks in advance,

Bob Hanson

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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