Hello professor,
Now I have a new question: how to label the selected CA atoms with strings
representing mutations, like "T123D", "K339R", etc?
I tried to use these commands:
select CAs, resi 123+339
mut = ["T123D", "K139R", "G223S", "M321S"]
label CAs, mut.pop
but I found that the labels are put in the wrong positions. So what is the
correct way the show the labels for mutations?
Best regards
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozdemir.gene...@gmail.com>
Send Time:2022年1月19日(星期三) 14:05
To:孙业平 <sunyep...@aliyun.com>
Subject:Re: [PyMOL] How to label atom at proper positions?
You can modify the previous script like this,
# ONE LETTER CODES
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "%s%s" % (one_letter[resn],resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping <sunyep...@aliyun.com>, 19 Oca 2022 Çar, 06:43 tarihinde şunu yazdı:
Dear Professor Halil İbrahim Özdemir,
Thank you for your help. The labels shown now are fomatted as "(THR339)",
"(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the
parentheses, like "T339", "S308".
Thank you again.
Best,
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozdemir.gene...@gmail.com>
Send Time:2022年1月18日(星期二) 18:50
To:孙业平 <sunyep...@aliyun.com>
Subject:Re: [PyMOL] How to label atom at proper positions?
Hi Sunyeping,
You can easily apply the following script from PyMOL terminal. Have a nice days.
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping via PyMOL-users <pymol-users@lists.sourceforge.net>, 18 Oca 2022 Sal,
13:14 tarihinde şunu yazdı:
Dear pymol users,
I select a series of CA atoms in a structure in pymol and show them as sphere
in pymol and want to label them. If using the label menu at the up-right conner
of pymol, the labels shown overlaps with spheres and can not be seen. So I wish
to show the labels at a bit distance from the seleccted atoms. Is there a
method to do that? I will appreciate to any help!
Best regards
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