[PyMOL] What's wrong with my pymol script?

[Dd H]

Hi everyone,
I want to render images of frames of my trajectory that loaded in pymol
with the script below. After running this script, pymol outputs images and
they are all the same. So what's wrong with my script?

for i in range(1, cmd.count_states()+1):
 cmd.set("state", i, "traj")
 cmd.png("%d.png" % (i), width=10, height=10, dpi=300)
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Re: [PyMOL] Modeling protein-dna complex

[Sampson, Jared M.]

Hi soumi - 

A command-line version of what David said is the following:

save new_complex.pdb, protein_selection or dna_selection

where `protein_selection` and `dna_selection` include all the atoms you want to 
have in the final PDB.  They could be object names if you have each protein and 
the DNA in separate objects.

Hope that helps.

Cheers,
Jared

> On Aug 13, 2016, at 12:15 PM, David Hall  wrote:
> 
> Select the protein you want and the dna, then save the selection as a PDB.
> 
> There are many ways to make a selection; visually, the easiest might be:
> 
> You said you’ve removed the DNA from the protein-dna complex, so now you 
> should have:
> 
> (1) an object that has just your protein that you want in the complex
> (2) an object that has just your DNA that you want in the complex
> 
> In the bottom right, where it typically says “Selecting Residues”, click 
> where it says Residues until that it says “Objects”
> 
> Click on your protein
> 
> Click on your dna
> 
> Click on File->Save Molecule and save “sele” as a PDB file.
> 
>> On Aug 13, 2016, at 8:22 AM, soumi  wrote:
>> 
>> Hi,
>>I carry on my research work on protein-dna complex system.I have one dna 
>> pdb and one protein-dna complex pdb.I want to make new protein-dna complex 
>> pdb taking  dna from single pdb and protein from protein-dna complex.Protein 
>> possess similar DNA-binding specificities.I superimpose two pdb file and 
>> remove dna from protein-dna complex pdb .But I can not save new protein-dna 
>> complex.Please let me know by pymol how I would be able to model of the 
>> referred paper was done.
>> Thanks
>> soumi
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>> patterns at an interface-level. Reveals which users, apps, and protocols are 
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
>> J-Flow, sFlow and other flows. Make informed decisions using capacity 
>> planning reports. 
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> 
> 
> --
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> patterns at an interface-level. Reveals which users, apps, and protocols are 
> consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
> J-Flow, sFlow and other flows. Make informed decisions using capacity 
> planning reports. http://sdm.link/zohodev2dev
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consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. http://sdm.link/zohodev2dev
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Re: [PyMOL] What's wrong with my pymol script?

[Sampson, Jared M.]

Hi Dd H -

`cmd.set` is the wrong command to use here.  (It's for changing settings, not 
for going through states, although some settings can be applied to only a 
specific state).

Instead, you should use `cmd.frame(i)` to move to that frame (state) number.

Note that the `width` and `height` arguments to 
`cmd.png` are in pixels unless you include 
a unit suffix like '10in' or '10cm', and it also takes a `ray` keyword argument 
if you want to ray trace for a nicer image.  Also, this is in a PyMOL (.pml) 
script instead of a Python (.py) script, you need to enclose any statement that 
requires multiple lines (i.e. loops, if/else, etc.) within a `python` block.

```
python
for i in range(1, cmd.count_states()+1):
 cmd.frame(i)
 cmd.png("%d.png" % (i), width='10in', height='10in', dpi=300, ray=1)
python end
```

Hope that helps.

Cheers,
Jared


On Aug 14, 2016, at 9:48 AM, Dd H mailto:ddhe...@gmail.com>> 
wrote:

Hi everyone,
I want to render images of frames of my trajectory that loaded in pymol with 
the script below. After running this script, pymol outputs images and they are 
all the same. So what's wrong with my script?

for i in range(1, cmd.count_states()+1):
 cmd.set("state", i, "traj")
 cmd.png("%d.png" % (i), width=10, height=10, dpi=300)

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. 
http://sdm.link/zohodev2dev___
PyMOL-users mailing list 
(PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. http://sdm.link/zohodev2dev___
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