Re: [PyMOL] How to label atom at proper positions?
Hello Professor,
That's great. Finally, is it possible to show mutation information in the
labels, like "T389S", "R201E", etc.?
Best
--
From:Halil İbrahim Özdemir
Send Time:2022年1月19日(星期三) 14:05
To:孙业平
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 , 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
Send Time:2022年1月18日(星期二) 18:50
To:孙业平
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 , 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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[PyMOL] Virtual Annual CCP4/APS Crystallographic School (2022) in the US
Dear Colleagues, We are pleased to announce the virtual annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 13-24, 2022 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2022/index.php. Dates: June 6 (Bioinformatics & setup) and June 13 through 24, 2022 (with a weekend break on June 18 and 19th) Location: Virtual/Remote The school comprises two parts: remote data collection workshop and virtual crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA at APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants’ crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft of the program, contact info and other details can be found at the School website. Note that for the virtual school, an additional day (June 6th, 2022) was scheduled to prepare for the main event, with lectures on generating AlphaFold models to use in later part of the school. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 15th, 2022. To apply, visit https://www.ccp4.ac.uk/schools/APS-2022/application.php. Fees: There is no fee for attending the virtual school for the chosen applicants. We hope to see you at the school. Charles, Andrey, Garib and Qingping ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
