Re: [PyMOL] sequence in the image

[Jason Vertrees]

Hi Osvaldo,

There is currently no way to do this. If you'd like to see it
implemented, please file it on the PyMOL open-source feature tracker.

Cheers,

-- Jason

On Fri, Jan 20, 2012 at 8:21 PM, Osvaldo Martin  wrote:
> Hi,
>
> PyMOL has an option to save the current view as an image, but it is possible
> to include the sequence in the image?
>
> Cheers,
>
> Osvaldo
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
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[PyMOL] Mutagenesis wizard

[James Starlight]

Dear PyMol users!

I've desided to make this topic for my questions linked with the
mutagenesis wizard setup.


First of all I've already tried to make some point mutations in my proteins
and all worked perfect. I just want ask about definition of the new
torsions for the mutated residue. E.g I have no problems with the backbone
torsions ( I've made it as in the old residue) but the new side chain is
always in the linnear possition. How I could define this Chi angles of the
mutated residue? E.g I have another pdb structure where such residue was
already present in the suitable orientations. How I could obtain Chi values
for this residue and copy it to the  mutated residue?



James
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Re: [PyMOL] Protein-ligand interactions

[James Starlight]

Thanks Thomas

I've just one extra question about ligand sites.

As I've said previously I can obtain information about polar contacts
between ligand and its surrounding residues via Present- ligand sites.

On the next step I mask all other non relevant parts of the protein ( wich
are represented as the cartoon) by

hide cartoon

so as the consequence I have only ligand and its environment ( other
residues and some water)

How I could select all this visible (relevant) part and save it in the
separate pdb?
I've not found such simple selection by the visible part in the selection
algebra :(

James

2012/1/20 Thomas Holder 

> Hi James,
>
>
>  1- Some of my proteins consist of ligand wich include some of amino
>> acids from sequence of my protein ( e.g fluorophores in GFP). So I'd
>> like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly
>> motif in GFP). How I could do it?
>>
>
> The preset selects hetatoms as ligands, so you could do:
>
> select motif, (pepseq SYG) and not (name C+N+O)
> alter motif, type="HETATM"
>
>
>  2- In some cases there are relatively long distances between polar
>> ligand groups and protein's polar residues where H-bond must be formed (
>> eg in some cases up to 3.5-3.7 A ). So the default  a-> present->ligands
>> sites-> cartoon  does not recognize that long H-bonds. How I could set
>> the H-bond cutoff distance in the above method?
>>
>
> there are several h_bond_* settings that control this. (I recommend
> http://pymolwiki.org/index.**php/Grepsetto
>  find settings) For example:
>
> set h_bond_cutoff_center, 5.0
> set h_bond_cutoff_edge, 4.0
>
>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
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