pymol-users Mailing List for PyMOL Molecular Graphics System

Thanks David. 
This worked flawlessly... I made one of my .pdb files a favorite in Dropbox app, set the iPad to airplane mode, so no wifi, back to Dropbox app, tapped the .pdb file, and selected open in pymol from the actions button.  My molecule was right there with no network connection.

Seems like this is likely a generally useful trick for getting the iPad to act more like a computer with a traditional file system.

Thanks again,
Steve

Sent from my iPad

On Nov 28, 2012, at 12:46 PM, David Hall <li...@co...> wrote:

> Hi Steve,
> 
> I'll suggest a workaround to having pymol cache the files:
> 
> (1) Install the DropBox app
> (2) Favorite your PDB files in that app, this will cache those files
> locally within the DropBox app for offline access
> (3) From the dropbox app, you can open PDB files in Pymol using the
> button in the upper right corner, since the dropbox app has cached
> them locally, PyMol just reads the file and doesn't need the internet
> 
> -David
> 
> On Wed, Nov 28, 2012 at 11:48 AM, Steve Williams <wi...@ap...> wrote:
>> I am a new subscriber to the pymol listserv.  I did look around a bit on the listserv site, but did not find a way to search previous postings and responses, so did not find if there is a known answer to my question.
>> Minor question: is there a way to search the pymol message archive, and if so, how to do it?
>> Major question: I have been playing with the iPad version of pymol from Schrodinger.  I know how to search pbd for structures,and how to view structures I have already found and saved to my pymol app folder on Dropbox.  But I need to show some structures to an audience where I may not have wifi access for my iPad, and I would like to have the pymol iPad app locally save structure files so I can use them when I am off line.  Is there a way to do this with the iPad?
>> 
>> Thanks,
>> Steve Williams
>> 
>> Sent from my iPad
>> ------------------------------------------------------------------------------
>> Keep yourself connected to Go Parallel:
>> INSIGHTS What's next for parallel hardware, programming and related areas?
>> Interviews and blogs by thought leaders keep you ahead of the curve.
>> http://goparallel.sourceforge.net
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...

Hi Steve,

I'll suggest a workaround to having pymol cache the files:

(1) Install the DropBox app
(2) Favorite your PDB files in that app, this will cache those files
locally within the DropBox app for offline access
(3) From the dropbox app, you can open PDB files in Pymol using the
button in the upper right corner, since the dropbox app has cached
them locally, PyMol just reads the file and doesn't need the internet

-David

On Wed, Nov 28, 2012 at 11:48 AM, Steve Williams <wi...@ap...> wrote:
> I am a new subscriber to the pymol listserv.  I did look around a bit on the listserv site, but did not find a way to search previous postings and responses, so did not find if there is a known answer to my question.
> Minor question: is there a way to search the pymol message archive, and if so, how to do it?
> Major question: I have been playing with the iPad version of pymol from Schrodinger.  I know how to search pbd for structures,and how to view structures I have already found and saved to my pymol app folder on Dropbox.  But I need to show some structures to an audience where I may not have wifi access for my iPad, and I would like to have the pymol iPad app locally save structure files so I can use them when I am off line.  Is there a way to do this with the iPad?
>
> Thanks,
> Steve Williams
>
> Sent from my iPad
> ------------------------------------------------------------------------------
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi Erik -

A more general question. It seems like there must be a better way to visualise a
polymer, say as a ball an stick image. Is there a more straight forward way of doing
this in pymol?

Not sure if you've found a solution to this already, but have a look at http://www.pymolwiki.org/index.php/Stick_ball, which may help with getting a ball-and-stick representation of your objects.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 398
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/



Thanks, Erik

--
Erik Nelson

Howard Hughes Medical Institute
6001 Forest Park Blvd., Room ND10.124
Dallas, Texas 75235-9050

p : 214 645 5981
f : 214 645 5948

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Greetings,

Minor answer: I usually go to 
http://www.mail-archive.com/pym...@li.../ to search 
the list.

Regards,
JP Cartailler

On 11/28/2012 10:48 AM, Steve Williams wrote:
> I am a new subscriber to the pymol listserv.  I did look around a bit on the listserv site, but did not find a way to search previous postings and responses, so did not find if there is a known answer to my question.
> Minor question: is there a way to search the pymol message archive, and if so, how to do it?
> Major question: I have been playing with the iPad version of pymol from Schrodinger.  I know how to search pbd for structures,and how to view structures I have already found and saved to my pymol app folder on Dropbox.  But I need to show some structures to an audience where I may not have wifi access for my iPad, and I would like to have the pymol iPad app locally save structure files so I can use them when I am off line.  Is there a way to do this with the iPad?
>
> Thanks,
> Steve Williams
>
> Sent from my iPad
> ------------------------------------------------------------------------------
> Keep yourself connected to Go Parallel:
> INSIGHTS What's next for parallel hardware, programming and related areas?
> Interviews and blogs by thought leaders keep you ahead of the curve.
> http://goparallel.sourceforge.net
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Steve.

> I am a new subscriber to the pymol listserv.  I did look around a bit on the listserv site, but did not find a way to search previous postings and responses, so did not find if there is a known answer to my question.

Welcome to the PyMOL community.


> Minor question: is there a way to search the pymol message archive, and if so, how to do it?

Yes, try here http://sourceforge.net/search/?group_id=4546&type_of_search=mlists.
You get there by mousing over "Mailing Lists" on the pymol-users
archive page (http://sourceforge.net/mailarchive/forum.php?forum_name=pymol-users).


> Major question: I have been playing with the iPad version of pymol from Schrodinger.  I know how to search pbd for structures,and how to view structures I have already found and saved to my pymol app folder on Dropbox.  But I need to show some structures to an audience where I may not have wifi access for my iPad, and I would like to have the pymol iPad app locally save structure files so I can use them when I am off line.  Is there a way to do this with the iPad?

Currently you need to be online to access your data. We'll fix this
for the next release.


Cheers,

-- Jason

--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

I am a new subscriber to the pymol listserv.  I did look around a bit on the listserv site, but did not find a way to search previous postings and responses, so did not find if there is a known answer to my question.
Minor question: is there a way to search the pymol message archive, and if so, how to do it?
Major question: I have been playing with the iPad version of pymol from Schrodinger.  I know how to search pbd for structures,and how to view structures I have already found and saved to my pymol app folder on Dropbox.  But I need to show some structures to an audience where I may not have wifi access for my iPad, and I would like to have the pymol iPad app locally save structure files so I can use them when I am off line.  Is there a way to do this with the iPad?

Thanks,
Steve Williams

Sent from my iPad

----------------------------------------
> From: jas...@sc...
> Date: Tue, 27 Nov 2012 12:37:41 -0600
> Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
> To: mar...@ho...
> CC: pym...@li...
>
> Mike,
>
> > Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case,
> > what pymol facilities are there for adding them? Apparently you have some editing
>
> h_add object_name
>
> Type, "help h_add" or check out h_add on the PyMOLWiki
> (http://www.pymolwiki.org/index.php/H_Add).

Thanks, applying to the pdb I had seems to have worked but it didn't think much of the double bonds
and added extra's but presumably I can delete and rotate more easily than adding all them manually.



>
> Cheers,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
 		 	   		  

Hi Erik,

This is a known bug introduced in OS X 10.8 and some video cards. To
fix this just type,

  set cylinder_shader_ff_workaround, 1

and all should be well. PyMOL uses an official rendering optimization
but some systems have difficulty with it, hence our workaround.

This is automatically fixed in PyMOL v1.5.0.5 and later (and in the
recent open-source code).

Cheers,

-- Jason



On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson <nel...@gm...> wrote:
>
> I use pymol to generate images of simple polymers by loading their
> coordinates as
> .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates.
> I connect
> them using the ribbon_trace option, and color them by varying b-factors in
> the .pdb
> file.
>
> I had created many different movies and figures this way, and I saved the
> sessions
> as .pse files. Just recently, I went back to view some of these sessions and
> they just
> loaded as blank screens.
>
> I tried creating more images as before - using the ribbon_trace option to
> connect the
> atoms - but it no longer works.
>
> I'm pretty sure I didn't change any options in pymol, so I'm wondering if
> pymol
> somehow updated itself, or some update of my mac airbook affected the pymol
> program. Neither of these seems very likely.
>
> What went wrong? Is there a way I can fix this?
>
> A more general question. It seems like there must be a better way to
> visualise a
> polymer, say as a ball an stick image. Is there a more straight forward way
> of doing
> this in pymol?
>
> Thanks, Erik
>
> --
> Erik Nelson
>
> Howard Hughes Medical Institute
> 6001 Forest Park Blvd., Room ND10.124
> Dallas, Texas 75235-9050
>
> p : 214 645 5981
> f : 214 645 5948
>
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Erik,

Can you please send me a copy of one of the problematic sessions?

Cheers,

-- Jason

On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson <nel...@gm...> wrote:
>
> I use pymol to generate images of simple polymers by loading their
> coordinates as
> .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates.
> I connect
> them using the ribbon_trace option, and color them by varying b-factors in
> the .pdb
> file.
>
> I had created many different movies and figures this way, and I saved the
> sessions
> as .pse files. Just recently, I went back to view some of these sessions and
> they just
> loaded as blank screens.
>
> I tried creating more images as before - using the ribbon_trace option to
> connect the
> atoms - but it no longer works.
>
> I'm pretty sure I didn't change any options in pymol, so I'm wondering if
> pymol
> somehow updated itself, or some update of my mac airbook affected the pymol
> program. Neither of these seems very likely.
>
> What went wrong? Is there a way I can fix this?
>
> A more general question. It seems like there must be a better way to
> visualise a
> polymer, say as a ball an stick image. Is there a more straight forward way
> of doing
> this in pymol?
>
> Thanks, Erik
>
> --
> Erik Nelson
>
> Howard Hughes Medical Institute
> 6001 Forest Park Blvd., Room ND10.124
> Dallas, Texas 75235-9050
>
> p : 214 645 5981
> f : 214 645 5948
>
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Mike,

> Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case,
> what pymol facilities are there for adding them? Apparently you have some editing

h_add object_name

Type, "help h_add" or check out h_add on the PyMOLWiki
(http://www.pymolwiki.org/index.php/H_Add).

Cheers,

-- Jason

--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

----------------------------------------
> From: jas...@sc...
> Date: Mon, 26 Nov 2012 10:37:52 -0600
> Subject: Re: was: [PyMOL] Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
> To: mar...@ho...
> CC: pym...@li...
>
> Hi Mike,
>
> > I was trying to figure out what to eat today so naturally I started looking for PDB libraries
> > with food components. I was looking for garlic related chemicals when I came across this,
> >
> > http://molecules.gnu-darwin.org/
> >
> > which seems to have many pdb files. My question I guess is, what does pymol have
> > for an "API" to get molecule structures from various locations or do you just have an
> > interface for pdb.org? Besides deciding on what to eat today, I was curious if
> > pymol has more generalized means of finding structure files.
>
> We have an API for accessing structures remotely. For example,
>
> load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
> myMolecule
>
> You could easily create a PyMOL plugin
> (http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes
> advantage of this site very simply using the load command and
> formatted URLs.

Thanks, I didn't know it would be that simple and that looks like a good way to learn
python. Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case,
what pymol facilities are there for adding them? Apparently you have some editing
capabilites and analyses, I thought there may be some way to guess approximately where
the hydrogens should go and then export the new file. This is probably obvious 
from a quick google search on basic capabilites but it also sounds as if there
may be less well known specialized tools for doing less common things like this.


>
> I hope your meal was tasty.
>
how can you enjoy it without the pdb file on the screen and optimizing in DFT? LOL.





> Cheers,

Thanks.

>
> -- Jason
>
>
> >> ----------------------------------------
> >> > From: jas...@sc...
> >> > Date: Fri, 2 Nov 2012 18:57:38 -0500
> >> > To: pym...@li...
> >> > Subject: [PyMOL] Mobile PyMOL Problem and Solution
> >> >
> >> > Greetings,
> >> >
> >> > On Oct 28th, the folks at the PDB made some changes to their PDB Web
> >> > Services interface. This change broke Mobile PyMOL's ability to search
> >> > for and download PDBs.
> >>
> >> I haven't bothered to look at this specific situation but this a problem with many sites
> >> and automated interaction. NCBI has a nice eutils interface that has remained stable
> >> for a while, I'd been trying to get more groups to offer a web interface designed for
> >> automated interactions. FWIW,
> >>
> >> http://www.ncbi.nlm.nih.gov/books/NBK25500/
> >>
> >>
> >> Do you have automated access to this library for example,
> >>
> >> http://www.ncbi.nlm.nih.gov/Structure/index.shtml
> >>
> >> they also have their own viwer, for example,
> >>
> >> http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
> >>
> >> but pymol seems a bit more extensive.
> >>
> >> >
> >> > I have updated Mobile PyMOL and will soon resubmit it to the AppStore
> >> > for verification and release. This process takes typically takes no
> >> > less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users
> >> > please use the following technique to acquire structures:
> >> > (1) Using Safari on the iPad browse to the www.pdb.org and find the
> >> > structure you want.
> >> > (2) Click "Download Files" from the upper right hand side of the
> >> > structure's page and then select "PDB File (Text)".
> >> > (3) Click "Open in PyMOL".
> >> >
> >> > Happily, as a long-term solution, I've established contact with the
> >> > PDB Web Services Group and we'll now be made aware of future changes.
> >> > The PDB is an extremely valuable resource in the community and I'm
> >> > glad we could work this out.
> >> >
> >> > Cheers,
> >> >
> >> > -- Jason
> >> >
> >> > --
> >> > Jason Vertrees, PhD
> >> > PyMOL Product Manager
> >> > Schrödinger, Inc.
> >> >
> >> > (e) Jas...@sc...
> >> > (o) +1 (603) 374-7120
> >> >
> >> > ------------------------------------------------------------------------------
> >> > LogMeIn Central: Instant, anywhere, Remote PC access and management.
> >> > Stay in control, update software, and manage PCs from one command center
> >> > Diagnose problems and improve visibility into emerging IT issues
> >> > Automate, monitor and manage. Do more in less time with Central
> >> > http://p.sf.net/sfu/logmein12331_d2d
> >> > _______________________________________________
> >> > PyMOL-users mailing list (PyM...@li...)
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
 		 	   		  

I use pymol to generate images of simple polymers by loading their
coordinates as
.pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates.
I connect
them using the ribbon_trace option, and color them by varying b-factors in
the .pdb
file.

I had created many different movies and figures this way, and I saved the
sessions
as .pse files. Just recently, I went back to view some of these sessions
and they just
loaded as blank screens.

I tried creating more images as before - using the ribbon_trace option to
connect the
atoms - but it no longer works.

I'm pretty sure I didn't change any options in pymol, so I'm wondering if
pymol
somehow updated itself, or some update of my mac airbook affected the pymol
program. Neither of these seems very likely.

What went wrong? Is there a way I can fix this?

A more general question. It seems like there must be a better way to
visualise a
polymer, say as a ball an stick image. Is there a more straight forward way
of doing
this in pymol?

Thanks, Erik

-- 
Erik Nelson

Howard Hughes Medical Institute
6001 Forest Park Blvd., Room ND10.124
Dallas, Texas 75235-9050

p : 214 645 5981
f : 214 645 5948

Hi Per 


If you're still having problems, you can try to install and run pymol under the X virtual frame buffer (xvfb).


Cheers,

Esben


Best Regards
Esben Peter Friis
Science Manager

Novozymes A/S
Krogshoejvej 36

2880 Bagsvaerd Denmark
Phone: +45 44461334
Mobile: +45 30771334
E-mail: ep...@no...

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-----Original Message-----
From: Jason Vertrees [mailto:jas...@sc...] 
Sent: 26. november 2012 17:48
To: Per Larsson
Cc: pym...@li...
Subject: Re: [PyMOL] Pymol in command mode - no output

Hi Per,

You'll probably want to use something like this:

# load the file

load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
myMolecule

# ray trace and save the image; you need to do this since you're running # PyMOL headlessly

png ~/foo.png, height=768, width=1024, ray=1


As far as missing output that's most likely because you're running remotely and the stdout/stderr are being piped elsewhere. This is common on clusters.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson <per...@sb...> wrote:
> Hi Pymol-users,
>
> I'm running a pml-script file to render some images on a remote server, using pymol 1.4, but I do not get any output at all. And no error message, so it is hard to troubleshoot, unfortunately.
>
> To reduce the complexity of my script, I have reduced it to basically just loading a pdb-file and saving as a png-image (two lines in the pml-script), but even that does not work. Any suggestions?
>
> I envoke the whole thing using
> $pymol -c script.pml
>
>
> Thanks
> /Per
>
>
>
>
> ----------------------------------------------------------------------
> -------- Monitor your physical, virtual and cloud infrastructure from 
> a single web console. Get in-depth insight into apps, servers, 
> databases, vmware, SAP, cloud infrastructure, etc. Download 30-day 
> Free Trial.
> Pricing starts from $795 for 25 servers or applications!
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--
Jason Vertrees, PhD
Director of Core Modeling Product Management Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

------------------------------------------------------------------------------
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Hi Alex,

the gaps and the scrambled sequence view have the same reason, it's the
internal ordering of atoms which is not consecutive. PyMOL does this
based on atom identifiers (chain, resi, etc.). I suggest assigning
ascending chain letters to the three parts before fusing.

alter nterminus, chain='A'
alter middlesub, chain='B'
alter cterminus, chain='C'
fuse ...

Cheers,
  Thomas

Alex Truong wrote, On 11/26/12 22:31:
> Hi All,
> 
> I recall asking a bunch of questions here about Fuse earlier this year,
> but I haven't needed to come back to it until now. Apologies if this has
> already been addressed elsewhere.
> 
> When I fuse, the two objects are manually attached in a reasonable way,
> correct? Does the cartoon representation accurately reflect that
> attachment? I just fused 3 subunits together, and there are some fairly
> noticeable gaps between subunits when looking at the cartoon view. Even
> though they look properly fused from the line view, since our
> publication will rely on the cartoon view for simplicity, these gaps
> are...unacceptable. Does anyone know the reason for them, and how to fix
> them? Additionally, the residue order in the sequence view is scrambled.
> They are attached in the correct order, but the middle subunit is
> displayed first, then the N-terminus, then the C-terminus.
> 
> Thanks,
> 
> Alex Truong

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Jon,

I'm stumped too, because that's the correct syntax. Can you send me a
copy of your session file?

The only thing I can think of at present is that a selection might need:

set sphere_scale, 5, (selection_name)

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 2:53 PM, Jonathan Grimes
<jon...@st...> wrote:
>
>    I wanted to changed the size of sphere_scale for all atoms in an
>    object, a selection of Calpha atoms.
>
>    I thought I could use the command
>
>    set sphere_scale, 5, object_name
>
>    this doesnt seem to work and am unclear as to the reason.
>
>     thanks
>     jon
>
>
>
>
>    does the command
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow
> University Research Lecturer
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: Jon...@st..., Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>
>
>
>
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
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-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Mary,

Just a hint for any future lists you might be on: most modern email
lists, including pymol-users, have footers with links to subscription
options. You simply click that to get to a subscription page where you
can unsubscribe.

In this case, I removed you from the list to save you the hassle.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 5:30 PM, Mary Hall <mh...@po...> wrote:
> How do I remove myself from the PyMOL users list? I'd like to stop receiving
> emails.
>
> Thank you.
>
> M. Hall
>
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

How do I remove myself from the PyMOL users list? I'd like to stop
receiving emails.

Thank you.

M. Hall

Morphing toward a target .pdb, or end-point analysis and 1) solvent box; or 2) vacuum?

gg...@oh...

On Nov 26, 2012, at 12:42 PM, "Hasan Demirci" <dem...@gm...> wrote:

> Dear all,
> I am trying to morph two protein-protein complex pdb files.
> Everything looks fine but somehow during the morphing the complex structure is also bouncing up and down instead of a morphing at a fix large catalytic reference domain of chain A.
> If I only use chain A of the complex it morphs perfectly, somehow including chain B makes things complicated.
> How can I morph these two pdb without extra bouncing.
> 
> With my best regards.
> 
> Hasan 
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
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Hi All,

I recall asking a bunch of questions here about Fuse earlier this year, but
I haven't needed to come back to it until now. Apologies if this has
already been addressed elsewhere.

When I fuse, the two objects are manually attached in a reasonable way,
correct? Does the cartoon representation accurately reflect that
attachment? I just fused 3 subunits together, and there are some fairly
noticeable gaps between subunits when looking at the cartoon view. Even
though they look properly fused from the line view, since our publication
will rely on the cartoon view for simplicity, these gaps
are...unacceptable. Does anyone know the reason for them, and how to fix
them? Additionally, the residue order in the sequence view is scrambled.
They are attached in the correct order, but the middle subunit is displayed
first, then the N-terminus, then the C-terminus.

Thanks,

Alex Truong

Hi Balaji,

the latest incentive builds (since v1.4, as far as I know) from
Schrödinger are shipped with python 2.7. If you are looking for the
open-source version, Christoph Gohlke has Windows builds with python2.7
as described on the PyMOLWiki:

http://pymolwiki.org/index.php/Windows_Install#Pre-compiled_PyMOL

Cheers,
  Thomas

Ban Arn wrote, On 11/26/12 18:10:
> Dear Thomas
> 
> Which version of pymol has python 2.7.
> 
> Is it free for academics or I have to purchase license from schrodinger.
> 
> Kindly advice.
> 
> Many Thanks
> Balaji

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

   I wanted to changed the size of sphere_scale for all atoms in an
   object, a selection of Calpha atoms.

   I thought I could use the command

   set sphere_scale, 5, object_name

   this doesnt seem to work and am unclear as to the reason.

    thanks
    jon




   does the command 
Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

Dear all,
I am trying to morph two protein-protein complex pdb files.
Everything looks fine but somehow during the morphing the complex structure
is also bouncing up and down instead of a morphing at a fix large catalytic
reference domain of chain A.
If I only use chain A of the complex it morphs perfectly, somehow including
chain B makes things complicated.
How can I morph these two pdb without extra bouncing.

With my best regards.

Hasan

Dear Thomas

Which version of pymol has python 2.7.

Is it free for academics or I have to purchase license from schrodinger.

Kindly advice.

Many Thanks
Balaji

Hi Heng,

> Hi, I am just wondering if there are some useful pymol cgo tutorials
> available ? such as how to visualize a  3D triangle object(vertex and
> triangle files are known ) in Pymol?

See https://www.google.com/?q=pymol%20cgo. There is a chapter
subsection on CGOs and also a few scripts the demonstrate their usage.


> In addition, is the pymol volume visualize (http://pymol.org/volume)
> available for educational use ?

Volume visualization is available in the Incentive version and
open-source builds, but not the free Educational version.

Cheers,

-- Jason

--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Per,

You'll probably want to use something like this:

# load the file

load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
myMolecule

# ray trace and save the image; you need to do this since you're running
# PyMOL headlessly

png ~/foo.png, height=768, width=1024, ray=1


As far as missing output that's most likely because you're running
remotely and the stdout/stderr are being piped elsewhere. This is
common on clusters.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson <per...@sb...> wrote:
> Hi Pymol-users,
>
> I'm running a pml-script file to render some images on a remote server, using pymol 1.4, but I do not get any output at all. And no error message, so it is hard to troubleshoot, unfortunately.
>
> To reduce the complexity of my script, I have reduced it to basically just loading a pdb-file and saving as a png-image (two lines in the pml-script), but even that does not work. Any suggestions?
>
> I envoke the whole thing using
> $pymol -c script.pml
>
>
> Thanks
> /Per
>
>
>
>
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120