pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] ccp4 map?

[Ben C. <ac...@em...>]

Thanks to all who replied.  I was going by the html manual, which said
that pymol only reads XPLOR/CNS maps.  I know that the manual is
out-of-date --- I should have dug harder. 

Thanks,

Ben

RE: [PyMOL] ccp4 map?

[Frank V. <Fra...@sy...>]

I believe pymol reads ccp4 maps...  at least, it did a few months ago :)
To do the conversion off-line, you'd have to install ccp4, then you
could use 
something like xdlmapman.  

phx.


> -----Original Message-----
> From: Ben Cornett [mailto:ac...@em...]
> Sent: Wednesday, March 20, 2002 12:48 PM
> To: pym...@li...
> Subject: [PyMOL] ccp4 map?
> 
> 
> Can anyone offer some advice on how to convert a ccp4 map to an XPLOR
> map for import into pymol?  I know next to nothing about
> crystallography, so perhaps the question is not even meaningful.
> 
> Thanks,
> 
> Ben
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


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[PyMOL] ccp4 map?

[Ben C. <ac...@em...>]

Can anyone offer some advice on how to convert a ccp4 map to an XPLOR
map for import into pymol?  I know next to nothing about
crystallography, so perhaps the question is not even meaningful.

Thanks,

Ben

RE: [PyMOL] turn

[DeLano, W. <wa...@su...>]

> From: Mirek Cygler [mailto:mir...@br...]

> 	I wonder if there is a command equivalent to "turn" in=20
> molscript? I would
> like to show a cartoon view of my molecule with some=20
> sidechains. When I use
> "show cartoon" and include a selection of sidechains, they=20
> appear far from
> the backbone worm.

Turn off "smooth loops" and "flat sheets" using the cartoon menu or the
commands

set cartoon_smooth_loops=3D0
set cartoon_flat_sheets=3D0

> 	Can I change the name of the object after loading the=20
> molecule into PyMol?

No, but you can create an identical copy and delete the original.

load test1.pdb
create test2=3Dtest1
delete test1

> When I save the molecule can I also save the secondary=20
> structure assignments
> with it?=20

I wish...this is on the "to do" list.

> Is there a facility within PyMol to detect secondary=20
> structure
> automatically?

Sort of.  util.ss make an attempt at it, but the algorithm in
unvalidated (something I just cooked up one morning).  For publication,
I encourage users to obtain secondary structure assignment via an
accepted algorithm.

load test1.pdb
util.ss test1
show cartoon

- Warren

[PyMOL] turn

[Mirek C. <mir...@br...>]

Hello,
	I wonder if there is a command equivalent to "turn" in molscript? I would
like to show a cartoon view of my molecule with some sidechains. When I use
"show cartoon" and include a selection of sidechains, they appear far from
the backbone worm.
	Cheers,

                                                Mirek

[PyMOL] question

[Mirek C. <mir...@br...>]

Hi,
	Can I change the name of the object after loading the molecule into PyMol?
When I save the molecule can I also save the secondary structure assignments
with it? Is there a facility within PyMol to detect secondary structure
automatically?
	Thanks for your help,

                                                Mirek

RE: [PyMOL] Colors and labels.

[DeLano, W. <wa...@su...>]

Mario,
> From: Mario Sanchez [mailto:sa...@if...]

> I have some questions using pymol and I wonder if someone can give me
> some help.
>=20
> At first I would like to know if there are any way to define=20
> more colors
> than that appearing in the menu. Is there some kind of "rgb"=20
> definition,
> for exemple?

the "set_color" command:

set_color khaki,[0.95,0.9,0.7]

> I also tried to change the colors of the sticks only, without success.
> When I chance the colors of the atoms in side chains it works, but
> changing color of carbon alpha causes change in cartoon too.=20
> Is there a
> way to do it?

Not with a single object, but remember that it is trivial to make copies
of objects in PyMOL which are shown using different representations and
coloring schemes.

In this case, create a copy of the object, then show the ribbon on the
original with one color scheme, and then show the sticks on the copy:

load orig.pdb
create cpy,(orig)
hide
show cartoon,orig
show sticks,cpy

You can now color the two independently.

> Finally I didn't find a way to put labels in residues -- like Tyr-25
> beside a tyrosine -- and to make "ray" of it.=20

You got me there: vectorized labels are on the TO DO list, but for now
you'll need to add labels manually.  The normal labels won't work
because they are rasterized into the OpenGL buffer...

Cheers,
Warren

[PyMOL] Colors and labels.

[Mario S. <sa...@if...>]

I have some questions using pymol and I wonder if someone can give me
some help.

At first I would like to know if there are any way to define more colors
than that appearing in the menu. Is there some kind of "rgb" definition,
for exemple?
I also tried to change the colors of the sticks only, without success.
When I chance the colors of the atoms in side chains it works, but
changing color of carbon alpha causes change in cartoon too. Is there a
way to do it?
Finally I didn't find a way to put labels in residues -- like Tyr-25
beside a tyrosine -- and to make "ray" of it.=20

I will appreciate very much any suggestion.

--=20
Mario Sanches,  PhD Student
Protein Crystallography Group
S=E3o Paulo University, S=E3o Carlos Physics Institute
Phone:  +55 (16) 273 9868
sa...@if...

Re: [PyMOL] b.pdb

[Warren L. D. <wa...@su...>]

Here is what is going on: PyMOL's atom selection mechanism has a set of
keywords (name,resi,chain,model,etc), which includes "b" and "q" --
B-factor and occupancy.   An object named "b" gets confused with the
"b" keyword.  Normally you are able to simply use an object name in a
selection, but with a object named "b", you'll need to prefix
it with the "model" keyword to make it clear what you're asking for...

load b.pdb

# ambiguous:
color red,(b)

# unambiguous:
color red,(model b)

It is an embarassing design deficiency, but most of the time, the
convenience of not using the "model" keyword is probably worth
it.  However, PyMOL should probably inform you if/when there is a
name-space conflict like this : )

Cheers,
Warren

On Wed, 13 Mar 2002, Robert Campbell wrote:

> 
> Lari Lehti? <le...@ma...> [2002-03-13 08:40] wrote:
> > Just a funny thing...
> > 
> > If I try to color my cartoon with rainbow. The file name can't be b.pdb. I get
> > an error:
> > 
> > Selector-Error: Misplaced ).
> > Selector-Error: Malformed selection.
> > ( ( ( byres ( b )<--
> > 
> > If I rename the file and load it, coloring works fine.
> > 
> 
> I noticed the same problem if I had read in any file name, but created a
> selection named "b".  I don't do that now!  :)  I guess "b" must be some
> other predefined object?
> 
> Cheers,
> Robert
> 

Re: [PyMOL] b.pdb

[Robert C. <rl...@k2...>]

Lari Lehti? <le...@ma...> [2002-03-13 08:40] wrote:
> Just a funny thing...
> 
> If I try to color my cartoon with rainbow. The file name can't be b.pdb. I get
> an error:
> 
> Selector-Error: Misplaced ).
> Selector-Error: Malformed selection.
> ( ( ( byres ( b )<--
> 
> If I rename the file and load it, coloring works fine.
> 

I noticed the same problem if I had read in any file name, but created a
selection named "b".  I don't do that now!  :)  I guess "b" must be some
other predefined object?

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] b.pdb

[<le...@ma...>]

Just a funny thing...

If I try to color my cartoon with rainbow. The file name can't be b.pdb. I get
an error:

Selector-Error: Misplaced ).
Selector-Error: Malformed selection.
( ( ( byres ( b )<--

If I rename the file and load it, coloring works fine.

-Lari-

Re: [PyMOL] MDL file

[Szilveszter J. <sz...@ri...>]

On Mon, Mar 11, 2002 at 10:47:17AM -0800, DeLano, Warren wrote:
[..]
> # Python code for reading an SD file with
> # identifier as separate SD field 'MOLID' 
[..]

Brilliant, now I only have to generate some environment around. Thanks!

Szilva

RE: [PyMOL] Create a double bond

[DeLano, W. <wa...@su...>]

By default, PyMOL creates single bonds when joining fragments.  To
change a bond valence, CTRL-right click on the bond to select it.  You
should see a "ring" about the bond.  Then press CTRL-W to cycle through
the possible bond valences: single, double, triple.

Note that it is essentially impossible right now to build complex
molecules in PyMOL without using some external molecular minimization
and mechanics program, since the "molecular sculpting" feature can only
maintain pre-existing atomic geometries. =20

For coarse modeling of protein-ligand interactions, I tend to use PyMOL
to draw the initial covalent structures, use MacroModel to perform
energy minimization, and then return the structure to PyMOL for purposes
modeling the complex.

- Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Guillaume Michaud [mailto:r1...@em...]
> Sent: Monday, March 11, 2002 12:43 PM
> To: pym...@li...
> Subject: [PyMOL] Create a double bond
>=20
>=20
> PLEASE WRITE BACK TO=20
> rp...@ma...
>=20
> Hi,
>=20
> I was just wondering how to create a=20
> double bond between two atoms (for=20
> example between a carbon and an oxygen=20
> or C=3DC).
>=20
> Thankx
> r1ck5p
> --=20
>=20
> _______________________________________________
> Sign-up for your own FREE Personalized E-mail at Email.com
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>=20
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[PyMOL] Create a double bond

[Guillaume M. <r1...@em...>]

PLEASE WRITE BACK TO 
rp...@ma...

Hi,

I was just wondering how to create a 
double bond between two atoms (for 
example between a carbon and an oxygen 
or C=C).

Thankx
r1ck5p
-- 

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RE: [PyMOL] MDL file

[DeLano, W. <wa...@su...>]

ChemPy has a an SDF class for processing SD files.  Here's an example of
using it to answer your question.

# Python code for reading an SDF file with
# identifier in first line of the MOL record

from pymol import cmd
from chempy.sdf import SDF
from string import join,strip

isdf =3D SDF("input.sdf")
while 1:
	r =3D isdf.read()
	if not r: break
	mol =3D r.get('MOL')
	ident =3D strip(mol[0])
	cmd.read_molstr(join(mol,''),ident)
isdf.close()

# Python code for reading an SD file with
# identifier as separate SD field 'MOLID'=20

from pymol import cmd
from chempy.sdf import SDF
from string import join

isdf =3D SDF("input.sdf")
while 1:
	r =3D isdf.read()
	if not r: break
	mol =3D r.get('MOL')
	ident =3D r.get_single('MOLID')
	cmd.read_molstr(join(mol,''),ident)
isdf.close()

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Szilveszter Juhos [mailto:sz...@ri...]
> Sent: Monday, March 11, 2002 9:27 AM
> To: pym...@li...
> Subject: [PyMOL] MDL file
>=20
>=20
> Dear Pymol Users/Developers,
>=20
> If I have an MDL (.sdf) file with multiple models, how can I=20
> ask pymol to
> load them into separate models? As I checked pymol is reading sdf with
> chempy's reader, so I could access the data field as well somehow.
>=20
> Cheers:
>=20
> Szilva
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] MDL file

[Szilveszter J. <sz...@ri...>]

Dear Pymol Users/Developers,

If I have an MDL (.sdf) file with multiple models, how can I ask pymol to
load them into separate models? As I checked pymol is reading sdf with
chempy's reader, so I could access the data field as well somehow.

Cheers:

Szilva

[PyMOL] Viewing Water molecules, problems with bond

[Alan W. S. da S. <al...@bi...>]

Hi List,

=09I'm trying to create a image of protein/subtrate + HOH.  The
problem is the HOH made connections where isn't supposed to be!  How can I
solve this?

Many thanks in advance,

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laborat=F3rio de F=EDsica Biol=F3gica
  Instituto de Biof=EDsica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

Re: [PyMOL] Loading non-standard PDB file

[Holly M. <mi...@ph...>]

Warren,

Thanks for the quick reply!

>
>    Right now PyMOL has pretty limited connectivity detection
> capabilities for "in-process" structures, which do not exhibit normal
> bond lengths and atom separations.   A workaround would be to passage
> the structure through energy minimization (using an external tool)
> before loading it into PyMOL (which will establish correct connectivity
> for the object) and to then load the original in-process coordinates as
> state 2 of the object.

I don't think that the structure has abnormal atom distances. Is it just
that the pdb file does not have HETATM or CONECT or other 'extras' ????

>
>   Alternatively, is there any way you could use HETATM records (instead
> of ATOM) and include explicit CONECT records?

I think this would solve the problem. I tried to search for a program/script
that would do this and didn't find one. Seems like there should be many of
these.

Again, I am sorry for taking up your time on this simple problem but I want
to use PyMol and I have been struggling with this for a week now.


Cheers,
Holly
--
____________________________________________________________________________

Holly Miller, Ph.D.              voice: 631 444-8018
Res. Asst. Prof.                 FAX:  631 444-7641
Dept. Pharm. Sci.                http://www.pharm.sunysb.edu/faculty/miller/

SUNY Stony Brook                 mi...@ph...
Stony Brook, NY 11794-8651

****************************************************************************

             Biomail--New references from Medline to your e-mail account
                      http://www.biomail.org
___________________________________________________________________________

RE: [PyMOL] Loading non-standard PDB file

[DeLano, W. <wa...@su...>]

Holly,

   Right now PyMOL has pretty limited connectivity detection
capabilities for "in-process" structures, which do not exhibit normal
bond lengths and atom separations.   A workaround would be to passage
the structure through energy minimization (using an external tool)
before loading it into PyMOL (which will establish correct connectivity
for the object) and to then load the original in-process coordinates as
state 2 of the object.

   Alternatively, is there any way you could use HETATM records (instead
of ATOM) and include explicit CONECT records?

   Before too long, PyMOL will have pattern-based connectivity
determination for normal PDB residues.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Holly Miller [mailto:mi...@ph...]
> Sent: Friday, March 08, 2002 10:57 AM
> To: PyMol Users
> Subject: [PyMOL] Loading non-standard PDB file
>=20
>=20
> Hi!
>=20
> I am a new PyMol user. I want to look at an 'in progress'=20
> structure from
> a collaborator. When I load the pdb into PyMol there are bonds between
> atoms that shouldn't be bonded. This is mostly (if not only) in the
> bound DNA part of the structure. Is it possible to change the=20
> parameters
> by which the bonds are automatically calculated (if this is how it
> works) or some other way to fix this, other than clicking on=20
> each wrong
> bond and deleting it (there are many).
>=20
> I apologize for asking such a simple question.
>=20
> Thank you,
> Holly
>=20
> --
> ______________________________________________________________
> ______________
>=20
> Holly Miller, Ph.D.              voice: 631 444-8018
> Res. Asst. Prof.                 FAX:  631 444-7641
> Dept. Pharm. Sci.
> http://www.pharm.sunysb.edu/faculty/miller/
> SUNY Stony Brook                 mi...@ph...
> Stony Brook, NY 11794-8651
>=20
> **************************************************************
> **************
>=20
>              Biomail--New references from Medline to your=20
> e-mail account
>=20
>                       http://www.biomail.org
> ______________________________________________________________
> _____________
>=20
>=20
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Loading non-standard PDB file

[Holly M. <mi...@ph...>]

Hi!

I am a new PyMol user. I want to look at an 'in progress' structure from
a collaborator. When I load the pdb into PyMol there are bonds between
atoms that shouldn't be bonded. This is mostly (if not only) in the
bound DNA part of the structure. Is it possible to change the parameters
by which the bonds are automatically calculated (if this is how it
works) or some other way to fix this, other than clicking on each wrong
bond and deleting it (there are many).

I apologize for asking such a simple question.

Thank you,
Holly

--
____________________________________________________________________________

Holly Miller, Ph.D.              voice: 631 444-8018
Res. Asst. Prof.                 FAX:  631 444-7641
Dept. Pharm. Sci.
http://www.pharm.sunysb.edu/faculty/miller/
SUNY Stony Brook                 mi...@ph...
Stony Brook, NY 11794-8651

****************************************************************************

             Biomail--New references from Medline to your e-mail account

                      http://www.biomail.org
___________________________________________________________________________

Re: [PyMOL] install

[Alan W. S. da S. <al...@bi...>]

I think ir you install Python 2.1 or you wait Pymol compiled to Python
2.2.


On Thu, 7 Mar 2002, Fei Xu wrote:

> Hi! Everyone:
> I am installing pymol.My versioin is 0.78 for window. I use python2.2.
> When I run pymol , it saiys that it can't find python21.dll.
> what should I do? does it require python21.dll absolutely?
>
> HAve a nice day!
>
> Fei  Xu

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laborat=F3rio de F=EDsica Biol=F3gica
  Instituto de Biof=EDsica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

[PyMOL] install

[Fei Xu <fe...@ru...>]

Hi! Everyone:
I am installing pymol.My versioin is 0.78 for window. I use python2.2.
When I run pymol , it saiys that it can't find python21.dll. 
what should I do? does it require python21.dll absolutely?

HAve a nice day!

Fei  Xu

Re: [PyMOL] display of densities, electrostatic maps

[Warren L. D. <wa...@su...>]

On Thu, 7 Mar 2002, Ingo Dramburg wrote:

> Hi out there,
> 
> Pymol is really amazing, I started to write a module to create and
> manipulate densities for pymol.

Awesome!  This is precisely the kind of user-driven participation
the project needs to thrive.  I am not up on what kinds of density
manipulation functions are needed by today's crystallographers, but if
users like yourself can contribute in this fashion, then we are going to
create some highly useful software together...

> Is it possible to create surfaces from contours (additional to isomesh and 
> isodot) something like isosurf ???

Funny you should ask -- I just added that feature a couple of weeks ago 
: ).  Hopefully this will also enable PyMOL to become useful for
scientists in the electron-microscopy reconstruction fields.  If you can
compile from the CVS repository, then you can use the "isosurf" command
right away.  It takes the same arguments as isomesh.  However, if you are
using a precompiled version (such as on windows), then just wait a couple
of weeks for the new (v0.80) release.

There is also a "map_new" command in the current source which allows
for creation of maps on-the-fly (any may be useful as an example of 
what you're trying to do).  Note that it isn't done yet, but if you have
a version compiled out of the current CVS tree, then you can try the
following preview...

load test/dat/pept.pkl
map_new esp,coulomb,0.5,pept,2.0
isosurf pos,esp,-0.25
isosurf neg,esp,0.25
color blue,pos
color red,neg

For the curious, a figure of the above can be found at 

http://pymol.sf.net/pmimag/prev.jpg

Please don't try to do any science with this feature yet (clearly I
have a sign flipped somewhere, I haven't yet applied proper units, and
the cutoff is still hard-coded).  Poisson-Boltzmann also still needs to be
coded-up -- but Grasp will soon face some stiff competition from PyMOL, as
electrostatics becoome an integral part of the package.

A key point here is that since PyMOL's map features are general purpose,
they can be used for density, masks, electrostatics, surfaces, averaging
of atomic positions, QM wavefunctions, EM, and any other kind of volume
visualization.  All it takes is a self-interested party with some
development skills and an open-source mindset to make this happen -- and
then it's done -- all of humanity is provided with a new tool that can
be used to enable exciting new scientific discoveries.

Let's all pool our efforts together in this manner in order to take PyMOL
to the next level!  What have we got to lose but our lack of good
software?

Cheers,
- Warren

[PyMOL] display of densities, electrostatic maps

[Ingo D. <dra...@Ma...>]

Hi out there,

Pymol is really amazing, I started to write a module to create and
manipulate densities for pymol.

Is it possible to create surfaces from contours (additional to isomesh and 
isodot) something like isosurf ???

Ingo
-- 
************************************************************
Ingo Dramburg 

Institute of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, D 35032 Marburg, Germany

Tel. + 49 6421 282 1313
Fax  + 49 6421 282 8994
e-mail dra...@ma...
http://www.agklebe.de/

Re: [PyMOL] About Surface

[Richard G. <re...@co...>]

Warren, I've used Varshney's surface code (written at UNC)
for many years now. There are some legal statements but I
checked with UNC and they told me they didn't care who used
copied or modified the code, so I consider it public domain
at this point. I would be happy to send you a copy. It is
C-code that can actually run in parallel and is quite fast.
The surface is the true solvent contact surface (piecewise
spheres and tori). It has a couple minor problems that are solvable:

   1. poor/degenerate triangulation in a few places
   2. needs better dynamic memory management

I would be happy to send you a copy of the code.
Sorry I have not time to work with PyMol yet,
perhaps someday.

Richard Gillilan
MacCHESS


"DeLano, Warren" wrote:

> Now, on to Alan's specific questions:
>
> >       I'm particularly interested in how pymol generate surface (a
> > internal algorithm?) and how to compare it to vdW, solvent,
> > Connolly and
> > MSMS surfaces.
>
> PyMOL's surfacing algorithm is just something I cooked up over a weekend
> a couple years back.  It is brute-force: 1. surface the atoms, 2.
> surface waters in contact with those atoms, and 3. merge the result into
> a continuous surface and try to cover up any glitches.  If a better (ie.
> faster) surfacing algorithm ever enters the public domain/BSD-licecnse
> software pool, then I would love to include it as an alternative.
>
> To get a better surface, select "Maximum Quality" from the "Display"
> menu, a go get a cup of coffee while you wait : ).  You may need extra
> RAM too...
>
> To make it transparent, "set transparency=1"
>
> Cheers,
> Warren
>
> _______________________________________________
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