Re: [PyMOL] (no subject)

[David Hall]

For some reason, the people doing brew have decided to stop supporting
compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain
pymol cannot use tcl-tk with aqua.

If you already had pymol installed, this seems to eliminate the external
gui. If you didn't, new installations of pymol will now crash randomly.

Here's how I got to the old version that worked

$ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/
$ git checkout 46e1ef94247cd2fb9555b724c051e8907996 -- tcl-tk.rb
$ cd ../../homebrew-science/
Edit the pymol.rb file so that it depends on "tcl-tk" instead of
"homebrew/dupes/tcl-tk"

$ brew remove tcl-tk python pymol
$ brew install pymol
$ brew pin tcl-tk

Really, I uninstalled all my homebrew packages and then reinstalled
everything because some of their changes over the last 6 months had made
things oddly broken. If you want to do the same, you can try this:

$ brew list > installed
$  wrote:

> Hi,
> pymol external gui menus missing, I have compiled pymol in mac os by using
> brew.
>
> Anyone can provide some suggestions?
>
> Jacky
>
> --
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Re: [PyMOL] (no subject)

[Vivien Schoonenberg]

This worked! Thank you Leandro and Jed!

 

From: jedg...@gmail.com [mailto:jedg...@gmail.com] On Behalf Of Jed Goldstone
Sent: Tuesday, April 4, 2017 11:35
To: Vivien Schoonenberg 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] (no subject)

 

Try using

remove not alt +A

to remove alternative conformations.

Jed

 

On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg 
mailto:vivienschoonenb...@gmail.com> > wrote:

Hi there,

 

I’m saving the sequences from each chain of the PDB via pymol with 

>>save something.fasta, chain A

 

This is the same sequence that is shown in pymol and seems to correspond to the 
structure I am looking at.

However, when I loaded new B-factors in my structure, I noticed something funny 
happened. The list which I made corresponding to the sequence I saved earlier 
was too short. 

I  found out by iterating that some residues repeated themselves(>>iterate 
(chain A and n. CA), print resn). They carry the same residue number, and are 
not shown in the sequence. However, when I load my B-factors my list shifts 
because of these repeats, making it too short for the complete chain and 
loading the wrong value onto residues. 

 

Does anyone know why this happens and how I can fix this?

 

Thank you,

Vivien


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Re: [PyMOL] (no subject)

[Jed Goldstone]

Try using

remove not alt +A

to remove alternative conformations.

Jed

On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> wrote:

> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
> This is the same sequence that is shown in pymol and seems to correspond
> to the structure I am looking at.
>
> However, when I loaded new B-factors in my structure, I noticed something
> funny happened. The list which I made corresponding to the sequence I saved
> earlier was too short.
>
> I  found out by iterating that some residues repeated themselves(>>iterate
> (chain A and n. CA), print resn). They carry the same residue number, and
> are not shown in the sequence. However, when I load my B-factors my list
> shifts because of these repeats, making it too short for the complete chain
> and loading the wrong value onto residues.
>
>
>
> Does anyone know why this happens and how I can fix this?
>
>
>
> Thank you,
>
> Vivien
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>



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Research Specialist
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Redfield 3-52 MS #32
Woods Hole, MA  02543
http://www.whoi.edu/hpb/Site.do?id=481
(508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)
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Re: [PyMOL] (no subject)

[Leandro Bortot]

Hi,

 You probably have a pdb file which has multiple possible conformations
for some residues. You can check this by visual inspection of such
residues. They have two side chains coming from the same CA. In the text
file you can see the conformations marked as A and B in the residue name
field, e.g. APHE BPHE.

 If that is the case, you have to choose one of them either manually or
with some other molecular modeling software, e.g. gromacs.

I hope it helps!
Regards,
Leandro



On Mon, Apr 3, 2017 at 5:47 PM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> wrote:

> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
> This is the same sequence that is shown in pymol and seems to correspond
> to the structure I am looking at.
>
> However, when I loaded new B-factors in my structure, I noticed something
> funny happened. The list which I made corresponding to the sequence I saved
> earlier was too short.
>
> I  found out by iterating that some residues repeated themselves(>>iterate
> (chain A and n. CA), print resn). They carry the same residue number, and
> are not shown in the sequence. However, when I load my B-factors my list
> shifts because of these repeats, making it too short for the complete chain
> and loading the wrong value onto residues.
>
>
>
> Does anyone know why this happens and how I can fix this?
>
>
>
> Thank you,
>
> Vivien
>
> 
> --
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [PyMOL] (no subject)

[Edward A. Berry]

On 04/19/2015 02:08 AM, leila karami wrote:
> Dear Marcelo
>
> Thanks for your quick answer.
>
> Unfortunately, I can't open the link (https://www.pymol.org/citing) you 
> suggested me.

perhaps your firewall or browser is blocking the https: connection or rejecting 
the certificate?
Try http: instead- they seem to reach the same content.
Just don't give your taxpayer ID number or bank password!

>
> Thanks in advance.
>
>
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Re: [PyMOL] (no subject)

[Marcelo Marcet]

Hi Leila,

No problem, here is the content of the site. If you need the reference manager 
files (BibTex or EndNote files), I am happy to email them to you as well.

Cheers,
Marcelo





Citation Format
Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the 
version number in accordance with your usage.  If you use BibTex or EndNote, 
download the handy citation files below.

PyMOL
The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

JyMOL
The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

AxPyMOL

The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 
Schrödinger, LLC.
 

BibTex Files
PyMOL BibTex Entries [.bib] 
For help with BibTex see:

http://en.wikipedia.org/wiki/BibTeX 
http://www.bibtex.org/Using/ 
EndNote Files
PyMOL EndNote Entries [.xml]  
(right-click and save this file to your computer; most browsers dont' render 
XML nicely)




> On Apr 19, 2015, at 12:08 AM, leila karami  wrote:
> 
> Dear Marcelo
> 
> Thanks for your quick answer.
> 
> Unfortunately, I can't open the link (https://www.pymol.org/citing 
> ) you suggested me.
> 
> Thanks in advance.
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF___
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Re: [PyMOL] (no subject)

[Jordan Willis]

PyMOL
The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

JyMOL
The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
 

AxPyMOL

The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 
Schrödinger, LLC.


> On Apr 18, 2015, at 11:08 PM, leila karami  wrote:
> 
> Dear Marcelo
> 
> Thanks for your quick answer.
> 
> Unfortunately, I can't open the link (https://www.pymol.org/citing 
> ) you suggested me.
> 
> Thanks in advance.
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF___
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Re: [PyMOL] (no subject)

[Marcelo Marcet]

Hi Leila,

Take a look at the link below:

https://www.pymol.org/citing 

Cheers,
Marcelo




> On Apr 18, 2015, at 11:55 PM, leila karami  wrote:
> 
> Dear all
> 
> How to cite pymol in my paper?
> 
> Thanks.
> --
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Re: [PyMOL] (no subject)

[Thomas Holder]

Hi Aliya,

yes, likely there is a clash. But that's hard to tell without seeing your data.

Cheers,
  Thomas

On 01 Jul 2014, at 11:34, Aliya Holland  
wrote:
> Hello,
> 
> I just created an animation of a conformational change of a specific domain 
> on a molecule. During the animation the domain rotates just as it should,  
> however other parts of the molecule moves with the conformation change. I was 
> wondering if that was part of the PyMOL programming or if there was a clash 
> between the end domain and the rotating section. Why would there be movement 
> in the entire molecule when only one section of it is morphing. 
> 
> Thank you 
> 
> A

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Re: [PyMOL] (no subject)

[Gianluigi Caltabiano]

Auto vyzdobena http://www.domarn.se/capcutgrahampatterson/?vhotmailID=gfesuzgz

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Re: [PyMOL] (no subject)

[Davi de Miranda Fonseca]

My PyMOL 1.5.0.5 works fine in Windows 8 (64 bits).

Try the following:
- Press Windows Key + Q
- This should open the search apps thingy, type pymol
- It should show all PyMOL shortcuts, try the "PyMOL + Tcl-Tk GUI + Console"
- Does PyMOL still refuses to open? Did you get any error message?

On 20/03/2013 03:11, Thomas Holder wrote:
> Hi Nina Marie,
>
> I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5
> runs fine on Windows 8.
>
> Cheers,
>Thomas
>
> Wolf, Nina Marie wrote, On 03/19/13 21:11:
>> Hi,
>>
>> I recently upgraded my computer to windows 8. Since then, pymol will not
>> open. Is the latest version of pymol incompatible with windows 8? Or is
>> there something I can do to get it working on my computer?


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Re: [PyMOL] (no subject)

[Thomas Holder]

Hi Nina Marie,

I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5
runs fine on Windows 8.

Cheers,
  Thomas

Wolf, Nina Marie wrote, On 03/19/13 21:11:
> Hi,
> 
> I recently upgraded my computer to windows 8. Since then, pymol will not
> open. Is the latest version of pymol incompatible with windows 8? Or is
> there something I can do to get it working on my computer?

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Re: [PyMOL] (no subject)

[Jason Vertrees]

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  wrote:
> How do I remove myself from the PyMOL users list? I'd like to stop receiving
> emails.
>
> Thank you.
>
> M. Hall
>
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Re: [PyMOL] (no subject)

[Thomas Holder]

Hi Noloofar and Lina,

>> I would like to calculate partial charges of my pdb. Is it possible to do it
> 
> In pymol:
> 
> Action-> compute -> partial charge sum

this doesn't calculate partial charges, sorry.

This does:
Action -> generate -> vacuum electrostatics

But better would be to use pdb2pqr:
http://www.poissonboltzmann.org/pdb2pqr

>> I have another question too, when aligning two structure in Pymol, there is
>> a RMSD for the total structure, is there any command to calculate the RMSD
>> for a specific region of the alignment.

If the two structures have the same sequence (same atom identifiers) and 
you don't need an "alignment", you can use rms_cur.

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

Cheers,
   Thomas

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Re: [PyMOL] (no subject)

[lina]

On Sun, Sep 4, 2011 at 8:37 PM, niloofar niknam
 wrote:
>
>
> Deal list,
> I would like to calculate partial charges of my pdb. Is it possible to do it

In pymol:

Action-> compute -> partial charge sum


> by Pymol? If not, Is anyone know any server
> or  software to do it?
> I have another question too, when aligning two structure in Pymol, there is
> a RMSD for the total structure, is there any command to calculate the RMSD
> for a specific region of the alignment.
> Any offer would be appreciated.
> kind regards.
> Niloofar
>
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lina

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Re: [PyMOL] (no subject)

[Nat Echols]

On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann wrote:

> Hi Chris,
>
> the emails are only sent to you because you subscribed to the pymol-users
> list.
> If you don't want them anymore you need to unsubscribe.
>
> Click on "Show details" at the top of this email. Click then on:
> unsubscribe Unsubscribe from this mailing-list
>
> That will do the magic.


Or click on the link at the bottom of *every email sent to the list*:


> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] (no subject)

[Thomas Juettemann]

Hi Chris,

the emails are only sent to you because you subscribed to the pymol-users list.
If you don't want them anymore you need to unsubscribe.

Click on "Show details" at the top of this email. Click then on:
unsubscribe Unsubscribe from this mailing-list

That will do the magic.


On Fri, May 28, 2010 at 10:42, Christian De Ford  wrote:
> Please stop sending me daily emails its very annoying, i would
> appreciate if you erase me from the list
> Thank you!
> --
>
>
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Re: [PyMOL] (no subject)

[Warren DeLano]

Rotem,

Try starting with the script below.  It will produce output like:

PRO A 1Chi-1:   20.6
GLN A 2Chi-1: -178.8
LEU A 5Chi-1:  -64.6
TRP A 6Chi-1:  -55.6
GLN A 7Chi-1:  -59.6
ARG A 8Chi-1:  -83.1
PRO A 9Chi-1:   34.9
LEU A 10   Chi-1:  -53.5
...

Cheers,
Warren

---

load $TUT/1hpv.pdb

select chi1, polymer & (br. */N) & (br. */CA) & (br. */CB) & (br. */CG)

N  = cmd.index("chi1 & */N ") 

CA = cmd.index("chi1 & */CA")

CB = cmd.index("chi1 & */CB")

CG = cmd.index("chi1 & */CG")

LABEL = []

iterate chi1 & */CA, LABEL.append(resn+" "+chain+" "+resi)

I = range(len(LABEL))

CHI1 = [0] * len(I)

for i in I: CHI1[i] = cmd.get_dihedral(N[i],CA[i],CB[i],CG[i])

for i in I: print "%-10s Chi-1: %6.1f" % (LABEL[i],CHI1[i])




From: Rotem Sertchook [mailto:rotem.sertch...@weizmann.ac.il] 
Sent: Tuesday, March 24, 2009 12:11 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)

Hi,
I'm looking for a way to calculate set of torsion angels from selected residues 
(for example Chi1 dihedral of all His residues). Is it possible to write PyMOL 
script for such task ? Any hints to write such script will be appreciated!
 
Thank you
Rotem
 





--
Rotem Sertchook, Ph.D.
Bioinformatics Unit, Biological Services
Weizmann Institute of Science,
Rehovot 76100, Israel.
--

Re: [PyMOL] (no subject)

[gilleain torrance]

Hi,

I think that it probably is possible to do this from within pymol, and
probably quite convenient for single molecules.

However, there are two other possible approaches, which would be
helpful for multiple molecules.

Firstly, there is a program called 'dang' made by the Richardson group:

http://kinemage.biochem.duke.edu/software/dang.php

and secondly, might I humbly submit that I have a program I call
'Tailor' that is intended for measuring and analysing (to a limited
extent) selected parts of proteins:

http://tailor.sourceforge.net/docs/index.html

gilleain

On Tue, Mar 24, 2009 at 7:06 AM, Rotem Sertchook
 wrote:
> Hi,
> I'm looking for a way to calculate set of torsion angels from selected
> residues (for example Chi1 dihedral of all His residues). Is it possible to
> write PyMOL script for such task ? Any hints to write such script will be
> appreciated!
>
> Thank you
> Rotem
>
>
>
>
>
>
> --
> Rotem Sertchook, Ph.D.
> Bioinformatics Unit, Biological Services
> Weizmann Institute of Science,
> Rehovot 76100, Israel.
> --
>
> --
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>

Re: [PyMOL] (no subject)

[Warren DeLano]

Justin,

Sorry about that...

"svn update" and rebuild.

I believe the warning is gone now.  It should only print if you
specifically request certain stereo modes.

Cheeers,
Warren
 

> -Original Message-
> From: Justin Lecher [mailto:j.lec...@fz-juelich.de] 
> Sent: Thursday, February 19, 2009 5:42 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Hello all especially Warren,
> 
> What does
> 
> "Sorry, time-sequential stereo 3D not available"
> 
> mean. It is printed out when I start pymol. I am using current HEAD.
> 
> Thanks justin
> 
> 
> --
> Justin Lecher
> Institute for  Neuroscience and Biophysics INB 2 - Molecular 
> Biophysics II Research centre Juelich GmbH,
> 52425 Juelich,Germany
> phone: +49 2461 61 5385
> 
> 
> 
> 

Re: [PyMOL] (no subject)

[DeLano Scientific]

Martin,

No, sorry, you will need an external tool to do this.

Cheers,
Warren


--
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sa...@delsci.com to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net 
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
> Of Martin Sztacho
> Sent: Monday, April 16, 2007 3:51 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Hello,
>  I would like to ask about building phosphate group at Tyr 
> residue. Is there any posibility to do it at PyMOL programe?
> Thank you for answer
> Martin Sztacho
> 
> --
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Re: [PyMOL] (no subject)

[Tsjerk Wassenaar]

Dear Bernhard,

The user manual is quite informative where it comes to making
selections. There is not a polar/nonpolar grouping made for you, but
you can easily select the residues based on their names (resn or r.).

select basic, (resn lys,his,arg)

As a side note, on this as well as all other user lists, it is
preferred that you set a subject line which reflects the question
you're asking. Since many of us are dedicating our own time to
answering, we usually make a preselection of the mails we could
possibly provide an answer to. Mails without subject are likely to be
thrown away unread.

Cheers,

Tsjerk


On 2/23/07, Bernhard Kleine  wrote:

Hello and good morning,

being newly arrived in this list, I am a molecular biologist working
recently in endocrinology and epigenetics and living in the black forest
in the south west of germany.

Since I am not fully content with the picture quality which I can get
with Rasmol, I am trying to use PyMOL. However, since I try to adopt my
rasmol script for use in PyMOL, I am unable to find how to select
individual amino acids, or e.g. polar or basic residues. I am quite
convinced that such shortcuts exist. But either the refmanual oder the
usermanual lack mentioning any typ of aminoacids, so far as I can say
(searching with Acrobat reader).

It would be a pleasure if anyone could point me to the proper
information.

Thanks a lot

Bernhard
--
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Padualaan 8
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The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Re: [PyMOL] (no subject)

[gilleain torrance]

Hi,

I don't know how simple you want it, but python lets you print just like:

   print cmd.distance(a, b)

assuming that a and b are strings that are atom selections. See

  http://www.pymolwiki.org/index.php/Translate_And_Measure

for a more complex example! :)

gilleain


On 11/7/06, Giacomo Bastianelli  wrote:


Dear Users,

I would like with a simple script to export
some data regarding distances.
Do any of you know how to write an output with
all distances that I set up?

Thanks in advance

Giacomo



Giacomo Bastianelli

EIMID Ph.D Fellow (www.eimid.org)

Marie Curie EST

gbast...@pasteur.fr

Unité de Bioinformatique Structurale

Institut Pasteur

25-28 Rue de Dr.Roux

75015 Paris, France

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Re: [PyMOL] (no subject)

[Donglu Xie]

Hi Warren,

Thank you very much. Under the help of one of PyMol users, at last figure
out the right configuration. It needs "AllowDFPStereo" on in LCD and
""XineramaStereoFlipping" on in CRT. Following is the part I changed:

== begin the partial xorg.conf 

# for CRT
Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
VendorName  "Videocard vendor"
BoardName   "NVIDIA Quadro FX3400"
BusID   "PCI:5:0:0"
Option  "Stereo" "3"
Screen 0
Option "UBB"   "1"
Option "NoPowerConnectorCheck"
Option   "XineramaStereoFlipping" "1"
EndSection


# for LCD
Section "Device"
Identifier  "Videocard1"
Driver  "nvidia"
VendorName  "Videocard vendor"
BoardName   "NVIDIA Quadro FX3400"
BusID   "PCI:5:0:0"
Screen  1
Option "UBB"   "1"
Option "Stereo"   "3"
Option "NoPowerConnectorCheck"
Option   "AllowDFPStereo" "1"
EndSection

== end 

Bests,
-Donglu


> Donglue,
>
> My suspicion is that stereo and windows spanning multiple displays may
> be mutually exclusive, possibly because the displays aren't necessarily
> sync'd on the VBL, or because the LCD context may not be stereo-capable.
>
> Cheers,
> Warren
>
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Donglu
> Xie
> Sent: Saturday, July 15, 2006 9:36 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
>
> Hi Dear Pymol-users,
>
> Sorry about this long message. I am struggling to configure X Windwo to
> enable stereo.
>
> Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One
> monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try
> to
> configure X widnow to enable stereo with Xinerama on so that application
> can cross the screen boundaries. There is no any error or warning
> message
> in Xorg.0.log (xorg.conf is below). However, when tried to run stereo
> application, such as PyMol or Coot, it doesn't work. It came out with
> different error messages.
>
> In PyMol, error is following:
> X Error of failed request:  BadValue (integer parameter out of range for
> operation)
>   Major opcode of failed request:  78 (X_CreateColormap)
>   Value in failed request:  0x0
>   Serial number of failed request:  14
>   Current serial number in output stream:  16
>  PyMOL: abrupt program termination.
>
> In Coot, the error is
> Gdk-ERROR **: BadValue (integer parameter out of range for operation)
>   serial 390 error_code 2 request_code 78 minor_code 0
>
> Googling doesn't get much useful information.
>
> I also tried to use Twinview. The stereo works well. However, the
> application interface cannot move cross the screen boundaries.
>
> The Xinerama enabled setting works perfect with systems connected with a
> CRT and a LCD monitors
> (2.4.20-6smp #1 SMP Thu Feb 27 09:36:38 EST 2003 i686 athlon i386
> GNU/Linux)
> (NVIDIA Quadro4 750 XGL).
>
> The system with stereo problem is
> 2.6.9-34.0.1.ELlargesmp #1 SMP Wed May 17 17:19:07 EDT 2006 x86_64
> x86_64
> x86_64 GNU/Linux
>
> xorg.conf and partial of Xorg.0.log files is below.
>
> Any help or suggestion is appreciated.
> Best,
> -Donglu Xie
>
> xorg.conf is following
> =
> Section "ServerLayout"
> Identifier "Dual Layout"
> Option "Xinerama" "true"
> Screen 0  "Screen0"
> Screen 1 "Screen1" RightOf "Screen0"
> InputDevice"Mouse0" "CorePointer"
> InputDevice"Keyboard0" "CoreKeyboard"
> EndSection
>
> Section "Files"
> RgbPath  "/usr/X11R6/lib/X11/rgb"
> FontPath "unix/:7100"
> EndSection
>
> Section "Module"
> Load  "dbe"
> Load  "extmod"
> Load  "fbdevhw"
> Load  "glx"
> Load  "glx"
> Load  "record"
> Load  "freetype"
> Load  "type1"
> #   Load  "dri"
> EndSection
>
> Section "InputDevice"
> Identifier  "Keyboard0"
> Driver  "kbd"
> Option  "XkbModel" "pc105"
> Option  "XkbLayout" "us"
> EndSection
>
> Section "InputDevice"
> Identifier  "Mouse0"
> Driver  "mouse"
> Option  "Protocol" "IMPS/2"
> Option  "Device" "/dev/input/mice"
> Option  "ZAxisMapping" "4 5"
> Option  "Emulate3Buttons" "yes"
> EndSection
>
> Section "Monitor"
> Identifier   "LCD"
> VendorName   "Viewsonic"
> ModelName"VP2030b"
> HorizSync24.0 - 92.0
> VertRefresh  50.0 - 85.0
> Option  "dpms"
> EndSection
>
> Section "Monitor"
> Identifier   "CRT"
> VendorName   "Viewsonic"
> ModelName"G225fb"
> HorizSync30.0 - 130.0
> VertRefresh  50.0 - 160.0
> Optio

Re: [PyMOL] (no subject)

[Andrea Spitaleri]

Hi,
for this purpose I have used caver program. You can download it free
of charge from here  http://loschmidt.chemi.muni.cz/caver/download.php

I hope this help

Regards

andrea

2006/3/27, srilath...@jubilantbiosys.com :
> dear sir
> iam a pymol user, do we can find area & volume of active site in
> pymol
> if we can, just tell me how to do it
> thanking you
> srilatha
> Thanks & Regards
> srilatha potlapelly
> MSc Biotechnology
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Re: [PyMOL] (no subject)

[gilleain torrance]

Hi,

I found out how to do ... something ... like this the other day.

RE: [PyMOL] (no subject)

[EPF (Esben Peter Friis)]

Hi Blanton

You are probably looking for the "symexp" command. I don't remember the exact 
syntax, but there is a small help text. You can also try to search the mail 
archive.


Best wishes

Esben


-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Blanton Tolbert
Sent: Sat 2006-03-04 15:01
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)
 
Hi pymol community

I would like to recapitulate the crystal packing arrangement of a  
protein structure to look for neighbor interactions.  Is it possible  
to do this in pymol?  If so, please provide me some insight.

Thanks,


Blanton Tolbert
Graduate Student
University of Rochester
Biophysics and Structural Biology
585-275-5189
blanton_tolb...@urmc.rochester.edu





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Re: [PyMOL] (no subject)

[Andrea Spitaleri]

Hi
try align or fit

regards

andrea

2006/3/3, srilath...@jubilantbiosys.com :
> dear all
> can we superimpose structures in pymol
> Thanks & Regards
> srilatha potlapelly
> MSc Biotechnology
> Drug discovery,
> #450,4th D Main, 12th cross,
> Mahalakshmipuram - 560086
> Bangalore
> Office: +9180-23495461-64  Extn.-1029
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RE: [PyMOL] (no subject)

[Warren DeLano]

Yes, the create command provide you with this ability, though at the end
of the process you end up with a new object.

create new_object, old_object1 | old_object2

In some cases, new_object can be the same name as either old_object1 or
old_object2:

create old_object1, old_object1 | old_object2

Also note that the vertical bar (the "or" operator) is optional in
recent betas, so

create old_object1, old_object1 old_object2

becomes legal.

Cheers,
Warren

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. 400 Oyster Point Blvd., Suite 213   
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> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Joseph Fernandez
> Sent: Sunday, September 25, 2005 11:19 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> There is a very useful functionality in Sybyl, whereby the 
> user can "merge" a residue from one molecular area, into 
> another molecular area.  The residue then becomes a part of 
> the latter moleculear area, without deleting it.  I wonder 
> whether there is such a functionality in PyMol.  
> 
> As an example, I have created a new object, consisting of 
> several residues that I have extracted from the active site 
> of a protein (using the create command). 
> I then deleted these residues from the original object 
> (active site of protein).  I now want to merge an additional 
> residue from the active site into the ligand object, and 
> delete the residue from the active site, but without deleting 
> the ligand object.
> 
> Any assistance on this matter would be appreciated.
> 
> Joe
> 
> 
>   
>   
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> 

RE: [PyMOL] (no subject)

[Warren DeLano]

Yi,

To stuff a bunch of identical object in one PDB file, you need to assign
a unique segment ID to each one.  For example:

load $PYMOL_PATH/test/dat/1tii.pdb

symexp s,1tii,1tii,5

names=cmd.get_names()
for a in range(len(names)): cmd.alter(names[a],"segi="+str(a))

save multi.pdb

Cheers,
Warren

--
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Principal Scientist

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. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
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> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of yi zhang
> Sent: Sunday, July 24, 2005 8:43 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Hi, everyone,
> 
> I used symexp command in pymol to generate symmetry-related 
> molecule, something like:
> 
> cmd.symexp('sym', 'obj', 'obj',10 )
> 
> of course, I can manually save each symmetry-related molecule 
> to *.pdb file by clicking save molecule button, but how can I 
> write a script to save all of them or part of them? the 
> symmetry-related objects are not appendable.
> 
> thanks!
> 
> yi
> 
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Re: [PyMOL] (no subject)

[lieven]

On Sunday 24 July 2005 05:42, yi zhang wrote:
> cmd.symexp('sym', 'obj', 'obj',10 )
>
> of course, I can manually save each symmetry-related
> molecule to *.pdb file by clicking save molecule
> button, but how can I write a script to save all of
> them or part of them? the symmetry-related objects
> are not appendable.

I have used something like this in the past:
#--
# get symmetry mates
objs = [ n for n in cmd.get_names() if n[0:3]=="sym" ]
for obj in objs:
if cmd.get_type(obj)!="object:molecule":
print "Something's wrong!"
else:
cmd.save(obj+".pdb",obj)
#--

Hope this helps,
-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

Re: [PyMOL] (no subject)

[Joel Tyndall]

Check out the post on "High end graphics". This will solve the problem. 
Basically you can ray-trace your molecule at a resolution bigger tahn 
teh screen size and then cut it down afterwards effectively generating a 
high resolution graphic from a 72 dpi starting point


Cheers

J

Kolli, Madhavi wrote:


Hi,

I’ve just started using PyMol for making some figures. I’m very happy 
that it is so easy to use. However the resolution of my pictures is 
very bad even after rendering them. When I print them they are very 
pixellated. I’m sure there is something I’m not doing right. Any help, 
suggestions will be appreciated.


Thanks.

Regards,

Madhavi Kolli

Graduate Student

UMass Medical School Worcester



--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


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RE: [PyMOL] (no subject)

[Warren DeLano]

Christian,

This isn't implemented yet, but it is on the to do list.

Cheers,
Warren
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Christian Rummey
> Sent: Thursday, April 22, 2004 2:35 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> 
> hi ppl,
> 
> is there a way to sort the list of objects/selections in the 
> panel on the right side other than loading/selecting stuff in 
> a specific order?
> 
> simple example: I compare several ligands in a specific site, 
> and save the data as pymol sessions; after adding new 
> ligands//site conformations I'd like to sort the sites 1st, 
> then the ligands. 
> 
> any hints?
> 
> thanks a lot,
> christian
> 
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RE: [PyMOL] (no subject)

[Warren DeLano]

Mohammed,

ray width, height
  png filename.png

for example, for a 5x4 figure at 300 dpi:

ray 1600,1200
  
  png hires.png
 (or use Save image... from the File menu after the ray command)

Cheers,
Warren


> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Mohammad Wadud Bhuiya
> Sent: Monday, April 05, 2004 5:53 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] (no subject)
> 
> Dear pymol usres
> 
> I want to increase the resolution of the figure but how? Save 
> file is png and resolution is very poor and print quality is 
> not good. I also make CA model by xfit and save file is 
> rasted3d and it is opened by pymol and save as png but figure 
> is not good quality for its low resolution. png file save as 
> windows resolution.  Could you suggest me how to increse 
> windows resolution I mean png resolution.
> 
> Thanks in advance
> Wadud
> 
> _
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> 
> 
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> 

Re: [PyMOL] (no subject)

[Matt Stephenson]

Hi Blanton,

Are you running the unstable tree, or have you just copied the 
pymol-0.90-2 package to stable, you either have to enable the unstable 
tree, or copy the numeric-py22 package from the unstable to stable, it 
can be found at '/sw/fink/dists/unstable/main/finkinfo/sci'


see here;

http://fink.sourceforge.net/faq/usage-fink.php#unstable

Matt

On Wednesday, Aug 20, 2003, at 12:01 Australia/Canberra, Tolbert, 
Blanton wrote:


I was attempting to install pymol 0.9 using fink and got the following 
error

message,

Failed: Can't resolve dependency "numeric-py22" for package 
"pymol-0.90-2"

(no matching packages/versions found)

Can anyone advise me on what to do to get around this?  Thanks in 
advance.



Blanton


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Re: [PyMOL] (no subject)

[Cameron Mura]

Hi Martin,
Visit Robert Campbell's repository of PyMOL scripts 
(http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find 
Python scripts  to import into PyMOL for drawing unit cell edges 
(draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff...


   Cameron



mkienetz wrote:


Dear All,

How do I show the unit cell using pymol?

Martin

Martin Kienetz
429 MSB
Department of Biochemistry
University of Alberta
Edmonton AB
T6G 2H7
(780) 492-2422



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Re: [PyMOL] (no subject)

[Kristian Rother]

Fei Xu wrote:

HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?


Dear Fei Xu:

1. You select an atom
2. You display it as a ball
3. You type:
set sphere_scale = 2.0

Here, the number is the size proportional to an original size of 1.0.

Unfortunately, settings for individual objects are not functional yet.


Kristian

RE: [PyMOL] (no subject)

[DeLano, Warren]

Question 1, CA-trace:  

show ribbon
set ribbon_sampling=1

(NOTE: requires all main chain atoms to be present, but not necessarily visible 
-- CA-only models will be supported later on).

Question 2, Alignment of structural homologs (requires version 0.82).

load prot1.pdb
load prot2.pdb
align prot1,prot2ca

This will perform a sequence alignment and then an iterative alpha-carbon 
superposition of matched residues.

Cheers,
Warren


-Original Message-
From: Craig Smith [mailto:boiler...@mac.com]
Sent: Wednesday, October 09, 2002 3:19 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] (no subject)


Hello, 


On the advice of a friend, I recently downloaded the OSX beta version of PyMOL. 
So far I'm very,very impressed. I have two questions: 1. How do you display a 
simple CA trace. I saw the selection for a backbone trace. 2. I want to rms-fit 
two structural homologs. How is this done in PyMOL? I tried using the fit 
command and kept getting errors. 


Thanks for you help 



Craig L. Smith, Ph. D. 
Molecular Microbiology 
Washington University School of Medicine 
660 South Euclid Box 8230 
Voice: (314) 362-9054 
Fax: (314) 362-1232 
e-mail: sm...@borcim.wustl.edu 

Re: [PyMOL] (no subject)

[Warren L. DeLano]

On Sun, 17 Feb 2002, Nat wrote:

> From an earlier reply...
> > The easiest way to use PyMOL as a module is to use PyMOL as your Python
> > interpreter.  It isn't trivial to launch PyMOL from within a running
> > Python interpreter, but it can be done under unix (only).  See pymol.com
> > and modules/launch_pymol.py for an example of how to do it.
> 
> Got this working.  Now, I'm trying to create movie frames from the
> command line; I've got two systems I've tried this on, one SuSE
> 7.something (compiled manually), the other RedHat 7.2 (rpms).  I'm
> wondering whether this is even possible.  I've modified pymol.com to
> launch my script instead; what it does is this:
> 

You shouldn't (need to) modify any of the launch
scripts.  Just use the "-c" option to get
PyMOL running in command-line only mode.
(see "help launching for all the command-line options")

pymol.com -c script.py
pymol.com -c script.pml

Cheers,
Warrren

Re: [PyMOL] (no subject)

[Warren L. DeLano]

On Thu, 22 Nov 2001, Sona Vasudevan wrote:
 
> Hi!
> 
> Just wondering if there is a way to save a pymol session like in Insight
> and setor if I want to get back to it.

PyMOL isn't quite as sophisticated as Insight II in this respect, however
the logging features can achieve session-like behavior.  It works sort-of
like Grasp but with log files that are much more straight-forward to edit
and modify, since they are written in the PyMOL command language (.pml
files) or using PyMOL's Python API (.pym files).  Example:

Select "Log..." from the file menu immediately after you start PyMOL to
start writing a ".pml" or ".pym" log file.  Go about your business.

When done, press the "Get View" button and quit the program.

To resume your "session", launch PyMOL and select "Resume..." from the
file menu.  Open your log file and *PRESTO* PyMOL should be in
the same state as when you left. Any additional actions you then take will
be appended on to the log.  

Note that any "ray", "png", or "save" operations will be repeated when you
resume the log file.  Thus, you may want to edit the log file and
remove these commands with a text editor (Notepad on Windows) before
resuming.  Perhaps it would be nice to have a setting which ignores this
kinds of commands when resuming.  Hmm...

- Warren

PS. There is only bug I know of in the logging feature of 0.68 which
affects conformational editing when logging to .pml files.  It will be
fixed in the next release, but for now just log to .pym files if you
are going to edit conformations.