Re: [PyMOL] [pymol] Assembly
Hi Matthias, try dragging the pdb file into the center of the Pymol Viewing screen, thanks:) On Sun, Sep 22, 2024 at 12:21 PM Matthias Mayer < m.ma...@zmbh.uni-heidelberg.de> wrote: > To whom it may concern, > > I wanted to load a cryoEM structure of a virus-like particle (7epp.pdb1) > into pymol 2.5.0. But instead of showing all the subunits, when I open > the file, it makes a movie out of it with individual framesIs there a > way to prevent this and just show the entire assembly? > > Also when I used the single file 7epp.cif and used the command generate > symmetry mates, it makes weird things, overlaying all the structures > with only a small translational offset and not rotation. > > Thanks for any suggestions. > > Best regards > > Matthias > > -- > = > Prof. Dr. Matthias P. Mayer, SFCSSI > Center for Molecular Biology of Heidelberg University (ZMBH) > Im Neuenheimer Feld 345, room 161 > D-69120 Heidelberg > Germany > > Tel. +49 6221 546829 > > > > _______ > 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 > ___ 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
Re: [PyMOL] [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US
Hello Crystallographic School please keep me in mind if in need of any instructors, profile below in bold and attached, thanks:), Joel 🚀 *Hello HR I hope you're well:).* *I am a 56 year old American Rutgers University PhD in Biomedical Informatics/Nanomedicine exhibiting expertise in ion channel Pannexin1 computational transmembrane protein design towards pharmacophore ligand discovery and am interested in the above position.SInce my PhD graduation in 2020 I have been computationally investigating Panx1 and completed its molecular modeling and am now optimizing the best ligand i.e. QM via ORCA.* *Best,* *Joel 🚀* On Thu, Aug 15, 2024 at 10:04 PM Xu, Qingping via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > Please note that we are still accepting applications, interested students > are encouraged to apply before the deadline. A draft program is available > at the course website. > > Charles, Andrey and Qingping > > -- > *From:* CCP4 bulletin board on behalf of Qingping > Xu <292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Monday, April 8, 2024 1:26 PM > *To:* ccp...@jiscmail.ac.uk > *Subject:* [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) > in the US > > This Message Is From an External Sender > This message came from outside your organization. > > > Dear Colleagues, > > We are pleased to announce the 16th annual CCP4/APS crystallographic > school “From data collection to structure refinement and beyond” will be > held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS), > Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All > details can be found at the school website: > https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. > This will be our first > work post the APS-U upgrade. > > > Dates: October 28 through November 4, 2024 > > Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near > > Chicago), Illinois, USA > > The school comprises two parts: data collection (provisional pending APS > availability) workshop and crystallographic computing workshop. Data > collection workshop includes beamline training, data collection on > GM/CA@APS beamlines, and data processing, using only the participants' > crystals. Crystallographic computation workshop will feature many modern > crystallographic software packages taught by authors and other experts. > This workshop will also introduce elements of CryoEM. The daily schedule > will be organized in three sections – lectures, tutorials, and hands-on > (interactive trouble-shooting of the technical difficulties the > participants face in their projects). We have had considerable success > resolving these problems in past years, attested by resulting > publications (see > https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). > A draft > program can be found at the School website. > > Applicants: The workshop strongly encourages students who need expert > help with difficulties/challenges in their own projects. 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. > > Application: Application deadline is August 31st, 2024. To apply, > visit > https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$ > > Fees: There is a $500 participation fee for the selected academic > students and $1500 for industrial researchers. No credit card will be > required for registration, students who are selected to participate will > be contacted to pay. The students will be responsible for their > transportation and lodging. The workshop organizers can assist in making > lodging reservations at the Argonne Guest House. The workshop will cover > all other expenses (including meals). > > > We hope to see you at the school. > > Charles, Andrey, Garib and Qingping > > > > To unsubscribe from the CCP4BB list, click the following > link:https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$ > > This mess
Re: [PyMOL] [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US
Please note that we are still accepting applications, interested students are encouraged to apply before the deadline. A draft program is available at the course website. Charles, Andrey and Qingping From: CCP4 bulletin board on behalf of Qingping Xu <292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk> Sent: Monday, April 8, 2024 1:26 PM To: ccp...@jiscmail.ac.uk Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US This Message Is From an External Sender This message came from outside your organization. Dear Colleagues, We are pleased to announce the 16th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. This will be our first work post the APS-U upgrade. Dates: October 28 through November 4, 2024 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection (provisional pending APS availability) workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines, and data processing, using only the participants' crystals. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. This workshop will also introduce elements of CryoEM. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). A draft program can be found at the School website. Applicants: The workshop strongly encourages students who need expert help with difficulties/challenges in their own projects. 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. Application: Application deadline is August 31st, 2024. To apply, visit https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$ Fees: There is a $500 participation fee for the selected academic students and $1500 for industrial researchers. No credit card will be required for registration, students who are selected to participate will be contacted to pay. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Andrey, Garib and Qingping To unsubscribe from the CCP4BB list, click the following link: https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$ This message was issued to members of https://urldefense.us/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUIlqrIeo$, a mailing list hosted by https://urldefense.us/v3/__http://www.jiscmail.ac.uk__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUyfFpMcY$, terms & conditions are available at https://urldefense.us/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUuFJW2bU$ ___ 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
Re: [PyMOL] Deprecation of MMTF-format files for the PDB archive
Jose, I have a few questions about the BCIF format. Adding pymol-users because there might be interest there as well (at least among developers). First, at PDBe, where is the link for downloading BCIF files for a given structure? I only see this, for example, at https://www.ebi.ac.uk/pdbe/entry/pdb/4hhb [image: image.png] Any plan to include BCIF there? Second, I am not finding a definitive description of distinguishing among MMFF and various types of BCIF files, since the same internal MessagePack format is used for all. Is there a reliable and future-proof way of doing this short of parsing the whole byte stream with a MessagePack reader and checking for map keys or values? That does not seem to me a very efficient way of processing byte streams. I had thought perhaps the initial map value for "encoder" would suffice, but now I see that that is not reliable. For example, the density server declaration in older BCIF files now refers to "volume-server". Suggestions? Bob ___ 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
[PyMOL] Antw: Re: .phs files in pymol
Thank you so much! Best, Urban >>> Takanori Nakane 30/07/2024 13:01 >>> Hi, Open the map in Coot and select [File]-[Export Map]. This allows you to save the map in .ccp4 (= .mrc) format, which PyMOL can read. Best regards, Takanori Nakane On 7/30/24 20:17, Urban Leitgeb via PyMOL-users wrote: > Hi, > > I calculated anomalous difference maps with shelx and got .phs > files as output. I can open them in coot, but not in pymol. > I have read that I have to convert them to .mtz or rather calculate > a map. Can anyone tell me how to do that? > > Thanks, > Urban > > > ___ > 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 ___ 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
[PyMOL] .phs files in pymol
Hi, I calculated anomalous difference maps with shelx and got .phs files as output. I can open them in coot, but not in pymol. I have read that I have to convert them to .mtz or rather calculate a map. Can anyone tell me how to do that? Thanks, Urban ___ 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
[PyMOL] open source installation on Windows broken?
At https://pymolwiki.org/index.php/Windows_Install the process fails for 3. Download the appropriate wheel files <http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source>, which is a dead link. Does anyone know how to run open source PyMOL on Windows OS? Bob Hanson ___ 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
[PyMOL] BCIF
Seeing as MMTF is being deprecated, I am wondering if efforts are underway to allow PyMOL to read the BinaryCIF format? Bob Hanson >From July 2024 the PDB file archive will not be offered in the compressed > MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF > format <https://github.com/molstar/BinaryCIF>, which has been available > since 2020. Details on how to access BinaryCIF (BCIF) data files for the > entire PDB archive are available here > <https://www.rcsb.org/docs/programmatic-access/file-download-services#pdb-entry-files> > . > RCSB PDB support is ready to assist with any issues or questions at i...@rcsb.org. --- Jose Duarte RCSB Protein Data Bank San Diego Supercomputer Center UC San Diego La Jolla CA, USA -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* ___ 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
[PyMOL] help
I want to ask for your help. The circumstances is I want to download a license file, but when I click it, it appears a error,just like the picture shows.So how can I solve that?<> ___ 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
Re: [PyMOL] [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US
hp__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. This will be our first work post the APS-U upgrade. Dates: October 28 through November 4, 2024 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection (provisional pending APS availability) workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines, and data processing, using only the participants' crystals. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. This workshop will also introduce elements of CryoEM. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). A draft program can be found at the School website. Applicants: The workshop strongly encourages students who need expert help with difficulties/challenges in their own projects. 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. Application: Application deadline is August 31st, 2024. To apply, visit https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$ Fees: There is a $500 participation fee for the selected academic students and $1500 for industrial researchers. No credit card will be required for registration, students who are selected to participate will be contacted to pay. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Andrey, Garib and Qingping To unsubscribe from the CCP4BB list, click the following link: https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$ This message was issued to members of https://urldefense.us/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUIlqrIeo$, a mailing list hosted by https://urldefense.us/v3/__http://www.jiscmail.ac.uk__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUyfFpMcY$, terms & conditions are available at https://urldefense.us/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUuFJW2bU$ ___ 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
Re: [PyMOL] How to obtain a PyMOL selection within Python
Here is the solution. Wonder if someone can help explain why the line below
gives an error about print is not defined:
out=x.cmd.do("iterate mysel and name CA, print(resi)")
Thanks!
import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20")
out=[]
def f(chain, resi): out.append((chain,resi))
myspace={'f':f}
x.cmd.iterate("mysel and name CA", "f(chain, resi)", space=myspace)
print(out)
From: Zhou, Yingyao
Sent: Tuesday, May 28, 2024 3:57 PM
To: pymol-users@lists.sourceforge.net
Subject: How to obtain a PyMOL selection within Python
Hi,
In the example code below, there is a selection object "myself" within PyMOL, I
try to obtain the selected residues within Python.
The "out=x.cmd.do" prints the selection to stdout, but the variable out remains
None. What would be a good way to get the selection without going through disk
I/O?
import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20")
out=x.cmd.do("iterate mysel and name CA, (resi)")
print(out)
A separate question, when I run the following line of Python, I got an error
(however the command works using PyMOL's command interface):
out=x.cmd.do("iterate mysel and name CA, print(resi)")
I got an error:
return _cmd.alter(_self._COb, selection, expression, True,
File "", line 1, in
NameError: name 'print' is not defined
What's the syntax error in this line?
Thank you,
Yingyao
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[PyMOL] How to obtain a PyMOL selection within Python
Hi,
In the example code below, there is a selection object "myself" within PyMOL, I
try to obtain the selected residues within Python.
The "out=x.cmd.do" prints the selection to stdout, but the variable out remains
None. What would be a good way to get the selection without going through disk
I/O?
import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20")
out=x.cmd.do("iterate mysel and name CA, (resi)")
print(out)
A separate question, when I run the following line of Python, I got an error
(however the command works using PyMOL's command interface):
out=x.cmd.do("iterate mysel and name CA, print(resi)")
I got an error:
return _cmd.alter(_self._COb, selection, expression, True,
File "", line 1, in
NameError: name 'print' is not defined
What's the syntax error in this line?
Thank you,
Yingyao
_______
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[PyMOL] Exporting movie as PNG frames produces only single frame
Hi, I'm currently trying out the improved movie functions of PyMOL 3.03 (timeline, scenes) which I think are a great improvement. However, I noticed when I want to write out a composition as single frames (PNG) using the 'Export movie' function only one frame gets written (the first one). When exporting as MPEG1 movie the composition is exported normally (all frames). I also noticed creating a composition does not trigger the display of the 'global frames panel', while in PyMOL 2.x adding a movie program (e.g. scene loop) would display (and update) the number of frames the movie contains. In contrast, creating a morph (e.g. over 30 states) will trigger the 'global frames' panel showing 30 frames. When creating a 'state sweep' movie from the morph using the movie commands the corresponding 60 frames are shown (and played) in the timeline, but the 'global frames' panel still shows only 30 frames. Also exporting the frames as PNGs will only export the first 30 frames representing the different states, while the MPEG1-export function will export the full state sweep movie. I tried this with PyMOL 3.03 running under Linux and also Windows 10. The observed behavior is the same. Is there anything that's wrong in my approach? Christoph ___ 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
[PyMOL] labels on nucleic acids
Hi Am using pymol 3. Am I correct in thinking that you can't use the 'label' dialogues to label nucleotides in a nucleic acid? Only proteins? Thanks Joel - Professor Joel Mackay School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 E: joel.mac...@sydney.edu.au<mailto:joel.mac...@sydney.edu.au> | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org> ___ 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
Re: [PyMOL] create new object from selection - version 3.0
Thanks very much for the response Jarrett – great to know it’s been ID-ed and is in the process of being mended. J - Professor Joel Mackay School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 E: joel.mac...@sydney.edu.au<mailto:joel.mac...@sydney.edu.au> | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org> From: Jarrett Johnson Sent: Tuesday, April 2, 2024 2:57 PM To: Joel Mackay Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] create new object from selection - version 3.0 Hi Joel, Thanks for your feedback. You're correct in both assessments. I can reproduce the first issue (the `copy to object` menu should produce a submenu), and should be able to get a fix for that very soon. There are some submenu quirks that are still being ironed out; some of which, at least for linux, are also being addressed this week--but all still ongoing. Best, Jarrett J. On Mon, Apr 1, 2024 at 10:16 PM Joel Mackay via PyMOL-users mailto:pymol-users@lists.sourceforge.net>> wrote: Hi I’ve always found the command allowing you to create a ‘cloned’ object from a selection to be extremely useful. That is, select a chain (for example) and then use: Action > copy to object > new This seems to be disabled in version 3. You can extract a chain that you’ve selected, but not make a fresh copy. Am I just missing something? [It also seems a bit strange that submenus now don’t disappear as you scroll down the list of possible actions, until you reach the next command that has a submenu – it’s a bit disconcerting] Thanks Joel [cid:image001.png@01DA8513.C8E14410] - Professor Joel Mackay School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 E: joel.mac...@sydney.edu.au<mailto:joel.mac...@sydney.edu.au> | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/N7OGCROND2unrxr95T91Df2?domain=mackaymatthewslab.org> _______ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net<https://url.au.m.mimecastprotect.com/s/PwWXCVARKgC0lYlrgizgjgY?domain=mail-archive.com> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://url.au.m.mimecastprotect.com/s/RukhCWLVXkUzjVj7DSKq6AH?domain=sourceforge.net> -- Jarrett Johnson | Senior Developer, PyMOL [Image removed by sender.] ___ 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
[PyMOL] create new object from selection - version 3.0
Hi I've always found the command allowing you to create a 'cloned' object from a selection to be extremely useful. That is, select a chain (for example) and then use: Action > copy to object > new This seems to be disabled in version 3. You can extract a chain that you've selected, but not make a fresh copy. Am I just missing something? [It also seems a bit strange that submenus now don't disappear as you scroll down the list of possible actions, until you reach the next command that has a submenu - it's a bit disconcerting] Thanks Joel [cid:image001.png@01DA84FA.CEE5D470] - Professor Joel Mackay School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 E: joel.mac...@sydney.edu.au<mailto:joel.mac...@sydney.edu.au> | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org> ___ 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
[PyMOL] parameters for cation-pi identification
Dear All, I am wondering what parameters (cutoff distance, angles, side chains relative orientations) are used by the functions implemented in pymol (distance (mode =7 and A>find>pi-cation))to define cation-pi interaction. I didn’t find it in the documentation. Is there any way to eventually tune these parameters? Thank you for your responses, Best, Julien När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/om-ki/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://staff.ki.se/data-protection-policy>. ___ 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
[PyMOL] Align command and alternate residue conformations
Dear all, I would like to compare two crystal structures of the same protein, one obtained by X-ray diffraction and the other by neutron diffraction. I used the Align command in PyMOL with zero cycles of refinement to align these structures and obtain a rmsd between all non-H/D protein atoms. However, I would like to understand how Align calculates the rmsd, specifically how does it handle alternate residue conformations. Does it pair side-chain conformations based on their name (e.g. A, B, C..) or on their spatial proximity (i.e., conformations are paired regarding their position). I can imagine 2 scenarios that might be problematic: 1) where the side-chain conformations closer in space have different names; 2) where one structure has a double side-chain conformation, and the other has a single conformation. Best regards, Joao Ramos ___ 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
[PyMOL] Questions about licenses
Hello, all. My name is Alex Zatuchney, and I am a full-time high school student that is looking to use PyMOL to generate renders for both self-study and a possible research paper for the AP Research program. At some point, I would like to publish this research. Since I am a full-time student, would I be able to include PyMOL renders in a hypothetical research paper with the free, educational-use license? Thank you so much in advance, Alex ___ 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
Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol
Hello, I installed PyMol 2.5.7 and ran APBS electrostatic. However, I got the error: Error encountered: No heavy atoms found. You may also see this message if PDB2PQR does not have parameters for any residue in your protein. The point is: I am evaluating molecules (acesulfame potassium, in this case) and not whole proteins. If the APBS has worked but could not compute, then I the answer is asnwered. Thank you. Sent with [Proton Mail](https://proton.me/) secure email. On Sunday, November 26th, 2023 at 1:13 PM, Luigi Marongiu, PhD via PyMOL-users wrote: > Hello, > I am using Version 2.5.0, if I not mistaken, I installed it via apt-get: > > sudo > > apt-get > > -y > > install > > pymol > > In the legacy tab, there is nothing... > Thank you > > On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) > wrote: > >> Hi Luigi , >> >> Please include the version of PyMOL that you are using. >> The APBS Tools are under the "legacy plugins" in the incentive version >> (2.5.7). >> These are absent in the open source PyMOL (2.5.0). >> >> There was a relatively recent change in the Python libraries used to generate >> the widgets in PyMOL. You may have gotten an error about a missing Pnw module >> when trying to load the plugin with a recent version of the open source >> PyMOL. >> To use the plugin on the Wiki, you try an older version of PyMOL. >> Hopefully, someone who is more knowledgeable about plugins will provide a >> better answer. >> >> Best regards, >> >> Blaine >> >> --- >> >> From: Luigi Marongiu, PhD via PyMOL-users >> Sent: Saturday, November 25, 2023 2:02 AM >> To: pymol-users@lists.sourceforge.net >> Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol >> >> Hello, >> I tried to install APBS by launching Plugin manager and giving the URL of >> the app: >> >> [http://www.pymolwiki.org/index.php/apbsplugin](https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$) >> >> The file has been written in ~/.pymol/startup but I got the error: >> >> Plugin "apbsplugin" has been installed but initialization failed. >> >> How do I properly launch this app? Please note I relaunched PyMol several >> times. >> Thank you. >> >> Sent with [Proton >> Mail](https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$) >> secure email.___ 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
Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol
Hello, I am using Version 2.5.0, if I not mistaken, I installed it via apt-get: sudo apt-get -y install pymol In the legacy tab, there is nothing... Thank you On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) wrote: > Hi Luigi , > > Please include the version of PyMOL that you are using. > The APBS Tools are under the "legacy plugins" in the incentive version > (2.5.7). > These are absent in the open source PyMOL (2.5.0). > > There was a relatively recent change in the Python libraries used to generate > the widgets in PyMOL. You may have gotten an error about a missing Pnw module > when trying to load the plugin with a recent version of the open source PyMOL. > To use the plugin on the Wiki, you try an older version of PyMOL. > Hopefully, someone who is more knowledgeable about plugins will provide a > better answer. > > Best regards, > > Blaine > > ------- > > From: Luigi Marongiu, PhD via PyMOL-users > Sent: Saturday, November 25, 2023 2:02 AM > To: pymol-users@lists.sourceforge.net > Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol > > Hello, > I tried to install APBS by launching Plugin manager and giving the URL of the > app: > > [http://www.pymolwiki.org/index.php/apbsplugin](https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$) > > The file has been written in ~/.pymol/startup but I got the error: > > Plugin "apbsplugin" has been installed but initialization failed. > > How do I properly launch this app? Please note I relaunched PyMol several > times. > Thank you. > > Sent with [Proton > Mail](https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$) > secure email.___ 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
[PyMOL] How to install APBS on PyMol
Hello, I tried to install APBS by launching Plugin manager and giving the URL of the app: http://www.pymolwiki.org/index.php/apbsplugin The file has been written in ~/.pymol/startup but I got the error: Plugin "apbsplugin" has been installed but initialization failed. How do I properly launch this app? Please note I relaunched PyMol several times. Thank you. Sent with [Proton Mail](https://proton.me/) secure email.___ 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
[PyMOL] How to drag molecule in the pane with pymol
Hello, I have one molecules and I am importing a second one in the same file. The second molecule comes on top of the first one. How do I drag the second molecule around so that it does not overlap with the first? If I choose 'drag matrix', I can rotate the second molecule in the z axis. How can I move along the x/y axis? Thank you___ 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
[PyMOL] Get list of bound residues for al poses on PyMol
I can find the polar contact between my target and a ligand, but is it possible to get a table with all the bound residues and for all the poses, instead of manually finding the involved residues one by one? Thank you.___ 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
[PyMOL] How to delete/hide unwanted poses in Pymol?
Hello, I have several poses from a docking to a protein and I have different ligands to compare. I can load on PyMol the different ligands on a same protein file, and I can look at each pose for the different ligands but only, let's say, in sync: pose 1 of ligand 1 together with pose 1 of ligand 2; pose 2 of ligand 1 together with pose 2 of ligand 2; and so forth. Let's say that I am interested in comparing pose 3 of ligand 1 and pose 8 of ligand 2. How can I hide or delete the unwanted poses? Thank you.___ 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
Re: [PyMOL] help with PyMOL rename command
Thank You a lot indeed explanation ways more clear than the wiki one https://pymolwiki.org/index.php/Rename https://pymolwiki.org/index.php/Rename I know I should have tried more Again Thanks___ 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
[PyMOL] help with PyMOL rename command
Hi need help with PyMOL rename command: from https://pymolwiki.org/index.php/Rename : Rename rename creates new atom names which are unique within residues. USAGE CURRENT rename object-name [ ,force ] force = 0 or 1 (default: 0) PROPOSED rename object-or-selection,force NOTES To regerate only some atom names in a molecule, first clear them with an "alter (sele),name=“ commmand, then use "rename” ... Does 'rename test' create 'test' atom name ?? If so how do I apply it to a selection ? I know how to use set_name to change an object/selection name : https://pymolwiki.org/index.php/Set_name or alter to change a property over a selection : https://pymolwiki.org/index.php?title=Alter&redirect=no Cannot figure out how rename works ___ 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
[PyMOL] PyMol Education license
Hello, I am teaching at the Hanze University Groningen and I have used PyMol in two courses (Bioinformatics and Biochemistry) for a couple of years now without any problems. However, this year I have tried twice to get the educational license, but I did not receive the file with the license as it did the previous years. Some of my colleagues have tried as well, but with the same result: no license file received. I hope you someone can help me get the license so we can use PyMol again for our courses. Thank you. Kind regards, Mark ___ 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
[PyMOL] Need help in calculating buried surface area
Hello Everyone, I am trying to find a way to calculate the buried surface area in a complex with 2 molecules using pymol. Can anyone direct me to the correct way to do it? I am currently trying out the following method, and I need to find out if there is anything else I need to do to do this calculation. (Sum of Obj1+Obj2 solvent accessible surface area)- (solvent accessible area of the complex of Obj1-Obj2) Thanks in advance! Best, Shreya This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ___ 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
[PyMOL] separate two molecule as an object from a complex of four molecules
Public Hello All, I am trying to separate out two molecules(one copy for each of RSVF F1 and F2) from one pdb (6OUS). It's a trimeric protein bound to a Fab. I want to separate out RSVF1 and F2 proteins as one object from the bound antibody, ie create one object with only chains A,C,E and B,D,F. If you could explain the commands to use that will be really helpful to me. Thanks, Shreya Shreya Mukhopadhyay, PhD. (She/Her) Post Doc Fellow (Infectious Diseases and Vaccines-Discovery) 770 Sumneytown Pike, West Point B46, 2048-C, PA 19486 [cid:image001.png@01D9C55F.2D2C6730] This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ___ 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
Re: [PyMOL] Help with selecting interface residues between two structures
Hi, Jarrett
This is more than helpful! I just need to fix my own mistake in the selection
cmd.select(base_interface, "byres((not (/base//H+L) & base) within 10 of
/base//H+L)")
Maybe one more question:
Selection: “not (/base//H+L)” returns all residues in pred, as well as the P
chain of base. I understand this.
However, why “not /base//H+L” returns an empty selection?
Thanks!
From: Jarrett Johnson
Sent: Thursday, June 29, 2023 6:31 AM
To: Zhou, Yingyao
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Help with selecting interface residues between two
structures
This Message is from an External Sender. Do not click links or open attachments
unless you trust the sender.
Hi,
There might be a cleaner way to do this, but I propose creating a mapping of
your chains from base to pred and use the `iterate` command to get the relevant
identifiers and map them back to the prediction. Here is a full script that
pulls from the PDB that attempts this idea.
from pymol
import cmd
# our reference
cmd.fetch('3hfm',
'base')
# dummy prediction
cmd.copy('pred',
'base')
# Heavy & Light chains in 3hfm are named L and H
# Antigen is Y so lets rename to A to simulate your case
cmd.alter('base & chain Y',
'chain="A"')
# change chain to emulate same residues different chain names
cmd.alter('pred & chain L',
'chain="A"')
cmd.alter('pred & chain H',
'chain="B"')
cmd.alter('pred & chain Y',
'chain="C"')
base_interface
= 'int_base'
cmd.select(base_interface,
'byres(base & (/base//H+L around 5))')
# After preparation:
# create a mapping of chains from base to pred
base_to_pred_chains
= {'L':
'A', 'H':
'B', 'A':
'C'}
# Create a list of identifiers in the interface from the selection
myspace
= {'int_set':
set()}
cmd.iterate(base_interface,
'int_set.add((chain, resi, resn))', space=myspace)
# Map them to a new selection onto the prediction
pred_interface
= 'int_pred'
cmd.select(pred_interface,
'none')
for
chain, resi,
resn in
myspace['int_set']:
new_chain
= base_to_pred_chains[chain]
# Add each pred residue to the selection
cmd.select(pred_interface,
f'pred & chain
{new_chain} & resi
{resi} & resn
{resn}',
merge=1)
Hope that helps,
Jarrett J
On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users
mailto:pymol-users@lists.sourceforge.net>>
wrote:
I am a relatively new PyMOL user and would like to get some helps from the
community.
I have two structures for the same antibody-antigen complex (with three chains:
light chain L, heavy chain H, and an antigen chain A) .
Structure “base” is the experimental true structure, structure “pred” is the
predicted structure. My goal is to determine how close the predicted interface
is w.r.t. the experimental truth.
I first select the interface residues as defined by “base”
load base.pdb
load pred.pdb
select int_base, byres(base & (/base//H+L around 5))
How do I select the same corresponding residues in object “pred”?
In addition, what if in the pred structure, chains are named A, B, and C,
corresponding to base structure L, H, A, respectively, how will I handle that?
(I was planning to rename the chains, if there is no nice trick to transfer the
selections from base to pred)
Thanks!
_______
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--
Jarrett Johnson | Senior Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]
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[PyMOL] Help with selecting interface residues between two structures
I am a relatively new PyMOL user and would like to get some helps from the community. I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) . Structure "base" is the experimental true structure, structure "pred" is the predicted structure. My goal is to determine how close the predicted interface is w.r.t. the experimental truth. I first select the interface residues as defined by "base" load base.pdb load pred.pdb select int_base, byres(base & (/base//H+L around 5)) How do I select the same corresponding residues in object "pred"? In addition, what if in the pred structure, chains are named A, B, and C, corresponding to base structure L, H, A, respectively, how will I handle that? (I was planning to rename the chains, if there is no nice trick to transfer the selections from base to pred) Thanks! ___ 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
[PyMOL] Pymol education uses for thesis
Hi, I am currently a master of philosophy student and am using Pymol education. I will need to write a thesis and was wondering if I can use this within my thesis or not. Thanks Lauren ___ 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
Re: [PyMOL] Generating of Rg for every state in PyMOL
Hi Jarrett,
Thank you very much for your kind and comprehensive advice, really appreciate
it!
I will try it out.
Kind regards,
Jessica Lim
From: Jarrett Johnson
Sent: Thursday, May 18, 2023 8:32 PM
To: #JESSICA LIM JIAYING#
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Generating of Rg for every state in PyMOL
Hi Jessica,
It seems in the gyradius psico script, by default it will calculate the radius
of gyration for the current state. You can provide a specific state to this
argument and generate the list yourself in a script.
```
from psico.querying import gyradius
from pymol import cmd
obj = "1nmr"
cmd.fetch(obj)
# for loop
for i in range(cmd.count_states(obj)):
print(f"State {i+1}: {gyradius(obj, state=i+1)}")
# list comprehension
gy_list = [gyradius(obj, state=i+1) for i in range(cmd.count_states(obj))]
print(gy_list)
```
Hope that helps,
Jarrett J
On Thu, May 18, 2023 at 8:05 AM #JESSICA LIM JIAYING# via PyMOL-users
mailto:pymol-users@lists.sourceforge.net>>
wrote:
Hi all,
I am having difficulty in trying to print out a list of the radius of gyration
for all states in my PDB file. I have several files of 100 states each and
would like to generate a list of the radius of gyration for every individual
state. However, I have only been successful at using the command gyradius as
part of the psico package in PyMOL but it only outputs a single value, and I
would have to click manually to the next state and re-enter the command to get
the next value. Hence, I would like to be able to obtain a list of values
without having to click through 100 different states.
Any advice or suggestions on how this can be done will be greatly appreciated,
thank you!
Kind regards,
Jessica Lim
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Jarrett Johnson | Senior Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]
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[PyMOL] Generating of Rg for every state in PyMOL
Hi all, I am having difficulty in trying to print out a list of the radius of gyration for all states in my PDB file. I have several files of 100 states each and would like to generate a list of the radius of gyration for every individual state. However, I have only been successful at using the command gyradius as part of the psico package in PyMOL but it only outputs a single value, and I would have to click manually to the next state and re-enter the command to get the next value. Hence, I would like to be able to obtain a list of values without having to click through 100 different states. Any advice or suggestions on how this can be done will be greatly appreciated, thank you! Kind regards, Jessica Lim ___ 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
[PyMOL] Opening grd files from the Open3DQSAR program
Hi, I try to open grd files from the Open3DQSAR program.I do not see some significant errors, but I see nothing in the visualization window. Here is the text log from Pymol program:https://pastebin.com/qqCHDzUjHow can I resolve this issue? ___ 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
Re: [PyMOL] PLEASE HELP
Thank you SO MUCH. My computer is going into overdrive. I want to use another terminal, but I’ve spent all last night and all day today trying to figure it out. My phone number is 562-360-7713. I’m really doing whatever it takes to make this work. Thank you again. Kyle Get Outlook for iOS<https://aka.ms/o0ukef> From: Jarrett Johnson Sent: Monday, March 27, 2023 4:23:30 PM To: Kyle Moorman Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PLEASE HELP EXTERNAL EMAIL : Exercise caution when responding, opening links, or opening attachments. Hi Kyle, The approach you listed looks about right to me. Using conda commands from the PyMOL commandline in the bundles don't seem to be working in those builds, but should be fine if you use another terminal. Either way, I will reach out to you directly. Best, Jarrett J. On Mon, Mar 27, 2023 at 3:46 PM Kyle Moorman via PyMOL-users mailto:pymol-users@lists.sourceforge.net>> wrote: To whom it may concern, While I am a licensed user of PyMol, h...@schrodinger.com<mailto:h...@schrodinger.com> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse. Below is all the information I have and what I’ve sent to h...@schrodinger.com<mailto:h...@schrodinger.com> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I’ve found on pymolwiki as well as various other sites I’ve come across are not very clear at all. Below is the message I sent to h...@schrodinger.com<mailto:h...@schrodinger.com> Could you help please? Thanks in advance: PyMOL 2.5.4 Windows-10-10.0.19041-SP0 ATI Technologies Inc. AMD Radeon(TM) HD8490 4.5.13399 Compatibility Profile Context 15.201.1151.1008 PyMOL Invoice #49406 01-mar-2024 Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37 I’m requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before: To whom it may concern, I have used the following commands in attempt to download psico: I used this file path: "C:\Users\admin\PyMOL\condabin\conda.bat" In order to install this code: conda install -c schrodinger pymol conda install -c schrodinger pymol-psico conda install -c rdkit rdkit conda install -c speleo3 csb I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now. I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help. Thanks so much in advance, Kyle ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=05%7C01%7Ckmoorman2023%40fau.edu%7Cc293b855a2484d080f6608db2f012a6c%7C63c3c9c1e824413fb4352f0cabb2828f%7C0%7C0%7C638155454309873971%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZovpU7sPBR0gIkBN6GFIxDfRMCVJJQxU5fi%2Fu5JTe5E%3D&reserved=0> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=05%7C01%7Ckmoorman2023%40fau.edu%7Cc293b855a2484d080f6608db2f012a6c%7C63c3c9c1e824413fb4352f0cabb2828f%7C0%7C0%7C638155454309873971%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e1O30bUEQSki1uoIfSoKA7HZfmHmhHsWmLX%2BuSn0BVE%3D&reserved=0> -- Jarrett Johnson | Senior Developer, PyMOL [https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download] ___ 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
[PyMOL] PLEASE HELP
To whom it may concern, While I am a licensed user of PyMol, h...@schrodinger.com<mailto:h...@schrodinger.com> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse. Below is all the information I have and what I've sent to h...@schrodinger.com<mailto:h...@schrodinger.com> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I've found on pymolwiki as well as various other sites I've come across are not very clear at all. Below is the message I sent to h...@schrodinger.com<mailto:h...@schrodinger.com> Could you help please? Thanks in advance: PyMOL 2.5.4 Windows-10-10.0.19041-SP0 ATI Technologies Inc. AMD Radeon(TM) HD8490 4.5.13399 Compatibility Profile Context 15.201.1151.1008 PyMOL Invoice #49406 01-mar-2024 Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37 I'm requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before: To whom it may concern, I have used the following commands in attempt to download psico: I used this file path: "C:\Users\admin\PyMOL\condabin\conda.bat" In order to install this code: conda install -c schrodinger pymol conda install -c schrodinger pymol-psico conda install -c rdkit rdkit conda install -c speleo3 csb I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now. I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help. Thanks so much in advance, Kyle ___ 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
[PyMOL] Unable to install PyTM plugin in PyMOL
Hello PyMOL support team, I am unable to install the post-translational modification (PyTM) plugin in my PyMOL. If I try to copy-paste the PyMOLwiki or the respective repository URL in the given box under the "Install new plugins" tab (Plugin manager), it shows some error (...sscl:504, 1407742e...etc.). I would appreciate it if you could kindly assist me in sorting this out. I am using the educational version of PyMOL on Windows. Thank you in advance. Sincerely, Mily. == Dr. Mily Bhattacharya, Ph.D. Assistant Professor School of Chemistry and Biochemistry, Thapar Institute of Engineering & Technology (Deemed to be University), Thapar Technology Campus, Post Box No. 32, Bhadson Road. Patiala - 147004, Punjab, India. Email: mily.bhattacha...@thapar.edu and mil...@gmail.com Homepage: https://sites.google.com/site/milybhattacharyamohali/home ORCID: http://orcid.org/-0003-2670-6709 ___ 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
Re: [PyMOL] [ccp4bb] 15th Annual CCP4/APS Crystallographic School (onsite)
This is a reminder for students interested in attending the upcoming onsite CCP4/APS school, please submit your applications. Thanks Charles, Andrey, Garib and Qingping On 1/3/23 08:37, Qingping Xu wrote: Dear colleagues, Happy new year! This is a reminder that the registration is open for the upcoming 2023 CCP4/APS school. Please note this year school is earlier than the usual summer date (before the APS upgrade starting in middle April). Please apply if you are interested in attending in person, or forward to students who may be interested. Thanks Charles, Andrey, Garib and Qingping On 10/20/22 12:13 PM, Qingping Xu wrote: Dear Colleagues, We are pleased to announce the 15th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on March 27th to April 3rd, 2023 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-2023/index.php. This will be our first post-COVID in person workshop, scheduled before the APS upgrade shutdown. Dates: March 27 through April 3, 2023 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@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 trouble-shooting 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 program can be found at the School website. Applicants: The workshop strongly encourages students who need expert help with difficulties/challenges in their own projects. 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. Application: Application deadline is Jan 31th, 2023. To apply, visit https://www.ccp4.ac.uk/schools/APS-2023/application.php Fees: There is a $500 participation fee for the selected academic students and $1500 for industrial researchers. No credit card will be required for registration, students who are selected to participate will be contacted to pay. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Andrey, Garib and Qingping To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ _______ 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
[PyMOL] Application
I am a student. I applied for a free download voucher on the website, but I haven't sent an email to me. I hope you can reply as soon as possible. Thank you??___ 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
[PyMOL] mutagenesis - dashed yellow lines hide?
During mutagenesis dashed yellow lines appear from the main chain of the new aa with distances attached and they remain when moving through the various rotamer states. Is there a way of hiding these lines and labels? ___ 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
[PyMOL] hiding the main chain for a named selection?
Newbie here. Is there a way to script hiding the main chain for a named selection as per the GUI (H-main chain)? ___ 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
[PyMOL] Gradient colouring
Hello everyone! I am interested to know how to apply gradient colouring to the protein of my interest based on user-defined values (not b factor or RMSD). What should be the type and format of this user defined file, specifying the values? And what is the command for implementing this? It would be really useful if you could guide me to do this. Thank you, Tanaya ___ 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
[PyMOL] Mutagenesis on apo structure and/or complex with adduct atoms removed?
A single residue change in the enzyme active site confers resistant to inhibitor (adduct). Structures of apo enzyme and complexed with adduct available. Should I do the mutagenesis on the apo or on the complex after removal of the adduct atoms and relaxing the structure? When I align the apo structure with the complex or the adduct-removed structure the RMSD values are 0.47 and 0.52, respectively. ___ 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
[PyMOL] How to use cmd.label command
Dear all,
I want to label residues with the resn+resi, and I tried the following command
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 CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
commands are written as:
cmd.select('CAs', 'obj & n. CAs')
cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
NameError: name 'resn' is not defined
So could anyone tell me how to correctly use the cmd.label command?
Thank you very much in advance
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[PyMOL] how to use cmd.label command
Dear all,
I want to label residues with the resn+resi, and I tried the following command
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 CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
commands are written as:
cmd.select('CAs', 'obj & n. CAs')
cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
NameError: name 'resn' is not defined
So could anyone tell me how to correctly use the cmd.label command?
Thank you very much in advance
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[PyMOL] why does coordinates not overlap with map
Dear pymol users, I have a coordinate file (pdb) and a map file (mtz), and I want to make a image that shows both the coordinate and the map. I generate a .map.ccp4 file using fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in pymol, I find the coordinates are out of the map. Please see the image at the following link: https://drive.google.com/file/d/1TmH-mFCnsCNghcq4RQJ9mNOBlTfCRsHW/view?usp=sharing Could anyone tell me how to map them overlap? Thank you in advance. Best regards___ 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
Re: [PyMOL] Virtual Annual CCP4/APS Crystallographic School (2022) in the US
Dear Colleagues This is a final reminder that the registration for the upcoming CCP4/APS school will be closed on Apr 15, 2022. Please submit your application soon if you plan to attend. Charles, Andrey, Garib and Qingping From: Xu, Qingping Sent: Monday, January 24, 2022 10:07 AM To: ccp...@jiscmail.ac.uk ; pymol-users@lists.sourceforge.net ; pheni...@phenix-online.org ; Ahrens, Kristin Subject: 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
[PyMOL] RMSD from DCD
I have been using VMD for most of my MD analysis, but I am trying to learn PyMol now. I know how to load a pdb and a dcd onto that pdb. But how do I measure the RMSD of each frame in the DCD aligned to the starting structure, and then output a graph like of RMSD vs frame? Doing this through scripting would be great. Thanks! ___ 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
Re: [PyMOL] Virtual Annual CCP4/APS Crystallographic School (2022) in the US
Dear Colleagues, Just a friendly reminder that the registration of the upcoming CCP4/APS virtual school is open. If you plan to attend the school, please submit your application before the Apr 15th, 2022 deadline, preferably sooner. The school schedule is available on the CCP4 school website (https://www.ccp4.ac.uk/schools/APS-2022/index.php). Charles, Andrey, Garib and Qingping On 1/24/22 10:07, Qingping Xu wrote: 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
Re: [PyMOL] How to label atom at proper positions?
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
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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Re: [PyMOL] distance-based selection of the side-chains
Hi Enrico,
I think it's because you are selecting side chains, glycine has no sidechain
and alanine has single carbon atom side chain so this representation won't work
for it. You would need to remove the sidechains from the selection to make it
apply to the backbone atoms, i.e. cmd.select('rep lines and poly)
Cheers,
Ali
On 27/1/22, 11:22 pm, "Enrico Martinez" wrote:
additional question in the same field:
as I've mentioned before, before applying distance-based filtering, I
would like to change the representation of the lines to ball-and-stick
for the residues involved in the interactions:
cmd.select('rep lines and sidechain')
cmd.show_as('sticks', 'sele')
cmd.set('stick_radius', '0.10')
cmd.set('stick_ball', 'on')
cmd.set('stick_ball_ratio', '2.2')
I've just noticed that some residues remain their "line"
representation, notably for hydrophobic (Gly, Ala) residues. How could
it be fixed ?
чт, 27 янв. 2022 г. в 12:38, Enrico Martinez :
>
> Thank you very much, Ali!!
> Cheers,
> Enrico
>
> чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay :
> >
> > Hi Enrico,
> >
> > You need to use the byres or br. Selection
(https://protect-au.mimecast.com/s/4MzUCROND2uvY6pqpi9A9Zw?domain=pymolwiki.org)
> >
> > I.e:
> > cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
> >
> > Also, consider hiding all protein residues and showing only the ones
near the protein, i.e.:
> > cmd.show('sticks','br. poly within 4 of resn XXX')
> > ^ Where 4 is the distance and XXX should be substituted with the
residue name of the ligand
> >
> > Cheers,
> >
> > Ali
> >
> > On 27/1/22, 10:12 pm, "Enrico Martinez" wrote:
> >
> > Dear Pymol Users!
> > I am working on the visualization of the protein-ligand contacts
> > identified using
> > preset.ligand_cartoon('pdb',_self=cmd)
> > Since the command also displays some residues, which are not
involved
> > in the interactions (with the radicals located too far away) with
the
> > ligand, I need to filter the displayed side-chains focusing only on
> > the important interactions. I am using a distance-based criterion
for
> > the selection of the residues which I am going to hide.
> >
> > this is what I've already tried:
> >
> > # display visible side chains as the sticks
> > cmd.select('rep lines and visible and sidechain')
> > cmd.show('sticks', 'sele')
> > # select all visible sticks of the sidechains far away from the
ligand
> > cmd.select('sidechain & (rep sticks & visible beyond 4 of not
polymer)')
> > cmd.hide('everything', 'sele')
> >
> > the problem is that the "select" command with such syntax, always
> > selects the ATOMS, but not the whole side-chains. Is it possible to
> > hide the whole side-chain using such syntax as well as it's
displayed
> > label?
> > Many thanks in advance!
> > Enrico
> >
> >
> > ___
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> >
> >
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Re: [PyMOL] distance-based selection of the side-chains
Hi Enrico,
You need to use the byres or br. Selection
(https://pymolwiki.org/index.php/Selection_Algebra)
I.e:
cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
Also, consider hiding all protein residues and showing only the ones near the
protein, i.e.:
cmd.show('sticks','br. poly within 4 of resn XXX')
^ Where 4 is the distance and XXX should be substituted with the residue name
of the ligand
Cheers,
Ali
On 27/1/22, 10:12 pm, "Enrico Martinez" wrote:
Dear Pymol Users!
I am working on the visualization of the protein-ligand contacts
identified using
preset.ligand_cartoon('pdb',_self=cmd)
Since the command also displays some residues, which are not involved
in the interactions (with the radicals located too far away) with the
ligand, I need to filter the displayed side-chains focusing only on
the important interactions. I am using a distance-based criterion for
the selection of the residues which I am going to hide.
this is what I've already tried:
# display visible side chains as the sticks
cmd.select('rep lines and visible and sidechain')
cmd.show('sticks', 'sele')
# select all visible sticks of the sidechains far away from the ligand
cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
cmd.hide('everything', 'sele')
the problem is that the "select" command with such syntax, always
selects the ATOMS, but not the whole side-chains. Is it possible to
hide the whole side-chain using such syntax as well as it's displayed
label?
Many thanks in advance!
Enrico
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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
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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Re: [PyMOL] How to label atom at proper positions?
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 ___ 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 ___ 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
[PyMOL] How to label atom at proper positions?
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 ___ 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
Re: [PyMOL] conversion of the small molecules from sdf to mol2
Hi,
You could try --append in openbabel to add the ID_STRUCTURE to the title of the
molecule sdf?
https://openbabel.org/docs/dev/Command-line_tools/babel.html#append-property-values-to-the-title
<https://openbabel.org/docs/dev/Command-line_tools/babel.html#append-property-values-to-the-title>
Chris
> On 14 Jan 2022, at 12:03, pymol-users-requ...@lists.sourceforge.net wrote:
>
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> than "Re: Contents of PyMOL-users digest..."
>
>
> Today's Topics:
>
> 1. conversion of the small molecules from sdf to mol2
> (Enrico Martinez)
>
>
> ------
>
> Message: 1
> Date: Thu, 13 Jan 2022 16:23:53 +0100
> From: Enrico Martinez
> To: pymol-users
> Subject: [PyMOL] conversion of the small molecules from sdf to mol2
> Message-ID:
>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Pymol users, dear Friends!
>
> I have a question regarding file conversion of the small organic
> molecules, which is not directly related to pymol but I believe that I
> may use it for the solution.
>
> I am dealing with the conversion of SDF file (2d formulas) to mol2
> format (3d coordinates)
> Usually I use it in one line command with babel
> obabel --gen3d -isdf ligands.sdf -omol2 > ligands.mol2
>
> It creates a multi-model mol2 file, that I may open in pymol and split
> the molecules manually using split_states command:
> pymol ligands.mol2
> cmd.split_states('ligands', 'prefix=conf')
> This creates several separate objects conf0001, conf0002 etc that I
> may save as the individual mol2.
> Alternatively I may obtain individual mol2 filles for each model of the SDF:
> obabel ./ligands.sdf -O ./babel/conf.mol2 --gen3d -m
> which creates separate files conf1.mol2 , conf2.mol2 .. confN.mol2
> that I may load in pymol in one command from terminal
> pymol ./babel/conf*.mol2
>
> The problem that the name of the initial model stored in the initial sdf, as:
>
> name_of_the_ligand
>
> always lost during conversion from sdf to mol2 (regardless of the way
> of the conversion). So the mol2 files always lack their initials
> defined from sdf :-)
>
> Could you suggest some trick to associate the name of the model (From
> initial sdf) to the corresponding object loaded in pymol or
> alternatively keep them during the conversion?
> Many thanks in advance!
> Enrico
>
>
>
> --
>
>
>
> --
>
> Subject: Digest Footer
>
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Re: [PyMOL] Set label for visible amino acids
Hi Enrico,
This is actually quite simple, see the PyMOL wiki:
https://pymolwiki.org/index.php/Aa_codes
Paste this python dictionary into PyMOL:
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'}
The one letter codes can be accessed with one_letter[resn]
To do something like Y-119:
label sele, '{}-{}'.format(one_letter[resn], resi) # front end command
cmd.label('sele', "'{}-{}'.format(one_letter[resn], resi)") # backend command
Cheers,
Ali
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
On 12/1/22, 11:26 pm, "Enrico Martinez" wrote:
exactly we may do it in the context meny for the particular selection
(we do not need to select a particular residues, so ..)
but may we create the same label using label command as well ??
cmd.label('sele', 'resn')
I think something should be used instead of 'resn'. there is also
option 'resi' which shows only the number of the amino acid. So I need
to combine "resn" and "resi"
:-)
вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh
:
>
> For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
>
>
>
> Vaheh
>
>
>
> From: Enrico Martinez
> Sent: Tuesday, January 11, 2022 12:34 PM
> To: pymol-users
> Subject: [PyMOL] Set label for visible amino acids
>
>
>
> Dear Pymol users!
> Here is the chain of the pymol commands that I am using to label the
> visible amino-acids shown as lines in the current pymol session.
> cmd.select('name CA and rep lines')
> cmd.label('sele', 'resn')
> cmd.set('label_font_id', '14')
> cmd.set('label_color', 'indigo')
> cmd.set('label_position', '3,0,0')
> It produces nice labeling according to the amino acid name (example
> Tyr). How it would be possible to indicate additionally the number of
> the amino acid like Tyr-119 or simply using one letter code + the
> number?
> Many thanks in advance
> Enrico
>
>
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Re: [PyMOL] surface representation of the protein-ligand interactions
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image:
https://pymolwiki.org/index.php/Rebuild
Cheers,
Ali
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
On 10/1/22, 11:10 pm, "Enrico Martinez" wrote:
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:
$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow, the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?
пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
>
> Hi Enrico,
>
> You can carve the protein surface around the ligand, i.e. show only the
surface behind the ligand, see this guide:
https://protect-au.mimecast.com/s/1Of6CNLJyQU0W9yVofmRSV0?domain=pymol.org
>
> You can also try and made the surface more transparent, but this doesn't
always give the best results, see:
https://protect-au.mimecast.com/s/vdsUCOMKzVTp8wQ53fvOudq?domain=pymolwiki.org,
i.e.:
>
> set transparency, 0.5
>
> It would help to see an image of what you are working with atm
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and
Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 10/1/22, 10:10 pm, "Enrico Martinez" wrote:
>
> Dear Pymol users!
> Working on the vizualisation of the protein-ligand interactions I
> would like to switch from cartoon to the surface representation of the
> protein, while still being capable to see the ligand-binding cavity
> (as well as non-covalent interactions)
>
> Could you suggest me some combination of the options which could helps
> me with such vizualisaiton?
> I have alread tried
> show surface, all within 5 of my_pdb and not polymer
> set surface_smooth_edges, onset surface_smooth_edges, on
> where my_pdb and not polymer corresponds to the selection of the
ligand
>
> Eventualy this create cool surface representation of the protein and
> but completely hides the ligand-binding cavity
> Many thanks in advance!
> Enrico
>
>
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Re: [PyMOL] surface representation of the protein-ligand interactions
Hi Enrico, You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://pymolwiki.org/index.php/Transparency, i.e.: set transparency, 0.5 It would help to see an image of what you are working with atm Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 On 10/1/22, 10:10 pm, "Enrico Martinez" wrote: Dear Pymol users! Working on the vizualisation of the protein-ligand interactions I would like to switch from cartoon to the surface representation of the protein, while still being capable to see the ligand-binding cavity (as well as non-covalent interactions) Could you suggest me some combination of the options which could helps me with such vizualisaiton? I have alread tried show surface, all within 5 of my_pdb and not polymer set surface_smooth_edges, onset surface_smooth_edges, on where my_pdb and not polymer corresponds to the selection of the ligand Eventualy this create cool surface representation of the protein and but completely hides the ligand-binding cavity Many thanks in advance! Enrico ___ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/cnxDCMwGxOtqr9lJjhwM0N6?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/ZXpPCNLJyQU0W9R6oh42rcB?domain=sourceforge.net ___ 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
Re: [PyMOL] Structure alignment -- general question
Hi George, You can do pairwise alignments, i.e. align 3 of the structures to one structure. You can also use the "extra_fit" method (https://pymolwiki.org/index.php/Extra_fit), i.e: extra_fit name CA, "object", super Replace object with the structure you want the other 3 to align to, this uses the "super" alignment method but you can also use "align", "cealign", "fit", etc. Depending on what gives the best results. Just a note, this will align all PyMOL objects to your selected object, you can make sub selections as needed. Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health On 4/1/22, 8:52 pm, "George Tzotzos via PyMOL-users" wrote: I’m dealing with 4 heterogeneous structures belonging to the same fold. I’d like to compare some conserved structural features and for this purpose it would be useful that the structures are aligned and then visualised in a grid. I understand that the align command works for 2 structures only. Is there another way achieve what I described above. Looking forward to any suggestions Many thanks in advance and all the best for 2022 ___ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/gt9KCVARKgCx661v8UGCdCY?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/W231CWLVXkU5KKvk8TxrS7w?domain=sourceforge.net ___ 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
[PyMOL] Structure alignment -- general question
I’m dealing with 4 heterogeneous structures belonging to the same fold. I’d like to compare some conserved structural features and for this purpose it would be useful that the structures are aligned and then visualised in a grid. I understand that the align command works for 2 structures only. Is there another way achieve what I described above. Looking forward to any suggestions Many thanks in advance and all the best for 2022 ___ 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
[PyMOL] Unable to run pymol from Linux command line
Hi, I installed pymol on Ubuntu 20.04 on WSL (Windows 10) using: sudo apt-get install -y pymol However, when I run pymol on the command line, I get this error: :1: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses qt.qpa.xcb: could not connect to display qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb. Aborted What should I do to get pymol to work? Best regards, Max _______ 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
[PyMOL] Distorted 3-10 helix
Dear All, My latest structure has several 3-10 helices present, however, a few of them in cartoon form shows the starting residue of the helix to be distorted/twisted. The structure is 2.2Ang and I can clearly see the position of the amide bond and the direction of carbonyl, but I cannot stop the twisting of the cartoon. I have tried altering that residue ss to a loop which “works” (as in the problem goes away) but I really wish to show the full helix. I have also run DSSPtoPDB and force it not to recognize the 3-10 helices as helices but in cartoon form you can see they are helices. Do anyone have suggestions or a way to force it to be a helix? [A close up of a toy Description automatically generated with low confidence] Thanks, Daniel [Text Frederick National Laboratory on a teal background] [LinkedIn icon]<https://www.linkedin.com/company/frederick-national-laboratory-for-cancer-research/> [Twitter icon] <https://twitter.com/FredNatLab> [Facebook icon] <https://www.facebook.com/FredNatLab> [Instagram icon] <https://www.instagram.com/frednatlab/> Daniel A Bonsor PhD | Scientist I RAS Structural Biology [Phone icon] office: 301-846-5134 / cell: 443-983-2930 [Email icon] daniel.bon...@nih.gov<mailto:daniel.bon...@nih.gov> [Contractor] [Location icon] Post Office Box B, Frederick, MD 21702 [Link icon] frederick.cancer.gov<https://frederick.cancer.gov/> The Frederick National Laboratory for Cancer Research is operated by Leidos Biomedical Research, Inc. for the National Cancer Institute. -- ___ 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
Re: [PyMOL] PyMOL for M1 macs
Hi, Thanks all will give it a try Cheers, Chris > On 6 Dec 2021, at 06:08, Jarrett Johnson > wrote: > > IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think) > than the previous x86. Your mileage may vary. > > Best, > Jarrett J > > On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <mailto:xinyu18...@gmail.com>> wrote: > It looks like while you can’t run it natively on M1, maybe you can do it > through rosetta2 translation via Conda install? > See here: https://pymol.org/2/support.html? > <https://pymol.org/2/support.html?> > Supported platform states M1 with rosetta2. Perhaps with some penalty for > efficiency though. Anyone tried? > > Sent from my iPhone > >> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson >> mailto:jarrett.john...@schrodinger.com>> >> wrote: >> >> >> Hi Chris, >> >> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac >> yet but it's on our radar to do so soon. >> >> Best, >> >> Jarrett J >> >> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users >> > <mailto:pymol-users@lists.sourceforge.net>> wrote: >> Hi, >> >> Is there a build of PyMOL for M1 Macs yet? >> >> Cheers, >> >> Chris >> >> >> _______ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> >> >> >> -- >> Jarrett Johnson | Senior Developer, PyMOL >> >> _______ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> > > -- > Jarrett Johnson | Senior Developer, PyMOL > ___ 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
[PyMOL] PyMOL for M1 macs
Hi, Is there a build of PyMOL for M1 Macs yet? Cheers, Chris ___ 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
Re: [PyMOL] Complement or Inverse Selection in Pymol
Hi Gret, No worries, In regards to the selection: “resi 25 and object” Its more so to ensure that you don’t accidently select “resi 25” from multiple chains or objects Like if you load two pdb files into PyMOL (say obj01 and obj02) and both have a resi 25, then resi 25 from both objects will be selected if you don’t include the object in the selection. On the other hand, If you: select chA, resi 25 and obj01 Then the chA selection will only contain resi 25 from obj01 and ignore obj02. Its more of a note about selections that you might already be familiar with Cheers, Ali From: Gert Kruger Date: Saturday, 27 November 2021 at 5:05 pm To: Ali Saad Kusay Cc: "pymol-users@lists.sourceforge.net" Subject: Re: [PyMOL] Complement or Inverse Selection in Pymol Dear Ali, Many thanks for your kind and very helpfull reply! One question: You wrote: "Doing something like resi 25 and object is safer". Do you mean: select chA, resi 25 And will that reflect as follows in my requirement: select other_waters, br. (resn WAT beyond 5 of chA, resi 25) Best wishes Gert Kruger On Fri, 2021-11-26 at 15:09 +, Ali Saad Kusay wrote: Hi Gert, These selection commands will generate a selection object called "other_waters " See https://pymolwiki.org/index.php/Selection_Algebra<https://protect-au.mimecast.com/s/h0hkCQnMBZfkPgpznSPf8vp?domain=protect-za.mimecast.com> You can do: select other_waters, br. (resn WAT and not sele) # after you make the selection in your email or select other_waters, br. (resn WAT beyond 5 of resi 25) A few notes: 1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br." 2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL To remove the unwanted water atoms, do: remove other_waters Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 On 27/11/21, 1:57 am, "Gert Kruger" wrote: Dear All, Apologies for my ignorance. I need to know which solvent molecules are in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to create a solvent waterbox in and around the enzyme. I found the following command that seems to find the Water molecules in the active site: > sele resn WAT within 5 sele resi 25 (ASP25 is in the active site). Now I want to remove ALL other water/solvent molecules (those that are not selected). Is there a method to achieve a complement or inverse selection (to hightlight ALL other watermolecules that are not currently selected?) I am able save the selection, but that is a bit more tedious. Question: Is there an easy way in Pymol to achieve a "complement" or "inverse" selection of waters in a solvent box? Thanks alot and best wishes Gert Kruger UKZN email disclaimer: The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University. ___ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/G7JzCXLW2mUXKGn89c6nIX_?domain=mail-archive.com<https://protect-au.mimecast.com/s/pyYTCVARKgCxym6OVtJhaUc?domain=protect-za.mimecast.com> Unsubscribe: https://protect-au.mimecast.com/s/ZungCYW8NocLlg3n9iGRDSs?domain=sourceforge.net<https://protect-au.mimecast.com/s/jj3uCXLW2mUXKjRplu9gQzs?domain=protect-za.mimecast.com> ___ 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
Re: [PyMOL] Complement or Inverse Selection in Pymol
Hi Gert, These selection commands will generate a selection object called "other_waters " See https://pymolwiki.org/index.php/Selection_Algebra You can do: select other_waters, br. (resn WAT and not sele) # after you make the selection in your email or select other_waters, br. (resn WAT beyond 5 of resi 25) A few notes: 1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br." 2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL To remove the unwanted water atoms, do: remove other_waters Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 On 27/11/21, 1:57 am, "Gert Kruger" wrote: Dear All, Apologies for my ignorance. I need to know which solvent molecules are in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to create a solvent waterbox in and around the enzyme. I found the following command that seems to find the Water molecules in the active site: > sele resn WAT within 5 sele resi 25 (ASP25 is in the active site). Now I want to remove ALL other water/solvent molecules (those that are not selected). Is there a method to achieve a complement or inverse selection (to hightlight ALL other watermolecules that are not currently selected?) I am able save the selection, but that is a bit more tedious. Question: Is there an easy way in Pymol to achieve a "complement" or "inverse" selection of waters in a solvent box? Thanks alot and best wishes Gert Kruger UKZN email disclaimer: The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University. ___ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/G7JzCXLW2mUXKGn89c6nIX_?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/ZungCYW8NocLlg3n9iGRDSs?domain=sourceforge.net ___ 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
[PyMOL] About contacting the PYMOL-creators
Hello, I wonder is there a way to contact the makers of Pymol for general question or to request certain program features? Regards, K. Zeghida.___ 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
Re: [PyMOL] Labeling residues for publication
Thank you both for the suggestions. I tried to upgrade. I get “pymol” is already at the latest version All the best George > On 28.10.2021, at 14:40, Jarrett Johnson > wrote: > > Hi George, > > This issue should've been addressed in PyMOL 2.5.1. I would consider > upgrading if you can. > > Best, > Jarrett J > > On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-users > <mailto:pymol-users@lists.sourceforge.net>> wrote: > Hi everybody, > > I’d be grateful for any suggestions regarding the editing of labels. > > I’ve labeled a few residues and I’m trying to give them a better placing in > the structure. I’m using mouse/2 button editing. Clicking on control and > then moving the labels works, but alas as soon as I release the control key > pymol crashes. > > I’m using > PyMOL(TM) 2.5.0 - Incentive Product > > Thanks in advance > > George > > _______ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> > > -- > Jarrett Johnson | Senior Developer > <https://www.schrodinger.com/> ___ 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
[PyMOL] Labeling residues for publication
Hi everybody, I’d be grateful for any suggestions regarding the editing of labels. I’ve labeled a few residues and I’m trying to give them a better placing in the structure. I’m using mouse/2 button editing. Clicking on control and then moving the labels works, but alas as soon as I release the control key pymol crashes. I’m using PyMOL(TM) 2.5.0 - Incentive Product Thanks in advance George ___ 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
Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.
Hi Zuben, I think I “solved” the problem. Converting “closed.py” to “closed.pse” does the trick. Many thanks for your suggestions George > On 14 Oct 2021, at 22:26, Brown, Zuben wrote: > > Hi George, > > The image came through. > > I think the problem is that it is assigning the same chain ID to multiple > chains. Can you give each protein (open, closed) unique chain IDs and see if > the problem persists? > > best, > Zuben > From: Brown, Zuben > Sent: Thursday, October 14, 2021 4:42 PM > To: George Tzotzos > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb. > > Hi George, > > It seems that image can't be loaded, possibly due to security settings with > my email. > > Anyway, if the issue only occurs after running closed.py then that must be > the issue. I assume loading open.pdb and closed.pdb without that script > shows no issue. > > Without knowing what closed.py is doing, it will be hard to troubleshoot. > If it isn't a long script, then perhaps you could post it? > > Best wishes, > Zuben > From: George Tzotzos > Sent: Thursday, October 14, 2021 2:29 PM > To: Brown, Zuben > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb. > > Zuben, thank you for the prompt response. > > Perhaps, I didn’t describe well the problem. I’m attaching a snapshot showing > the loaded scripted structure (“closed.py". It shows anti-correlated movement > of backbone atoms of my protein in “closed” conformation. The same protein > also adopts an “open” conformation, say “open.pdb”. I know want to load > open.pdb in the same pymol session with closed.py. Upon opening/loading > open.pdb, the protein can be seen in the pymol window but it is total > garbled. Somehow, it seems that the script of closed.py affects the > appearance of open.pdb. That is before I even attempt to align the two > conformations. > > Once again, many thanks > > George > > > > > >> On 14 Oct 2021, at 18:34, Brown, Zuben > <mailto:zb2...@cumc.columbia.edu>> wrote: >> >> Have a look here to see if this is what you want: >> >> https://pymolwiki.org/index.php/Align >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=> >> Align - PyMOLWiki >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=> >> align performs a sequence alignment followed by a structural superposition, >> and then carries out zero or more cycles of refinement in order to reject >> structural outliers found during the fit.align does a good job on proteins >> with decent sequence similarity (identity >30%).For comparing proteins with >> lower sequence identity, the super and cealign commands perform better. >> pymolwiki.org >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pymolwiki.org_&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=G-DVox001clYfvlqDJi_SO3fjxMwUnWEXG1mDewzLoA&e=> >> >> best wishes, >> Zuben >> From: George Tzotzos via PyMOL-users > <mailto:pymol-users@lists.sourceforge.net>> >> Sent: Thursday, October 14, 2021 12:06 PM >> To: pymol-users@lists.sourceforge.net >> <mailto:pymol-users@lists.sourceforge.net> >> > <mailto:pymol-users@lists.sourceforge.net>> >> Subject: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb. >> >> Apologies if this is trivial but I’m rather new to Pymol. >> >> I’m loading a script (x.py) that allows me to visualise correlations in the >> atomic movements of my protein. I have no problems with this. >> >> My next task is to load the native pdb file (e.g y.pdb) of the same protein >> but in a different conformation. Once I do this, y.pdb comes out garbled. My >> goal is to superimpose the y to x to check if the atomic correlations >> correspond to the conformation of y. >> >> Many thanks in advance for any suggestions >> >> George &
[PyMOL] Superposition of native pdb to scripted pdb.
Apologies if this is trivial but I’m rather new to Pymol. I’m loading a script (x.py) that allows me to visualise correlations in the atomic movements of my protein. I have no problems with this. My next task is to load the native pdb file (e.g y.pdb) of the same protein but in a different conformation. Once I do this, y.pdb comes out garbled. My goal is to superimpose the y to x to check if the atomic correlations correspond to the conformation of y. Many thanks in advance for any suggestions George ___ 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
[PyMOL] How to label on surface
Dear Pymol users, I wish to label the one-letter residue names for a bunch of selected resides on surface representation of a protein, but I found the labels cannot be seen on the image. It seems that these labels can been seen on cartoon representation when the surface is hide. Could you tell to how to show the labels on the surface? I will appreciate any help! Best regards___ 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
[PyMOL] How to import anaconda packages in Pymol?
Dear all, I installed Pymol in CentOS from source following the guide in "https://pymolwiki.org/index.php/Linux_Install";. I compiled Pymol with the Python from anaconda, but I found that I cannot import anaconda packages (such as pandas, numpy, etc.) in Pymol. The "import pandas" command will return "no such module named pandas" error. Could yuo tell me how to let pymol use the anaconda packages? I will appreciate any help. Best regards ___ 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
Re: [PyMOL] pymol installation error
Dear Mr. Jarrett, Yes, with the glm of version 0.0.9, pymol can be installed successful. Thank you very much:) -- From:Jarrett Johnson Send Time:2021年9月13日(星期一) 01:30 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] pymol installation error Hello, Looks like the glm version that you're currently using (I'm assuming 0.9.6--default package for Centos 7) is not up to date with the ones we're currently using (0.9.9). The location for glm headers within their library have changed a bit since the last several years. I might have to think of a way to reconcile these issues sometime this week. In the meantime if you'd like, I suggest picking up the latest package from https://github.com/g-truc/glm; alternatively, currently stick with your version and include and use `glm::epsilonEqual` over `glm::equal` on lines 31 and 32 of that source file. Hope that helps, Jarrett J On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users wrote: Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: e
Re: [PyMOL] pymol installation error
Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Woul
[PyMOL] pymol installation error
Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much of any help. Best regards.___ 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
[PyMOL] small GUI font size
I know this has been asked before, but for older versions of pymol. I just updated my pymol version to 2.5 by installing from sbgrid. I installed on a Macbook Pro using OSX 10.15.7. The font size in the GUI is extremely small now and I cannot find a setting to change this to a readable size. Any suggestions on how to change this? Thanks Ursula -- Ursula Schulze-Gahmen, PhD Staff Research Scientist The J David Gladstone Institutes 1650 Owens St. San Francisco, CA 94158 (415) 734 4835 ___ 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
Re: [PyMOL] Farewell
Dear Thomas Holder, Thank you for helping out PyMOL users like myself. Also putting up user friendly advise for the over the years who use PyMOL. I tend to read your email correspondence with other users, since they seem to be more thought through than my few emails I asked in these forums. I hope a lot more experts can do the same for people who are teaching molecular modeling or learning PyMOL. Sincerely, David Gae > On Apr 30, 2021, at 7:14 AM, Thomas Holder > wrote: > > Dear PyMOL community - > > The time has come for me to hand over my PyMOL development > responsibilities at Schrödinger. It's been an incredible journey for > me to get involved with the PyMOL community, to become a PyMOL fellow > in 2011 and to start working full time for the project in 2012. I'm > extremely grateful to all the people at Schrödinger who made this > possible, and of course to all of you - the user community - who've > shown me every day that my work is meaningful. > > PyMOL has a unique place within Schrödinger, and a highly motivated > and skilled team of developers and scientists stand behind it. They > have some great plans and I'm excited to watch how they will take > PyMOL to the next level. > > I don't think that my PyMOL journey is over yet. But for the next > chapter in my career, I'll "just" be a user and a member of the > community. See you around. > > Cheers, > Thomas > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > > ___ > 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 ___ 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
[PyMOL] How to label residue name on top of sphere representation
Dear all, I wish to label residue name on top of sphere representation, but I find it is difficult. I tried the following command select sele, c. A & resi 47 & name CB show sphere, c. A & resi 47 lable sele, "Y47" I and the "Y47" label is hidden inside the sphere and cannot be seen. Even if I set the sphere to be 80 % transparency, the label cannot be seen yet. So what the the correct way to make such a labelling? Best regards, Yeping Sun___ 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
[PyMOL] Calculating r.m.s.d values for ligands once proteins have been aligned
Dear all, I hope you are keeping safe and well. I am a new user to PyMOL and had a query that I hope someone can help me with. I have performed an alignment of two homologs with the super command on PyMOL, I have generated a rmsd value for this alignment using the C-alpha atoms as comparison. Both these proteins had ligands bound, and I would like to compare how closely these respective ligands match in space/binding pose. Would someone please be able to tell me how to calculate an rmsd value now for these ligands together once the proteins have been superimposed, without changing the coordinates of the ligands? Thank you so much! All the best, Sacha ___ 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
[PyMOL] Virtual Annual CCP4/APS Crystallographic School (2021) 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 14-25, 2021 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-2021/index.php. Dates: June 14 through 25, 2021 (with a weekend break on June 19 and 20th) 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 sample program, contact info and other details can be found at the School website. 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 1st, 2021. To apply, visit https://www.ccp4.ac.uk/schools/APS-2021/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, 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
[PyMOL] algorithm used by Pymol to detect interior cavities in protein
Hello, I am writing a paper on tunnels for small molecule access to buried active sites in proteins. I have noticed that tunnel prediction programs like CAVER and MOLE predict tunnels that align pretty well with the interior cavities displayed by Pymol. However, the size of the cavities predicted by Pymol are generally bigger than the diameter of the tunnel predicted by CAVER/MOLE, even after adjusting for probe size. My question therefore is "What type of algorithm (grid based, sphere based, etc) is used by Pymol to detect cavities?". Since the corroboration of tunnels predicted by CAVER and interior cavities predicted by Pymol bolster the computational prediction of tunnels, I would like to add this dual method to the paper. But I would need to account for the discrepancy in diameter. I hope that someone would be able to help me with an answer. Best wishes. And a happy new year. Rahul Banerjee University of Minnesota ___ 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
[PyMOL] is there a way to update ribbon, sticks, etc. with new coordinates?
Hi, I have PyMol figures containing objects such as ribbons, sticks, spheres, etc. However, I have done a bit more refinement of the models and I wouldlike to read the new coordinates into the pymol .pse file and redrawthese objects from the new coordinates. Is there an easy way to do this? Matt ___ 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
[PyMOL] Dose the thickness of residues reflect b-factor in cartoon putty representation?
Dear all, When you use "cartoon putty[, selection]" command in pymol, you will get the cartoon putty representation of your selection. And the backbond of the selection show different thickness. So dose the thickness of residues reflect b-factor in cartoon putty representation? Best regards Yeping Sun___ 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
Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi, Blaine,
Thank you, that's helpful. But a problem with creating a new object is that the
conformation of the newly created object for the selection is sightly different
from its counterpart in the original object. If the original object is shown as
cartoon, then both the putty presentation of new object and the cartoon
presentation of its counterpart in the original object at site of the
conformational difference will appear in the image produced in this way, and
that's ugly. Is there a way the avoid this shortcoming?
Best,
--
From:Mooers, Blaine H.M. (HSC)
Sent At:2020 Oct. 27 (Tue.) 18:09
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] [EXTERNAL] present b factor putty on select
I am sorry. I am wrong. I should have tested by suggestion.
Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.
create test, resi 100:150
preset.b_factor_putty("test")
The above worked with pdb file 4dgr.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
From: Mooers, Blaine H.M. (HSC) [blaine-moo...@ouhsc.edu]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping,
You are right; there is a way via the command line:
preset.b_factor_putty(selection='all')
Replace "all" with your selection.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
____
From: sunyeping via PyMOL-users [pymol-users@lists.sourceforge.net]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select
Dear all,
I know that if you want to visualize b facotor of a objector in pymol, you can
use A>Present>b factor putty. However, how can show the b factor putty on a
certain selection of the object? Is there any command line to do this or do I
have to create a new object for the selection and still use the A>Present>b
factor putty operation?
Thank you,
Best regards
___
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[PyMOL] present b factor putty on select
Dear all, I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation? Thank you, Best regards___ 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
Re: [PyMOL] Help ASPB
Dear Clarisa, > On Sep 10, 2020, at 2:56 AM, Clarisa Alvarez > wrote: > > Dear David > Thank you very much!you do not know how much you helped me!!Thanks! > I have two questions: > - with you sent I only saw lateral chains, how could I see backbone? You want to click on “H” button and hide all. Then click on “S” ribbons to see backbone atoms. > - I might have missed the amino acid grouping, I do not understand. The group refer to acid and base and non-charge groups that play factor in generating the electrostatic potential. I am just curious have you tried this type of simple model: q1q2/4*Pier^2 Best Regards, David > Thank you again! > Have a good day. > Clarisa. > > El mié., 9 sept. 2020 a las 19:11, David Gae ( <mailto:dd...@ucdavis.edu>>) escribió: > > select pos,(resn arg+lys+his) > show sticks, (pos and !name c+n+o) > color marine,pos > disable pos > select neg,(resn glu+asp) > show sticks, (neg and !name c+n+o) > color red,neg > disable neg > select neutral, (resn > gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe) > show sticks, (neutral and !name c+n+o) > color yellow, neutral > > I might have missed the amino acid grouping, I hope you check it before you > use it. > Hope this helps, > > > >> On Sep 9, 2020, at 4:28 AM, Clarisa Alvarez > <mailto:clarisae.alva...@gmail.com>> wrote: >> >> GenScript >> Dear all, Thanks in advance. >> I have this problem, I have two pockets with electrostatic potential made by >> APSB, does anyone know how I could tell which residue contributes to each >> potential in each protein? >> Thanks in advance. >> Regards, >> Clarisa. >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> ___ 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
Re: [PyMOL] Help ASPB
select pos,(resn arg+lys+his) show sticks, (pos and !name c+n+o) color marine,pos disable pos select neg,(resn glu+asp) show sticks, (neg and !name c+n+o) color red,neg disable neg select neutral, (resn gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe) show sticks, (neutral and !name c+n+o) color yellow, neutral I might have missed the amino acid grouping, I hope you check it before you use it. Hope this helps, > On Sep 9, 2020, at 4:28 AM, Clarisa Alvarez > wrote: > > GenScript > Dear all, Thanks in advance. > I have this problem, I have two pockets with electrostatic potential made by > APSB, does anyone know how I could tell which residue contributes to each > potential in each protein? > Thanks in advance. > Regards, > Clarisa. > ___ > 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 ___ 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
[PyMOL] How to select s series of residues that contain the selected atom
Dear pymol user, I select a series of atoms with the follow command in pymol: select atoms, chian A within 4 of chain B I wonder how to select the resides containing the selected "atoms", and how to return the names and indexes of these residues. Thank you in advance! Best regards, Yeping Sun___ 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
[PyMOL] May I hire you to assist me
Hello I wish to hire someone to assist me with the demonstration of active sites and molecular structure and function. A knowledge of the use of PDB is also helpful. my email is dr.cmor...@yahoo.ca ___ 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
Re: [PyMOL] 13th CCP4/APS Crystallographic School in the US
Dear colleagues, The 2020 CCP4 School at APS has been cancelled. Due to the pandemic, it is not possible to find a timeslot for the gathering at Argonne for the rest of the year. We are very sorry for the inconvenience. We want to thank the registrants for their interest in the School. The registration information will be carried over for the next event (Let us know if you are no longer interested). Hope to see everybody next year! Stay safe! The CCP4 School at APS Organizers From: Xu, Qingping Sent: Wednesday, April 1, 2020 7:18 AM To: ccp...@jiscmail.ac.uk; pheni...@phenix-online.org; pymol-users@lists.sourceforge.net Subject: RE: 13th CCP4/APS Crystallographic School in the US Dear colleagues, Due to the on-going pandemic, the 2020 CCP4/APS workshop (originally scheduled for June 15-22, 2020) is postponed. We will try to schedule the workshop at a later date. If no suitable date is found, the event will be cancelled. Further notice will be announced in the CCP4 bulletin board. In the meantime, the registration site remains open. We are sorry for the inconvenience. The CCP4/APS school organizers From: Xu, Qingping mailto:q...@anl.gov>> Sent: Monday, January 6, 2020 12:04 PM To: ccp...@jiscmail.ac.uk<mailto:ccp...@jiscmail.ac.uk>; pheni...@phenix-online.org<mailto:pheni...@phenix-online.org>; pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: 13th CCP4/APS Crystallographic School in the US Dear Colleagues, We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 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-2020/index.php. Dates: June 15 through 22, 2020 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@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 trouble-shooting 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 sample program, contact info and other details can be found at the School website. 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 1st, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, 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
Re: [PyMOL] Effect of different align method
Hello Julien Cappèle, Thank you for your response. I didn't mean to keep the input file in secrete. I have changed the access right to them, so you can download them freely. Best, Yeping Sun -- From:Julien CAPPELE Sent At:2020 Jun. 17 (Wed.) 17:05 To:孙业平 Subject:Re: [PyMOL] Effect of different align method Hello Sunyeping, I would suggest you to try TM-align, and a very good way to use it for multi-protein alignment is to use their server mTM-align. TM-align is a very robust alignment tool that will in most of the case, give you a better structural based alignment with low to zero input from the sequence. https://yanglab.nankai.edu.cn/mTM-align/ Also, if you are not working on secret stuff, you can give me access so I can rework the output files from mTM-align server to give you a RMSD-colored alignment in PyMOL. On PyMOL only, I didn't try to implement TM-align because I use Windows, but the developers said that a linux implementation could be possible if you are a bit familiar with compiling softwares. - Julien Cappèle Doctorant - 2ème année - ED C2MP Université de Lorraine CRM² - UMR CNRS 7036 julien.capp...@univ-lorraine.fr Tel: (+33)6 99 18 59 03 - Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users a écrit : Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ 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 ___ 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
[PyMOL] Effect of different align method
Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ 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
Re: [PyMOL] PyMOL-users Digest, Vol 169, Issue 9
> On Jun 7, 2020, at 17:28, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Re: View two proteins from one pdb file (Joel Tyndall) > > > -- > > Message: 1 > Date: Sun, 7 Jun 2020 22:28:14 + > From: Joel Tyndall > To: Neena Susan Eappen , pymol-users > > Subject: Re: [PyMOL] View two proteins from one pdb file > Message-ID: > <0c934fa5962a487081d581b2ad311...@its-mail-p02.registry.otago.ac.nz> > Content-Type: text/plain; charset="utf-8" > > Hi Neena, > > Use the command ?split_states clusters?, just type it into the command line > > J > > From: Neena Susan Eappen > Sent: Monday, 8 June 2020 10:01 am > To: pymol-users > Subject: [PyMOL] View two proteins from one pdb file > > Hello PyMOL users, > > I have a PDB file with coordinates for two proteins listed one after another > (attached). However, when i open the file on pymol, I only see one protein > (shown below) or it might be a sum of those 2 coordinates. How to view both > structures? > > [image.png] > > Many thanks, and Take care, > Neena > -- next part -- > An HTML attachment was scrubbed... > -- next part -- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 30449 bytes > Desc: image001.png > > -- > > > > -- > > Subject: Digest Footer > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > > End of PyMOL-users Digest, Vol 169, Issue 9 > *** ___ 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
Re: [PyMOL] volume representation is extremely dark colored
Thanks Thomas and Akbar! "set precomputed_lighting" did the trick and everything looks normal now. Vitali -Original Message- From: Thomas Holder Sent: Wednesday, May 27, 2020 2:24 AM To: Stanevich, Vitali [JRDUS] Cc: Mooers, Blaine H.M. (HSC) ; pymol-users@lists.sourceforge.net Subject: [EXTERNAL] Re: [PyMOL] volume representation is extremely dark colored Hi Vitali, Try this: set precomputed_lighting Or upgrade to the latest PyMOL version which has this setting by default. It's an Intel Graphics driver issue, you can read about it in this bug report: https://github.com/schrodinger/pymol-open-source/issues/15 Cheers, Thomas > On May 27, 2020, at 4:26 AM, Stanevich, Vitali [JRDUS] via PyMOL-users > wrote: > > Hi Blaine, > > Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher > improves brightness but makes representation not very "esthetically pleasing" > - the color is definitively oversaturated. > > Thanks, > Vitali > > -Original Message- > From: Mooers, Blaine H.M. (HSC) > Sent: Tuesday, May 26, 2020 6:31 PM > To: Stanevich, Vitali [JRDUS] ; > pymol-users@lists.sourceforge.net > Subject: [EXTERNAL] RE: volume representation is extremely dark colored > > WARNING: This email originated from outside the company. Do not click on > links unless you recognize the sender and have confidence the content is > safe. If you have concerns about this email, send it as an attachment to > 'suspiciousem...@its.jnj.com'. > > Hi Vitali, > > Maybe ambient was set to a large negative value. > Doing so has not impact on line drawings. > > Try resetting it to the default value. > > set ambient, 0.1 > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Molecular Biology College of Medicine > University of Oklahoma Health Sciences Center S.L. Young Biomedical Research > Center (BRC) Rm. 466 > 975 NE 10th Street, BRC 466 > Oklahoma City, OK 73104-5419 > > ____ > From: Stanevich, Vitali [JRDUS] via PyMOL-users > [pymol-users@lists.sourceforge.net] > Sent: Tuesday, May 26, 2020 4:32 PM > To: pymol-users@lists.sourceforge.net > Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored > > Hello everyone, > > I have a problem of creating useful volume representations in Pymol version > 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. > Lines representation behaves as expected, but anything volume related > (sticks, surface, cartoon) is drawn as a very dark surface, see example image > at the link below: > https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=> > > Is there setting in Pymol which can bring volume-related representation to > something more normal? Or do you think it's non-Pymol problem with drivers > compatibility and etc issues? > > Thanks in advance! > > Vitali Stanevich, PhD > Scientist > Janssen R&D > > > > ___ > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ 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
Re: [PyMOL] volume representation is extremely dark colored
Hi Blaine, Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher improves brightness but makes representation not very "esthetically pleasing" - the color is definitively oversaturated. Thanks, Vitali -Original Message- From: Mooers, Blaine H.M. (HSC) Sent: Tuesday, May 26, 2020 6:31 PM To: Stanevich, Vitali [JRDUS] ; pymol-users@lists.sourceforge.net Subject: [EXTERNAL] RE: volume representation is extremely dark colored WARNING: This email originated from outside the company. Do not click on links unless you recognize the sender and have confidence the content is safe. If you have concerns about this email, send it as an attachment to 'suspiciousem...@its.jnj.com'. Hi Vitali, Maybe ambient was set to a large negative value. Doing so has not impact on line drawings. Try resetting it to the default value. set ambient, 0.1 Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 From: Stanevich, Vitali [JRDUS] via PyMOL-users [pymol-users@lists.sourceforge.net] Sent: Tuesday, May 26, 2020 4:32 PM To: pymol-users@lists.sourceforge.net Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored Hello everyone, I have a problem of creating useful volume representations in Pymol version 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below: https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=> Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it's non-Pymol problem with drivers compatibility and etc issues? Thanks in advance! Vitali Stanevich, PhD Scientist Janssen R&D ___ 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
