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Hi pymolers,

I wrote a script to use a personal plugin directory.

http://pymolwiki.org/index.php/PluginDirectory

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

I made a mistake. I meant command-line

pymol *pdb or pymol A.pdb B.pdb

etc. Not load *pdb.

Maia Cherney wrote:
> Also you can use
>
> load A.pdb B.pdb C.pdb
>
> or load *pdb
>
>
>
> leila karami wrote:
>> Dear all
>>
>> very thanks for your time and attention.
>>
>> my problem was solved by
>> load A.pdb
>> load B.pdb
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------ 
>>
>> All of the data generated in your IT infrastructure is seriously 
>> valuable.
>> Why? It contains a definitive record of application performance, 
>> security threats, fraudulent activity, and more. Splunk takes this 
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

Also you can use

load A.pdb B.pdb C.pdb

or load *pdb

leila karami wrote:
> Dear all
>
> very thanks for your time and attention.
>
> my problem was solved by
> load A.pdb
> load B.pdb
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security 
> threats, fraudulent activity, and more. Splunk takes this data and makes 
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> ------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

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      <br>
      I am writing to alert the Pymol community that I will be
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      <br>
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      session. If you are currently conducting protein X-ray
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      <br>
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    <br>
    <div class="moz-signature">-- <br>
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for local files, apart from using load:

load pdb1; load pdb2; load pdb3; load pdbN

there is another shortcut: you put all the PDB files you need to load in 
the fetch_path of pymol. To find out the current fetch_path, use command:

get fetch_path

Then you can simply load all pdb at once using:

fetch pdb1 pdb2 pdb3 pdb4 pdbN

On 06/29/2011 03:56 PM, Hongbo Zhu wrote:
> would python module multiprocessing meet your need?
> is that simultaneity the kind of simultaneity you want?
>
> On 06/29/2011 03:36 PM, leila karami wrote:
>> Dear Hongbo
>>
>> very thanks for your attention.
>>
>> None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not
>> help me.
>> I need to load two separate pdb files simultaneously.
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de

Are you referring to files on your computer?  You should just be able to use File -> Open to open one file, then do it again to open the next.

-David

On Jun 29, 2011, at 6:36 AM, leila karami <kar...@gm...> wrote:

> Dear Hongbo
> 
> very thanks for your attention.
> 
> None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help me.
> I need to load two separate pdb files simultaneously.
> 
> 
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security 
> threats, fraudulent activity, and more. Splunk takes this data and makes 
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

would python module multiprocessing meet your need?
is that simultaneity the kind of simultaneity you want?

On 06/29/2011 03:36 PM, leila karami wrote:
> Dear Hongbo
>
> very thanks for your attention.
>
> None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not
> help me.
> I need to load two separate pdb files simultaneously.
>
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de

Dear all

very thanks for your time and attention.

my problem was solved by
load A.pdb
load B.pdb

Dear all

very thanks for your time and attention.

my problem was solved by

load A.pdb
load B.pdb

Hello

Have you tried

load A.pdb
load B.pdb

If this does not work for you, could you please define the what
"simultaneous" means to you, i.e what exactly are you trying to do
that requires simultaneous loading of two files?
Marius

On Wed, Jun 29, 2011 at 3:36 PM, leila karami <kar...@gm...> wrote:
> Dear Hongbo
>
> very thanks for your attention.
>
> None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help
> me.
> I need to load two separate pdb files simultaneously.
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear Hongbo

very thanks for your attention.

None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help
me.
I need to load two separate pdb files simultaneously.

this also works:

fetch 1A00 or 1A07 or 1A08

but not:
load 1A00 or 1A07 or 1A08

On 06/29/2011 03:07 PM, leila karami wrote:
> Daer users
>
> I want to know how to load two separate pdb files simultaneously.
>
> any help will highly appreciated.
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de

In one PyMOL instance you can load many structures. They can be load 
into different objects, or different states of the same object.

If you mean using one command line to load multiple structures, since 
its grammar is very similar to python, I think you can always use 
semicolon to separate two commands:

fetch 1A00; fetch 1A07

this command will load both 1A00 and 1A07, but one after the other, not 
simultaneously.

On 06/29/2011 03:07 PM, leila karami wrote:
> Daer users
>
> I want to know how to load two separate pdb files simultaneously.
>
> any help will highly appreciated.
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de

Daer users

I want to know how to load two separate pdb files simultaneously.

any help will highly appreciated.

Matthias Schmidt wrote, On 06/28/11 13:37:
> I am making a movie in pymol that I prepared with g_morph
> 
> g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4)
> 
> Pymol does not assign the secondary structure.
> 
> load movie.pdb
> dss, movie

PyMOL calculates the consensus secondary structure over all states. You 
may produce distorted intermediates with g_morph, so that consensus 
might not be appropriate. To only consider first and last state, do this:

dss movie, state=-4

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi

I am making a movie in pymol that I prepared with g_morph

g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4)

Pymol does not assign the secondary structure.

load movie.pdb
dss, movie

assigns incorrect secondary structure. In my case, dss models a
complete transmembrane helix as a coil. Trying a manual repair in the
form of

alter resi1-resi2/, ss='H'

does change the representation of the bespoke helix from a coil into a
helix cartoon. But in a few frames of movie.pdb, the representation is
changed to a "tube".

Why is that and how can I fix it?

Best,

Matthias

Hi jpd,

if your selection is named "sele", then try this:

# previous resi
iterate name C and neighbor byres sele, print (resi,resn)

# next resi
iterate name N and neighbor byres sele, print (resi,resn)

More on selection operators:
http://pymolwiki.org/index.php/Selection_Algebra

Cheers,
   Thomas

jp d wrote, On 06/24/11 22:57:
> hi,
> is there a way in pymol/python scripts to
> determine what the next or previous resi would be?
> 
> it needs to handle insertions and deletions
> 
> thanks
> jpd

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

hi,
is there a way in pymol/python scripts to
determine what the next or previous resi would be?

it needs to handle insertions and deletions

thanks
jpd

Greetings,

Application instructions and deadlines for the Summer 2011 PyMOL Open
Source Fellowship have been posted here http://pymol.org/fellowship.
Interested applicants, please review the instructions before applying.
 The deadline is about a month away.

Good luck!

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Hi Amanda,

> I am using the command:
> cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts")
>
>to find the polar contacts.
>
> This command creates an object in the panel but I cannot figure out
> how to print the information I am seeing, like the distance and the
> atoms involved, in the viewer to a file.

as far as I know the "raw data" of distance objects cannot be accessed.

Have a look at the attached script, it does a very similar job to the 
distance command but returns atom pairs with (model,index) keys.

pairlist = polarpairs("exp_interest", "exp_interest", cutoff=3.6, \
     name="interest_polar_conts")

You can drop the 'name' argument if you don't need the object for visual 
inspection but only the pair list.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

Hello All, 

I am attempting to write a script that take a single residue of interest in a protein and then creates a selection that is all residues within 4 Angstroms of that residue. Then I would like to find the polar contacts within that new expanded selection and print out the pair of residue names, residue numbers, the atom names involved in the contact and the distance to a text file.
#select interest, resi 463
cmd.select ("interest","(resi 463)")

#Action, modify, expand, by 4 A, residues
cmd.select("exp_interest","(byres (interest expand 4))",enable=1)

# show lines for all within 4 Ang
cmd.show("lines"     ,"exp_interest")

#show sticks for residue of interest
cmd.show("sticks"    ,"interest")

#Action, find, polar contact, within selection
#distance exp_interest_polar, exp_interest, exp_interest, 3.6, 2
cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts")

I am using the command:
cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts")
to find the polar contacts.

This command creates an object in the panel but I cannot figure out how to print the information I am seeing, like the distance and the atoms involved, in the viewer to a file.

Thanks for the help,

Amanda

This depends on how you touch pad is configured and what mode you
selected froum the Mouse menu.
I would suggest a trial and error approach to your problem. Try doing
something and see what it does.
Also Google is your friend. http://www.google.fr/search?q=pymol+mouse

Marius

On Thu, Jun 23, 2011 at 4:25 PM, Chandan Choudhury <ii...@gm...> wrote:
>
> Hi PyMol users,
>
> How can be I friendly with PyMol using the touch pad (MacBook Pro). What are
> the touch pad controls.
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
> ------------------------------------------------------------------------------
> Simplify data backup and recovery for your virtual environment with vRanger.
> Installation's a snap, and flexible recovery options mean your data is safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> _______________________________________________
> 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 PyMol users,

How can be I friendly with PyMol using the touch pad (MacBook Pro). What are
the touch pad controls.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA

Hi Sean,

You can poke around pymol/modules/pymol/movie.py for more info.
Here's some help, though:

filename = output file
mode = 0=normal; 1=draw; 2=ray
first = start frame
last = end frame
preserve = if 0 then cleanup frames from temp directory; if 1 then
leave temp directory & frames
encoder = which encode to use, defaults to freemol's mpeg_encode
quality = integer 0..100, for visual quality of final movie;
corresponds to movie_quality setting
quiet = verbosity

This should probably end up on the PyMOLWiki.

Cheers,

-- Jason

On Wed, Jun 22, 2011 at 1:16 AM, Sean Law <mag...@ho...> wrote:
> Hi PyMOLers,
> Can somebody offer an explanation for the possible values that can be used
> with the "movie.produce" command?
> produce filename [, mode [, first [, last [, preserve [, encoder [, quality
> [, quiet ]]]]]]]
> Any clarification of the scope of each option would be appreciated.
> Thanks
> Sean
> ------------------------------------------------------------------------------
> Simplify data backup and recovery for your virtual environment with vRanger.
> Installation's a snap, and flexible recovery options mean your data is safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> _______________________________________________
> 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
PyMOL Product Manager
Schrodinger, LLC

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

Hi PyMOLers,Can somebody offer an explanation for the possible values that can be used with the "movie.produce" command?produce filename [, mode [, first [, last [, preserve [, encoder [, quality [, quiet ]]]]]]]Any clarification of the scope of each option would be appreciated.ThanksSean 		 	   		  

2001	Jan	Feb	Mar	Apr	May	Jun	Jul	Aug	Sep	Oct (13)	Nov (22)	Dec (35)
2002	Jan (33)	Feb (46)	Mar (56)	Apr (29)	May (56)	Jun (30)	Jul (64)	Aug (54)	Sep (86)	Oct (106)	Nov (50)	Dec (67)
2003	Jan (78)	Feb (98)	Mar (51)	Apr (95)	May (53)	Jun (103)	Jul (93)	Aug (64)	Sep (87)	Oct (93)	Nov (78)	Dec (86)
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2008	Jan (69)	Feb (81)	Mar (60)	Apr (34)	May (47)	Jun (65)	Jul (46)	Aug (49)	Sep (84)	Oct (43)	Nov (33)	Dec (30)
2009	Jan (62)	Feb (48)	Mar (123)	Apr (73)	May (72)	Jun (69)	Jul (78)	Aug (72)	Sep (99)	Oct (82)	Nov (70)	Dec (53)
2010	Jan (112)	Feb (95)	Mar (127)	Apr (110)	May (135)	Jun (91)	Jul (91)	Aug (79)	Sep (136)	Oct (63)	Nov (38)	Dec (64)
2011	Jan (59)	Feb (109)	Mar (191)	Apr (130)	May (94)	Jun (90)	Jul (89)	Aug (127)	Sep (135)	Oct (113)	Nov (136)	Dec (140)
2012	Jan (158)	Feb (131)	Mar (151)	Apr (88)	May (121)	Jun (85)	Jul (82)	Aug (56)	Sep (55)	Oct (125)	Nov (87)	Dec (65)
2013	Jan (81)	Feb (64)	Mar (90)	Apr (77)	May (80)	Jun (92)	Jul (92)	Aug (70)	Sep (69)	Oct (60)	Nov (99)	Dec (50)
2014	Jan (89)	Feb (66)	Mar (52)	Apr (70)	May (68)	Jun (44)	Jul (68)	Aug (81)	Sep (152)	Oct (106)	Nov (74)	Dec (57)
2015	Jan (93)	Feb (48)	Mar (60)	Apr (107)	May (82)	Jun (64)	Jul (74)	Aug (38)	Sep (49)	Oct (99)	Nov (105)	Dec (51)
2016	Jan (68)	Feb (87)	Mar (55)	Apr (90)	May (68)	Jun (25)	Jul (25)	Aug (41)	Sep (35)	Oct (55)	Nov (24)	Dec (26)
2017	Jan (59)	Feb (49)	Mar (24)	Apr (50)	May (45)	Jun (63)	Jul (36)	Aug (26)	Sep (22)	Oct (23)	Nov (26)	Dec (29)
2018	Jan (17)	Feb (21)	Mar (30)	Apr (34)	May (24)	Jun (47)	Jul (65)	Aug (30)	Sep (24)	Oct (52)	Nov (21)	Dec (17)
2019	Jan (9)	Feb (39)	Mar (32)	Apr (22)	May (30)	Jun (69)	Jul (40)	Aug (48)	Sep (17)	Oct (26)	Nov (30)	Dec (19)
2020	Jan (32)	Feb (26)	Mar (16)	Apr (34)	May (50)	Jun (87)	Jul (51)	Aug (23)	Sep (25)	Oct (48)	Nov (32)	Dec (6)
2021	Jan (12)	Feb (31)	Mar (15)	Apr (31)	May (13)	Jun (13)	Jul (24)	Aug (9)	Sep (11)	Oct (28)	Nov (26)	Dec (25)
2022	Jan (47)	Feb (22)	Mar (22)	Apr (12)	May (4)	Jun (26)	Jul (17)	Aug (2)	Sep (13)	Oct (6)	Nov (13)	Dec (4)
2023	Jan (7)	Feb (6)	Mar (13)	Apr (2)	May (25)	Jun (13)	Jul (12)	Aug (10)	Sep (5)	Oct (13)	Nov (19)	Dec (7)
2024	Jan (3)	Feb (12)	Mar (1)	Apr (13)	May (11)	Jun	Jul (20)	Aug (4)	Sep (4)	Oct (5)	Nov (4)	Dec (6)
2025	Jan (16)	Feb (8)	Mar (10)	Apr (6)	May (13)	Jun (7)	Jul (4)	Aug (1)	Sep (2)	Oct (1)	Nov	Dec

S	M	T	W	T	F	S
			1 (5)	2	3	4 (4)
5 (2)	6 (3)	7	8 (6)	9 (12)	10 (2)	11
12	13 (1)	14 (4)	15 (5)	16 (11)	17 (8)	18
19	20 (2)	21	22 (2)	23 (2)	24 (4)	25
26 (1)	27	28 (2)	29 (13)	30 (1)

pymol-users Mailing List for PyMOL Molecular Graphics System

PyMOL is an OpenGL based molecular visualization system

pymol-users — Collaborative support and tips for PyMOL users