pymol-users Mailing List for PyMOL Molecular Graphics System

Ah, indeed, the latest revision 3969 has a correctly working distance 
command.

Thanks Jason.


Andreas


On 29/09/2011 3:08, Jason Vertrees wrote:
> Hi Andreas,
>
> It was a bug with the invalidation system. I just pushed a fix to source forge.
>
> Thanks for bringing this to our attention.
>
> Cheers,
>
> -- Jason
>


-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

Hi Andreas,

It was a bug with the invalidation system. I just pushed a fix to source forge.

Thanks for bringing this to our attention.

Cheers,

-- Jason

2011/9/29 Andreas Förster <doc...@gm...>:
> Hi all,
>
> Has anyone noticed that the distance command behaves oddly.  Has this
> been recently introduced?
>
> fetch 1ubq
> zoom 1ubq
> dist 9/cg2, 73/cd2
> # output:  object dist01 is created
> # distance of 10.2 is shown, but no dashed line
> # now check this out:
> # several repetitions of the next two lines
> disable dist01
> enable dist01
> # eventually lead to the appearance of the dashed line
> # but it gets better
> disable dist01
> enable dist01
> # The distance is enabled but neither number nor dashed line are visible
> disable dist01
> enable dist01
> # Now the number and the dashed line are back
>
> When dist01 is enabled but invisible, disabling 1ubq brings it back, but
> it disappears again when 1ubq is re-enabled.
>
> With other pdb files, the distance command doesn't work at all.  It
> returns a distance of 0.0A to the screen that is only visible when the
> associated pdb object is disabled.
>
> I've observed this with
> pymol-py26 1.4-7 installed with fink on a MacBook running 10.6
> and with
> pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1
>
> Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine.
>
> Recently introduced bug?
>
>
> Andreas
>
>
>
> --
>         Andreas Förster, Research Associate
>         Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>             http://www.msf.bio.ic.ac.uk
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> 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,

 My pymol 1.4.1 works fine.
 can you try to ray trace and see if your objects are available but just not
displayed on the standard screen?

cheers,


2011/9/29 Andreas Förster <doc...@gm...>

> Hi all,
>
> Has anyone noticed that the distance command behaves oddly.  Has this
> been recently introduced?
>
> fetch 1ubq
> zoom 1ubq
> dist 9/cg2, 73/cd2
> # output:  object dist01 is created
> # distance of 10.2 is shown, but no dashed line
> # now check this out:
> # several repetitions of the next two lines
> disable dist01
> enable dist01
> # eventually lead to the appearance of the dashed line
> # but it gets better
> disable dist01
> enable dist01
> # The distance is enabled but neither number nor dashed line are visible
> disable dist01
> enable dist01
> # Now the number and the dashed line are back
>
> When dist01 is enabled but invisible, disabling 1ubq brings it back, but
> it disappears again when 1ubq is re-enabled.
>
> With other pdb files, the distance command doesn't work at all.  It
> returns a distance of 0.0A to the screen that is only visible when the
> associated pdb object is disabled.
>
> I've observed this with
> pymol-py26 1.4-7 installed with fink on a MacBook running 10.6
> and with
> pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1
>
> Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine.
>
> Recently introduced bug?
>
>
> Andreas
>
>
>
> --
>         Andreas Förster, Research Associate
>         Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>             http://www.msf.bio.ic.ac.uk
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> 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 all,

Has anyone noticed that the distance command behaves oddly.  Has this 
been recently introduced?

fetch 1ubq
zoom 1ubq
dist 9/cg2, 73/cd2
# output:  object dist01 is created
# distance of 10.2 is shown, but no dashed line
# now check this out:
# several repetitions of the next two lines
disable dist01
enable dist01
# eventually lead to the appearance of the dashed line
# but it gets better
disable dist01
enable dist01
# The distance is enabled but neither number nor dashed line are visible
disable dist01
enable dist01
# Now the number and the dashed line are back

When dist01 is enabled but invisible, disabling 1ubq brings it back, but 
it disappears again when 1ubq is re-enabled.

With other pdb files, the distance command doesn't work at all.  It 
returns a distance of 0.0A to the screen that is only visible when the 
associated pdb object is disabled.

I've observed this with
pymol-py26 1.4-7 installed with fink on a MacBook running 10.6
and with
pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1

Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine.

Recently introduced bug?


Andreas



-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

Hi Anasuya,

This sound like one of those very good reasons to have a go at Python,
and leave Perl behind... Together with all the plain reasons to leave
Perl behind :) First of all, check http://xkcd.com/353/

Assuming the file is called list.txt and you have all pdb files at
hand (which is not strictly necessary, as PyMOl can download them for
you), make a file called process.py with the following content



from pymol import cmd

def process_line(x):
  pdbid,res,chain,num = x.split()
  cmd.load(pdbid+".pdb")
  cmd.select("zone1","byres all within 4.5 of (chain %s and resn %s
and resi %s)"%(chain,res,num))
  cmd.select("zone2","(byres all within 4.5 of zone1) and not zone1)")
  cmd.save("%s-%s-%s-%s-zone1.pdb"%(pdbid,res,chain,num),zone1)
  cmd.save("%s-%s-%s-%s-zone2.pdb"%(pdbid,res,chain,num),zone2)
  cmd.delete(pdbid)

def process_all(filename):
  for line in open(filename):
    process_line(line)

process_all("list.txt")


#======

After saving the file, do

pymol -c process.py

And that's it. Unless I made an error somewhere :P I haven't actually
tested this. But the proper solution should lie along these lines :)

Hope it helps,

Tsjerk
On Thu, Sep 29, 2011 at 8:58 AM, Anasuya Dighe
<an...@mb...> wrote:
> Hello,
> I have a .txt file which has data in the following fashion:
>
>          19gs BSP A 1
>          1a2d PYX A 117
>          9rsa ADU A 125
>          7kme PRR J 382
>          1a0r ACE B 1
>          1a0r FAR G 72
>          .
>          .
>          .
>
> Fields: <PDB ID>  <LIGAND NAME>  <CHAIN TO WHICH IT IS ATTACHED>  <RESIDUE
> SEQUENCE NUMBER>
>
> In such  a way, I have data of around 19,200 unique pdb files which have one or
> more ligands attached to them. [PLEASE NOTE THAT there can be multiple ligands
> to a particular .pdb file attached at different positions ]
>
> For each .pdb file, I need to extract complete residues which fall within a
> radius of 4.5 Angstroms of the ligand. I am calling such zones as ZONE1.I mean
> residues that have any atom within 4.5 Angstroms of the ligand => zone1
> Then after extracting ZONE1, I also want to extract complete residues which fall
> within a radius of 4.5 Angstroms of ZONE1.. I am calling these zones as ZONE2. I
> mean, residues that have any atom within 9.0 Angstroms of the ligand, but are
> not already in ZONE1 => ZONE2
>
> I am looking for a way to automate Pymol by writing a .pml script, such that
> foreach pdb file, I have 2 additional files generated such that they are called
> as: 19gs_BSP_z1.pdb [for ZONE1] and 19gs_BSP_z2.pdb [for ZONE2],
> 1a2d_PYX_z1.pdb, 1a2d_PYX_z2.pdb and so on...
>
> Can this be done through PERL?
> Please suggest me an efficient way of achieving the desired output..
>
> Thanks,
>
> -Anasuya
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hello,
I have a .txt file which has data in the following fashion:

          19gs BSP A 1
          1a2d PYX A 117
          9rsa ADU A 125
          7kme PRR J 382
          1a0r ACE B 1
          1a0r FAR G 72
          .
          .
          .

Fields: <PDB ID>  <LIGAND NAME>  <CHAIN TO WHICH IT IS ATTACHED>  <RESIDUE
SEQUENCE NUMBER>

In such  a way, I have data of around 19,200 unique pdb files which have one or
more ligands attached to them. [PLEASE NOTE THAT there can be multiple ligands
to a particular .pdb file attached at different positions ]

For each .pdb file, I need to extract complete residues which fall within a
radius of 4.5 Angstroms of the ligand. I am calling such zones as ZONE1.I mean
residues that have any atom within 4.5 Angstroms of the ligand => zone1
Then after extracting ZONE1, I also want to extract complete residues which fall
within a radius of 4.5 Angstroms of ZONE1.. I am calling these zones as ZONE2. I
mean, residues that have any atom within 9.0 Angstroms of the ligand, but are
not already in ZONE1 => ZONE2

I am looking for a way to automate Pymol by writing a .pml script, such that
foreach pdb file, I have 2 additional files generated such that they are called
as: 19gs_BSP_z1.pdb [for ZONE1] and 19gs_BSP_z2.pdb [for ZONE2],
1a2d_PYX_z1.pdb, 1a2d_PYX_z2.pdb and so on...

Can this be done through PERL?
Please suggest me an efficient way of achieving the desired output..

Thanks,

-Anasuya



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Hi Lina,

atom properties can be changed with the "alter" command. It takes a 
selection (the atoms that should be modified) and an assignment 
expression in python syntax.

Example:
alter name H01, name="H22"

It's important to quote strings in the assignment expression!

More details and examples:
http://pymolwiki.org/index.php/Alter

Cheers,
   Thomas

On 09/27/2011 09:35 AM, lina wrote:
> Hi,
>
> how can I change the atom such as
>
> H01 to H22 in command
>
> Thanks ahead,
>
> --
> Best Regards,
>
> lina

-- 
Thomas Holder
MPI for Developmental Biology

Hi,

how can I change the atom such as

H01 to H22 in command

Thanks ahead,

-- 
Best Regards,

lina

Hi Lina,

If you have an atom that you want to identify you can right click on the atom which give you the atom name (pdb format).

Your command "select o, name o" does work on the latest windows install 1.4.1 where it selects all oxygens and creates a selection called (o).

Hope this helps

Joel

_________________________________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034

From: lina [mailto:lin...@gm...]
Sent: Sunday, 25 September 2011 11:11 p.m.
To: pym...@li...
Subject: [PyMOL] get atom name

Hi,

how can I get the atoms name (except label)

when I use
select o, name o

not work.

Here I will the .pse file in the following email.

--
Best Regards,

lina

Hi,

how can I get the atoms name (except label)

when I use
select o, name o

not work.

Here I will the .pse file in the following email.

-- 
Best Regards,

lina

Hi all,

since there were two "selection by distance" related questions this 
week, I put a table on the wiki that compares the different distance 
operators available in the PyMOL selection language.

http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators

Cheers,
   Thomas

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

Hi Anasuya,

> I have around 19,200 unique PDB files. Each of them have one or more
> ligands in it. For each ligand, I have to extract a zone which
> contains complete residues within 4.5Angstroms of the ligand [ i.e.
> ZONE1] and then extract another zone, which has complete residues
> within 4.5Angstroms of ZONE1, [i.e.ZONE2] I need to store these two
> zones in two separate .pdb files.
> How can this be done? So far I have managed to extract ZONE1 for all
> the PDB ID's and saved their corresponding .pdb files, but, I was
> stuck at the next step.

I guess you mean residues that have any atom within 4.5 Angstroms of the 
ligand? And for ZONE2 residues that have any atom within 9.0 Angstroms 
of the ligand, but are not already in ZONE1, right?

# select first ligand
select ligand, byres (first organic)

# zone 1
select ZONE1, byres (ligand around 4.5)

# zone 2
select ZONE2, byres (ligand around 9.0) and not ZONE1

# save to files
save zone1.pdb, ZONE1
save zone2.pdb, ZONE2

Have a look at
http://pymolwiki.org/index.php/Selection_Algebra

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

hi all,
I am writing this email with regards to the following problem.
Statement of the problem:

I have around 19,200 unique PDB files. Each of them have one or more ligands in it.
For each ligand, I have to extract a zone which contains complete residues
within 4.5Angstroms of the ligand [ i.e. ZONE1] and then extract another zone,
which has complete residues within 4.5Angstroms of ZONE1, [i.e.ZONE2]
I need to store these two zones in two separate .pdb files.
How can this be done? So far I have managed to extract ZONE1 for all the PDB
ID's and saved their corresponding .pdb files, but, I was stuck at the next
step.
Please let me know how I can solve this problem.


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

And to save it, add this python block

python
for PDB in PDBs:
    cmd.save("%s-K.pdb"%PDB,"%s"%PDB)
python end

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE <" rel="nofollow">http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/9/22 Troels Emtekær Linnet <tl...@gm...>

> # Firs load files in dirextory with:
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
> # load_sep.py
> # Load multiple PDB files into a multiple PyMOL objects
> #  e.g. load_sep prot_*.pdb, prot
> # will create objects with names, prot1, prot2, prot3, etc.
>
> # Now the rest
> cd /home/tlinnet/Desktop
>
> # Test protein
> fetch 4INS, async=0
>
> # Get all loaded PDB object names in pymol
> PDBs = cmd.get_names()
>
> python
> ### We need to find a way to get the information of chain and resi from the
> loaded list
> ### Create empty list
> ProtChainResiList = []
> for PDB in PDBs:
>     #print PDB
>     ### Get the ID numbers of CA atom in protein
>     CAindex = cmd.identify("%s and name CA"%PDB)
>     for CAid in CAindex:
>         ### We need to find a way to get the information of chain and resi
> from ID
>         pdbstr = cmd.get_pdbstr("%s and id %s"%(PDB,CAid))
>         pdbstr_lines = pdbstr.splitlines()
>         chain = pdbstr_lines[0].split()[4]
>         resi = pdbstr_lines[0].split()[5]
>         #print "CAid: %s Chain: %s resi: %s"%(CAid, chain,resi)
>         ProtChainResiList.append([PDB,chain,resi])
> #for entry in ProtChainResiList:
> #    print entry
> python end
>
> ### We devide it up in several python blocks, so python dont speed ahead:
> python
> ### Start the wizard
> cmd.wizard("mutagenesis")
> ###### REMOVE [0:3]
> for p,c,r in ProtChainResiList[0:4]:
>     #print p,c,r
>     cmd.do("refresh_wizard")
>     cmd.get_wizard().set_mode("LYS")
>     selection="/%s//%s/%s"%(p,c,r)
>     #print selection
>     cmd.get_wizard().do_select(selection)
>     ### Select frame 1, which is most probable
>     cmd.frame(1)
>     cmd.get_wizard().apply()
> ### Stop the wizard
> cmd.set_wizard("done")
> python end
>
> Troels Emtekær Linnet
>
>
>
> 2011/9/22 Fabio Gozzo <fg...@gm...>
>
>>  Hi Pymolers,
>>
>> I need to perform a batch operation but I need a help with script
>> modification.
>> A have a set (~100) of pdb files that I would like to mutate all residues
>> to lysine. I modified mutate02.py script in pymol to perform this task, but
>> I would need two extra "features":
>>
>> 1) the script would need to save the file with a different name. For
>> example, load test.pdb, mutate all residues to lysine and then save the
>> mutated version to test_K.pdb
>> 2) the script would need to perform this task for all the pdb files in a
>> directory.
>>
>> Right now, I am not concerned about the possible rotamers of lysine, any
>> lysine rotamer would work.
>> Could anyone give a hint on how to do it ?
>> Thanks !
>> Fabio.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2dcopy1
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

# Firs load files in dirextory with:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
# load_sep.py
# Load multiple PDB files into a multiple PyMOL objects
#  e.g. load_sep prot_*.pdb, prot
# will create objects with names, prot1, prot2, prot3, etc.

# Now the rest
cd /home/tlinnet/Desktop

# Test protein
fetch 4INS, async=0

# Get all loaded PDB object names in pymol
PDBs = cmd.get_names()

python
### We need to find a way to get the information of chain and resi from the
loaded list
### Create empty list
ProtChainResiList = []
for PDB in PDBs:
    #print PDB
    ### Get the ID numbers of CA atom in protein
    CAindex = cmd.identify("%s and name CA"%PDB)
    for CAid in CAindex:
        ### We need to find a way to get the information of chain and resi
from ID
        pdbstr = cmd.get_pdbstr("%s and id %s"%(PDB,CAid))
        pdbstr_lines = pdbstr.splitlines()
        chain = pdbstr_lines[0].split()[4]
        resi = pdbstr_lines[0].split()[5]
        #print "CAid: %s Chain: %s resi: %s"%(CAid, chain,resi)
        ProtChainResiList.append([PDB,chain,resi])
#for entry in ProtChainResiList:
#    print entry
python end

### We devide it up in several python blocks, so python dont speed ahead:
python
### Start the wizard
cmd.wizard("mutagenesis")
###### REMOVE [0:3]
for p,c,r in ProtChainResiList[0:4]:
    #print p,c,r
    cmd.do("refresh_wizard")
    cmd.get_wizard().set_mode("LYS")
    selection="/%s//%s/%s"%(p,c,r)
    #print selection
    cmd.get_wizard().do_select(selection)
    ### Select frame 1, which is most probable
    cmd.frame(1)
    cmd.get_wizard().apply()
### Stop the wizard
cmd.set_wizard("done")
python end

Troels Emtekær Linnet



2011/9/22 Fabio Gozzo <fg...@gm...>

> Hi Pymolers,
>
> I need to perform a batch operation but I need a help with script
> modification.
> A have a set (~100) of pdb files that I would like to mutate all residues
> to lysine. I modified mutate02.py script in pymol to perform this task, but
> I would need two extra "features":
>
> 1) the script would need to save the file with a different name. For
> example, load test.pdb, mutate all residues to lysine and then save the
> mutated version to test_K.pdb
> 2) the script would need to perform this task for all the pdb files in a
> directory.
>
> Right now, I am not concerned about the possible rotamers of lysine, any
> lysine rotamer would work.
> Could anyone give a hint on how to do it ?
> Thanks !
> Fabio.
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Thanks Marius 

With the second it works 

A bientot 

Stephane

-----Message d'origine-----
De : Marius Retegan [mailto:mar...@gm...] 
Envoyé : jeudi 22 septembre 2011 18:02
À : intra\sa175950
Objet : Re: [PyMOL] Write in a file the number of water at a distance from a

Hello Stephane,

Water molecules are composed of 3 atoms, so this
print cmd.count_atoms("WATER_firstshell")/3
should give you the right answer.

If you really want it your way:
print cmd.count_atoms("firstshell_WATER and elem O")

P.S. I haven't tried any of these commands. I hope they work.

Best regards,
Marius

--
Dr. Marius Retegan
Postdoctoral Fellow

Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0) 4 76 63 44 03

GnuPG http://db.tt/rr7Hd0Y



On Thu, Sep 22, 2011 at 5:38 PM, intra\sa175950 <ste...@ce...>
wrote:
> Hi All,
>
> With the help of Thomas Holder (thanks to him), now I can show and obtain
> the number of water in the first shell of my six peptides (an amyloid
> fibrils). However, I have a little problem with the command count_atoms in
> my script
>
> Below my script (*.pml) for Pymol 1.3 :
>
> mstop
> dss
> hide all
>
> select CL, resn CL
> delete CL
>
> ## Select WATER with residue ID SOL
> select WATER, resn SOL
>
> ## Select Amyloid, resi 1-54
> select Amyloid, resi 1-54 and not WATER
>
> ## Show in cartoon Amyloid
> show cartoon, Amyloid
>
> ## Show in different colors peptides because it is nice.
> set cartoon_color, black, resi 2-8
> set cartoon_color, red, resi 11-17
> set cartoon_color, green, resi 20-26
> set cartoon_color, blue, resi 29-35
> set cartoon_color, yellow, resi 38-44
> set cartoon_color, chocolate, resi 47-53
>
> ## Not use for the moment
>
> ##set cartoon_color, gray50, resi 56-62
> ##set cartoon_color, wheat, resi 65-71
> ##set cartoon_color, aquamarine, resi 74-80
> ##set cartoon_color, pink, resi 83-89
> ##set cartoon_color, orange, resi 92-98
> ##et cartoon_color, forest, resi 101-107
>
> ## Select water in the first shell (e.g. within 3.5 A of the Amyloid
atoms)
> select WATER_firstshell, WATER within 3.5 A of Amyloid
>
> ## Give the number of water in the first shell of the fibrils
> ## Works ---> Give number of water atoms (including oxygen and Hs)
> print cmd.count_atoms("WATER_firstshell")
>
> ## Print the residu ID of each water in the first shell
> iterate ("WATER_firstshell"), print resi
>
> set cartoon_fancy_helices=1
> set cartoon_discrete_colors, on
> set antialias = 1
>
> ray
>
> -------------------
>
> As you can imagine the "firstshell_WATER" variable contains the water O
and
> H atoms. It is not what I want! Indeed I want that count_atoms command
> counts only the number of Water oxygen. So I use
>
> count_atoms("firstshell_WATER" and elem O)
>
>  This command works if I use the pymol GUI but If I use the command in my
> script. Indeed
>
> print cmd.count_atoms("firstshell_WATER" and elem O) show a syntax error
>
>
> Thanks in advance for your help.
>
> Stephane
>
> ------------------------------
>
> Message: 7
> Date: Thu, 22 Sep 2011 11:14:36 +0200
> From: Thomas Holder <sp...@us...>
> Subject: Re: [PyMOL] Write in a file the number of water at a distance
>        from a protein surface
> To: ABEL Stephane 175950 <Ste...@ce...>
> Cc: "pym...@li..."
>        <pym...@li...>
> Message-ID: <4E7...@us...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Stephane,
>
> you can select those waters using the "within" or "gap" selection
> operators. "within" measures from the atom centre, whereas "gap" takes
> the VDW radius into accout but selects everything beyond instead of
> near. Have a look at those examples:
>
> # use '... within ...'
> select firstshell, solvent within 3.5 of polymer
>
> # or use 'not (... gap ...)'
> select firstshell, solvent and not (polymer gap 0.5)
>
> # shows the selected water molecules as a sphere
> show spheres, firstshell and elem O
>
> # writes the results in a file
> python
> stored.out = open('/tmp/water-IDs.txt', 'w')
> print >> stored.out, '## At 0.5 Ang of the protein surface there are',
> print >> stored.out, cmd.count_atoms('firstshell and elem O'),
> print >> stored.out, 'water molecules'
> print >> stored.out, '## Water ID and resi are'
> cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
> stored.out.close()
> python end
>
> http://www.pymolwiki.org/index.php/Selection_Algebra
> http://www.pymolwiki.org/index.php/Iterate
>
> Hope that helps,
>
> Cheers,
>   Thomas
>
> On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
>> Hi All,
>>
>> I have simulated a protein in water cubic box and I would like to
>> know how to show and obtain the number of water in the first shell of
>> the protein (or at x Ang of the protein surface) using a pymol
>> script. I can to do this using the pymol GUI but I would prefer that
>> the script :
>>
>> - shows the selected water molecules as a sphere
>> - and writes the results in a file with the water ID (i.e. residue
>> number), for example like this:
>>
>> ## At x Ang of the protein surface there are XX water molecules
>> ## Water ID  are
>>
>> Thanks in advance for your help.
>>
>> Stephane
>
> --
> Thomas Holder
> MPI for Developmental Biology
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 22 Sep 2011 10:05:46 +0000
> From: ABEL Stephane 175950 <Ste...@ce...>
> Subject: [PyMOL] RE : Write in a file the number of water at a
>        distance from a protein surface
> To: Thomas Holder <sp...@us...>
> Cc: "pym...@li..."
>        <pym...@li...>
> Message-ID:
>        <3E3...@EX...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you for your response, i will try your suggestion
>
> A bientot
>
> Stephane
> ________________________________________
> De : Thomas Holder [ad...@th...] de la part de Thomas Holder
> [sp...@us...]
> Date d'envoi : jeudi 22 septembre 2011 11:14
> ? : ABEL Stephane 175950
> Cc : pym...@li...
> Objet : Re: [PyMOL] Write in a file the number of water at a distance from
a
> protein surface
>
> Hi Stephane,
>
> you can select those waters using the "within" or "gap" selection
> operators. "within" measures from the atom centre, whereas "gap" takes
> the VDW radius into accout but selects everything beyond instead of
> near. Have a look at those examples:
>
> # use '... within ...'
> select firstshell, solvent within 3.5 of polymer
>
> # or use 'not (... gap ...)'
> select firstshell, solvent and not (polymer gap 0.5)
>
> # shows the selected water molecules as a sphere
> show spheres, firstshell and elem O
>
> # writes the results in a file
> python
> stored.out = open('/tmp/water-IDs.txt', 'w')
> print >> stored.out, '## At 0.5 Ang of the protein surface there are',
> print >> stored.out, cmd.count_atoms('firstshell and elem O'),
> print >> stored.out, 'water molecules'
> print >> stored.out, '## Water ID and resi are'
> cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
> stored.out.close()
> python end
>
> http://www.pymolwiki.org/index.php/Selection_Algebra
> http://www.pymolwiki.org/index.php/Iterate
>
> Hope that helps,
>
> Cheers,
>   Thomas
>
> On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
>> Hi All,
>>
>> I have simulated a protein in water cubic box and I would like to
>> know how to show and obtain the number of water in the first shell of
>> the protein (or at x Ang of the protein surface) using a pymol
>> script. I can to do this using the pymol GUI but I would prefer that
>> the script :
>>
>> - shows the selected water molecules as a sphere
>> - and writes the results in a file with the water ID (i.e. residue
>> number), for example like this:
>>
>> ## At x Ang of the protein surface there are XX water molecules
>> ## Water ID  are
>>
>> Thanks in advance for your help.
>>
>> Stephane
>
> --
> Thomas Holder
> MPI for Developmental Biology
>
>
>
> ------------------------------
>
>
----------------------------------------------------------------------------
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 64, Issue 17
> *******************************************
>
>
>
>
----------------------------------------------------------------------------
--
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> 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 All, 

With the help of Thomas Holder (thanks to him), now I can show and obtain
the number of water in the first shell of my six peptides (an amyloid
fibrils). However, I have a little problem with the command count_atoms in
my script

Below my script (*.pml) for Pymol 1.3 : 

mstop
dss
hide all

select CL, resn CL
delete CL

## Select WATER with residue ID SOL 
select WATER, resn SOL 

## Select Amyloid, resi 1-54 
select Amyloid, resi 1-54 and not WATER

## Show in cartoon Amyloid
show cartoon, Amyloid

## Show in different colors peptides because it is nice.  
set cartoon_color, black, resi 2-8
set cartoon_color, red, resi 11-17
set cartoon_color, green, resi 20-26
set cartoon_color, blue, resi 29-35
set cartoon_color, yellow, resi 38-44
set cartoon_color, chocolate, resi 47-53

## Not use for the moment

##set cartoon_color, gray50, resi 56-62
##set cartoon_color, wheat, resi 65-71
##set cartoon_color, aquamarine, resi 74-80
##set cartoon_color, pink, resi 83-89
##set cartoon_color, orange, resi 92-98
##et cartoon_color, forest, resi 101-107

## Select water in the first shell (e.g. within 3.5 A of the Amyloid atoms)
select WATER_firstshell, WATER within 3.5 A of Amyloid 

## Give the number of water in the first shell of the fibrils
## Works ---> Give number of water atoms (including oxygen and Hs)
print cmd.count_atoms("WATER_firstshell")
  
## Print the residu ID of each water in the first shell
iterate ("WATER_firstshell"), print resi

set cartoon_fancy_helices=1
set cartoon_discrete_colors, on 
set antialias = 1

ray

-------------------

As you can imagine the "firstshell_WATER" variable contains the water O and
H atoms. It is not what I want! Indeed I want that count_atoms command
counts only the number of Water oxygen. So I use 

count_atoms("firstshell_WATER" and elem O)

 This command works if I use the pymol GUI but If I use the command in my
script. Indeed

print cmd.count_atoms("firstshell_WATER" and elem O) show a syntax error 


Thanks in advance for your help.

Stephane

------------------------------

Message: 7
Date: Thu, 22 Sep 2011 11:14:36 +0200
From: Thomas Holder <sp...@us...>
Subject: Re: [PyMOL] Write in a file the number of water at a distance
	from a protein surface
To: ABEL Stephane 175950 <Ste...@ce...>
Cc: "pym...@li..."
	<pym...@li...>
Message-ID: <4E7...@us...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Stephane,

you can select those waters using the "within" or "gap" selection 
operators. "within" measures from the atom centre, whereas "gap" takes 
the VDW radius into accout but selects everything beyond instead of 
near. Have a look at those examples:

# use '... within ...'
select firstshell, solvent within 3.5 of polymer

# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)

# shows the selected water molecules as a sphere
show spheres, firstshell and elem O

# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print >> stored.out, '## At 0.5 Ang of the protein surface there are',
print >> stored.out, cmd.count_atoms('firstshell and elem O'),
print >> stored.out, 'water molecules'
print >> stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
stored.out.close()
python end

http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate

Hope that helps,

Cheers,
   Thomas

On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
> Hi All,
>
> I have simulated a protein in water cubic box and I would like to
> know how to show and obtain the number of water in the first shell of
> the protein (or at x Ang of the protein surface) using a pymol
> script. I can to do this using the pymol GUI but I would prefer that
> the script :
>
> - shows the selected water molecules as a sphere
> - and writes the results in a file with the water ID (i.e. residue
> number), for example like this:
>
> ## At x Ang of the protein surface there are XX water molecules
> ## Water ID  are
>
> Thanks in advance for your help.
>
> Stephane

-- 
Thomas Holder
MPI for Developmental Biology



------------------------------

Message: 8
Date: Thu, 22 Sep 2011 10:05:46 +0000
From: ABEL Stephane 175950 <Ste...@ce...>
Subject: [PyMOL] RE : Write in a file the number of water at a
	distance from a protein surface
To: Thomas Holder <sp...@us...>
Cc: "pym...@li..."
	<pym...@li...>
Message-ID:
	<3E3...@EX...>
Content-Type: text/plain; charset="iso-8859-1"

Thank you for your response, i will try your suggestion

A bientot

Stephane
________________________________________
De : Thomas Holder [ad...@th...] de la part de Thomas Holder
[sp...@us...]
Date d'envoi : jeudi 22 septembre 2011 11:14
? : ABEL Stephane 175950
Cc : pym...@li...
Objet : Re: [PyMOL] Write in a file the number of water at a distance from a
protein surface

Hi Stephane,

you can select those waters using the "within" or "gap" selection
operators. "within" measures from the atom centre, whereas "gap" takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:

# use '... within ...'
select firstshell, solvent within 3.5 of polymer

# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)

# shows the selected water molecules as a sphere
show spheres, firstshell and elem O

# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print >> stored.out, '## At 0.5 Ang of the protein surface there are',
print >> stored.out, cmd.count_atoms('firstshell and elem O'),
print >> stored.out, 'water molecules'
print >> stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
stored.out.close()
python end

http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate

Hope that helps,

Cheers,
   Thomas

On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
> Hi All,
>
> I have simulated a protein in water cubic box and I would like to
> know how to show and obtain the number of water in the first shell of
> the protein (or at x Ang of the protein surface) using a pymol
> script. I can to do this using the pymol GUI but I would prefer that
> the script :
>
> - shows the selected water molecules as a sphere
> - and writes the results in a file with the water ID (i.e. residue
> number), for example like this:
>
> ## At x Ang of the protein surface there are XX water molecules
> ## Water ID  are
>
> Thanks in advance for your help.
>
> Stephane

--
Thomas Holder
MPI for Developmental Biology



------------------------------

----------------------------------------------------------------------------
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1

------------------------------

_______________________________________________
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PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users


End of PyMOL-users Digest, Vol 64, Issue 17
*******************************************

Hi Pymolers,

I need to perform a batch operation but I need a help with script
modification.
A have a set (~100) of pdb files that I would like to mutate all residues to
lysine. I modified mutate02.py script in pymol to perform this task, but I
would need two extra "features":

1) the script would need to save the file with a different name. For
example, load test.pdb, mutate all residues to lysine and then save the
mutated version to test_K.pdb
2) the script would need to perform this task for all the pdb files in a
directory.

Right now, I am not concerned about the possible rotamers of lysine, any
lysine rotamer would work.
Could anyone give a hint on how to do it ?
Thanks !
Fabio.

On 12 sept. 2011, at 14:20, Jason Vertrees wrote:

> Greetings,
> 
> One chance encounter at ACS couple weeks ago turned into a multi-day
> discussion about using the new volume visualization for presenting
> field data. Leroy Laverman from UCSB now has some example movies
> showing how the electrostatic field extends beyond the molecular
> surface and how the volumes help us visualize this. I thought they
> were useful and worth sharing. You can view his sample movies here:
> http://www.chem.ucsb.edu/~laverman/Freeman/ESP.html. Leroy welcomes
> feedback at the email address listed on the page.
> 
> Hope this helps.

Amazing feature, very rich in informations!

Now I'm dreaming for the same feature in coot ;-)

Florian.

Thank you for your response, i will try your suggestion

A bientot

Stephane
________________________________________
De : Thomas Holder [ad...@th...] de la part de Thomas Holder [sp...@us...]
Date d'envoi : jeudi 22 septembre 2011 11:14
À : ABEL Stephane 175950
Cc : pym...@li...
Objet : Re: [PyMOL] Write in a file the number of water at a distance from a protein surface

Hi Stephane,

you can select those waters using the "within" or "gap" selection
operators. "within" measures from the atom centre, whereas "gap" takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:

# use '... within ...'
select firstshell, solvent within 3.5 of polymer

# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)

# shows the selected water molecules as a sphere
show spheres, firstshell and elem O

# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print >> stored.out, '## At 0.5 Ang of the protein surface there are',
print >> stored.out, cmd.count_atoms('firstshell and elem O'),
print >> stored.out, 'water molecules'
print >> stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
stored.out.close()
python end

http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate

Hope that helps,

Cheers,
   Thomas

On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
> Hi All,
>
> I have simulated a protein in water cubic box and I would like to
> know how to show and obtain the number of water in the first shell of
> the protein (or at x Ang of the protein surface) using a pymol
> script. I can to do this using the pymol GUI but I would prefer that
> the script :
>
> - shows the selected water molecules as a sphere
> - and writes the results in a file with the water ID (i.e. residue
> number), for example like this:
>
> ## At x Ang of the protein surface there are XX water molecules
> ## Water ID  are
>
> Thanks in advance for your help.
>
> Stephane

--
Thomas Holder
MPI for Developmental Biology

Hi Stephane,

you can select those waters using the "within" or "gap" selection 
operators. "within" measures from the atom centre, whereas "gap" takes 
the VDW radius into accout but selects everything beyond instead of 
near. Have a look at those examples:

# use '... within ...'
select firstshell, solvent within 3.5 of polymer

# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)

# shows the selected water molecules as a sphere
show spheres, firstshell and elem O

# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print >> stored.out, '## At 0.5 Ang of the protein surface there are',
print >> stored.out, cmd.count_atoms('firstshell and elem O'),
print >> stored.out, 'water molecules'
print >> stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
stored.out.close()
python end

http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate

Hope that helps,

Cheers,
   Thomas

On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
> Hi All,
>
> I have simulated a protein in water cubic box and I would like to
> know how to show and obtain the number of water in the first shell of
> the protein (or at x Ang of the protein surface) using a pymol
> script. I can to do this using the pymol GUI but I would prefer that
> the script :
>
> - shows the selected water molecules as a sphere
> - and writes the results in a file with the water ID (i.e. residue
> number), for example like this:
>
> ## At x Ang of the protein surface there are XX water molecules
> ## Water ID  are
>
> Thanks in advance for your help.
>
> Stephane

-- 
Thomas Holder
MPI for Developmental Biology

Hi Horacio,

> a) where could we find information about the SASA method it uses so we can speed and accuracy increment test with our own method

http://www.mail-archive.com/pym...@li.../msg01618.html
http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Surface-Related
http://www.pymolwiki.org/index.php/Get_Area
http://www.pymolwiki.org/index.php/Surface

And, you'll need to read the code in pymol/layer2/RepSurface.c

> b) same question for the method pymol uses to graphically render the molecular surface

pymol/layer2/RepSurface.c

Cheers,

-- Jason

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

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

Hi All, 

I have simulated a protein in water cubic box and I would like to know how to show and obtain the number of water in the first shell of the protein (or at x Ang of the protein surface) using a pymol script. I can to do this using the pymol GUI but I would prefer that the script :

- shows the selected water molecules as a sphere
- and writes the results in a file with the water ID (i.e. residue number), for example like this: 

## At x Ang of the protein surface there are XX water molecules
## Water ID  are 

Thanks in advance for your help. 

Stephane

On Wed, Sep 21, 2011 at 11:02 PM, Thomas Holder <
sp...@us...> wrote:

> Hi Lina,
>
> if you are looking for a way to "zoom in", use your right mouse button or
> type:
>

Thanks, are there some command is equal to the right mouse button?
just curious.

>
> move z, 10
>
it's not so simple to figure out the x,y,z direction by eyes.

>
> The "zoom" command however will set the current view to cover the given
> atom selection (or all if no selection is given).
>
> " rel="nofollow">http://pymolwiki.org/index.**php/Move<http://pymolwiki.org/index.php/Move>
> " rel="nofollow">http://pymolwiki.org/index.**php/Zoom<http://pymolwiki.org/index.php/Zoom>

Thanks for the links.

>
>
> Cheers,
>  Thomas
>
>
> On 09/21/2011 04:47 PM, lina wrote:
>
>> Hi,
>>
>> I tried to zoom in, make it large,
>>
>> but seems not work, neither,
>> zoom
>> zoom complete 1 or 0
>> zoom center
>>
>> Thanks for some suggestions,
>>
>> --
>> Best Regards,
>>
>> lina
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
>



-- 
Best Regards,

lina

Hi Lina,

if you are looking for a way to "zoom in", use your right mouse button 
or type:

move z, 10

The "zoom" command however will set the current view to cover the given 
atom selection (or all if no selection is given).

http://pymolwiki.org/index.php/Move
http://pymolwiki.org/index.php/Zoom

Cheers,
   Thomas

On 09/21/2011 04:47 PM, lina wrote:
> Hi,
>
> I tried to zoom in, make it large,
>
> but seems not work, neither,
> zoom
> zoom complete 1 or 0
> zoom center
>
> Thanks for some suggestions,
>
> --
> Best Regards,
>
> lina

-- 
Thomas Holder
MPI for Developmental Biology