Hi there,
This works perfect. Indeed, I was wondering how to extract position data.
This is very useful.
Thanks a million!
On Tue, May 6, 2014 at 7:58 PM, Sampson, Jared <jared.samp...@nyumc.org>wrote:
> Hi Mary -
>
> If you already know which state has the conformation you want to use for
> your measurement, or if you want to create a pseudoatom for each state, you
> can do so by passing the `state` keyword to pseudoatom:
>
> set state, 1 # or 2, 3, etc.
> pseudoatom test, pdbfile_0001 and chain A and resi 100 and n.
> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue, state=1 # or 2, 3, etc.
>
> You also may be interested in the iterate_state function.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
> On May 6, 2014, at 9:32 AM, M. Faridounnia <faridoun...@gmail.com> wrote:
>
> Thanks a lot for the tip and explaining the whole thing, Jared. I
> learned a lot from that. It worked but here is why I had a problem at the
> beginning (and tried the command I emailed), still same problem persists.
>
> I had tried similar command on one of the models after splitting the pdb
> file (split_states pdbfile, ) and it was not working.
> >split_states pdbfile,
> >pseudoatom test, pdbfile_0001 and chain A and resi 100 and n.
> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue
>
>
> Now, I tried exactly what you mentioned. After splitting the states it
> doesn't work, but when I don't do split_states, the same command works and
> creates a pseudoatom. The problem is that the NMR structure I have been
> doing split_states on is an average structure of 20 models. So, I need to
> create the pseudoatom on one of the 20 structure models ( the closest to
> the average or the lowest energy). It is not a big deal for now because for
> these two residues all the 20 structure are very similar but I still wonder
> why isn't it possible!
>
> I mean it would make more sense that the command doesn't work on the
> average structure, because it doesn't refer to a real coordinate in the
> file and it can take any of the twenty models, but when it knows which
> model to take, it is more probable to work because it refers to the right
> coordinates. Any comments on that?
>
> Cheers
> Mary
>
>
> On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared <jared.samp...@nyumc.org>wrote:
>
>> Hi Mary -
>>
>> There are a couple problems here. First, you’re giving the pseudoatom
>> command a positional argument out-of-order (and after keyword parameters).
>> Keyword parameters can appear in any order, but only if you use the
>> keyword. Otherwise, you must list them in the order specified by the
>> function. So, you either need to use the keyword and enclose the selection
>> in quotes (selection=“n. …”) or simply move it to its proper position, like
>> this:
>>
>> pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue
>>
>>
>> For the full order of arguments, see
>> http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom`
>> on the PyMOL command line.
>>
>> Second, your current selection is going to use any atom named
>> cg+cd1…etc. in the entire session, not just in your single Phe residue.
>> This is because the resi=100 and color=tv_blue are used to determine the
>> properties of the new pseudoatom, and not to determine or refine the
>> selection. If you want to use the ring of Phe 100 only, the selection
>> argument needs to include that information. If you have more than one
>> object or chain that includes resi 100, you will also need to specify that.
>>
>> So I’m guessing what you probably want is something along the lines of
>> (replacing “myobject” and “A” with appropriate values):
>>
>> pseudoatom test, myobject and chain A and resi 100 and n.
>> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue
>>
>>
>> which will create a tv_blue-colored pseudoatom in the center of the
>> ring of residue 100.
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>>
>>
>>
>> On May 4, 2014, at 2:12 PM, M. Faridounnia <faridoun...@gmail.com> wrote:
>>
>> Hi there,
>>
>> I want to measure the distance and angle between an aromatic ring
>> (phenylalanin and a residue backbone) like this:
>> http://www.pymolwiki.org/index.php/File:Pseu1.png
>>
>> I learned from here that I need to make a pseudoatom but I cannot make
>> it work.
>>
>> I tried
>> pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2
>>
>> and some other ways! I don't know how should I choose the write atoms
>> and make the pseudoatom. After this probably distance and angle measurement
>> would be straightforward.
>>
>> Best regards
>> Mary
>>
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