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From: Norbert S. <st...@bb...> - 2024-09-22 19:17:03
|
Dear Matthias, use: set assembly, 1 set all_states, 1 fetch 7epp GUI "generate symmetry mates" does not work as the unit cell is defined as: CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 resulting in symmetry mates shifted by 1.0 Ang. in x y z. We need a "generate biological assembly" command. Best, Norbert Am 22.09.2024 um 12:02 schrieb Matthias Mayer: > 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 > |
From: Joel S. <mjs...@al...> - 2024-09-22 12:17:40
|
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....@zm...> 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/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > |
From: Matthias M. <m....@zm...> - 2024-09-22 10:18:12
|
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 |
From: Joel S. <mjs...@al...> - 2024-08-16 05:50:09
|
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 < pym...@li...> 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Qingping > Xu <0000292fcbdb7ebe-dmarc-request@JISCMAIL.AC.UK> > *Sent:* Monday, April 8, 2024 1:26 PM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@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/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > |
From: Xu, Q. <qx...@an...> - 2024-08-15 20:02:11
|
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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Qingping Xu <0000292fcbdb7ebe-dmarc-request@JISCMAIL.AC.UK> Sent: Monday, April 8, 2024 1:26 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@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$ |
From: Georg M. <geo...@un...> - 2024-08-14 16:17:24
|
Dear Pymol community, I am trying since hours to turn off the interpolation for a few scenes in my script. However I am just able to turn off interpolation totally by using "mview uninterpolate" at the end of the script. Writing "scene 001, animate=0" seems to be obsolete. Also using mview .... , cut=1.0 and other keywords from mview which should stop or change interpolation are not working. https://pymolwiki.org/index.php/Mview This would be a testing script: reinitialize load $TUT/1hpv.pdb util.cbc turn x,180 orient as cartoon scene 001, store show sticks, organic orient organic scene 002, store hide cartoon show lines, byres organic expand 5 turn x,45 turn y,45 scene 003, store # 2) Specify a 30-second movie -- state 1, 900 frames at 30 frames per second. mset 1 x900 mview store, 1, scene=001 mview store, 240, scene=001 turn y,-30 mview store, 70, cut=1.0 turn y,60 mview store, 170, cut=1.0 mview store, 300, scene=002 mview store, 540, scene=002 turn y,-30 mview store, 370 turn y,60 mview store, 470 mview store, 600, scene=003 mview store, 840, scene=003 turn y,-30 mview store, 670 turn y,60 mview store, 770 Many thanks in advance for any tips, br Georg. |
From: Robert H. <ha...@st...> - 2024-08-13 13:57:20
|
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 |
From: Urban L. <urb...@bo...> - 2024-07-30 12:39:40
|
Thank you so much! Best, Urban >>> Takanori Nakane <tna...@os...> 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/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Takanori N. <tna...@os...> - 2024-07-30 12:01:29
|
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/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Urban L. <urb...@bo...> - 2024-07-30 11:33:39
|
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 |
From: Thomas H. <th...@th...> - 2024-07-28 15:44:41
|
Hi Bob, Looks like Christoph Gohlke has moved his wheels to Github: https://github.com/cgohlke/pymol-open-source-wheels/ Another option would be the conda-forge channel: https://anaconda.org/conda-forge/pymol-open-source Cheers, Thomas On Mon, Jul 22, 2024 at 4:46 AM Robert Hanson via PyMOL-users <pym...@li...> wrote: > > At > https://pymolwiki.org/index.php/Windows_Install > the process fails for > > 3. Download the appropriate wheel files, > > 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/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Jarrett J. <jar...@sc...> - 2024-07-24 16:26:38
|
Hi Istvan, I have not yet come across a better way to do this (perhaps someone has a clever way to approach this), but I do think that adding a range of states to the create function is reasonable. The other idea that came to mind was to do a full copy with `create` and just delete states, but it seems deleting states is not yet implemented (although I have seen a few requests for this before). I'll see if I can address this for PyMOL 3.1. The Timeline programs select a range to view in the movie, but doesn't actually alter the structure data. Jarrett J. On Fri, Jul 19, 2024 at 6:46 PM Istvan Kolossvary <iko...@gm...> wrote: > Hi, > > It seems that the Create command can only copy either a single state or > all states but no ranges. The range option would be very useful in > stitching together a trajectory from parts of other trajectories. This > functionality is readily available in the Timeline, but AFAIK not available > in Create. Right now the only solution seems to use a hugely inefficient > loop copying a whole range state by state. Does anyone know a better > solution? > > Thanks, > > Istvan > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Robert H. <ha...@st...> - 2024-07-22 02:41:33
|
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 |
From: Lei S. <le...@gm...> - 2024-07-21 03:33:00
|
Hi Jarrett, I feel it is easy enough for you to test in the scripting mode that whether "cmd.movie.produce(moviename,mode='ray',quality=85,quiet=0)" would produce the same with pymol3 and pymol2 after you load a 1000-frame dcd file to an object with load_traj. If not, do you have any suggestions how to let pymol3 behave like pymol2? Of course, I can always switch back to use pymol2, like I am doing now. Thanks, Lei On Sat, Jul 20, 2024 at 9:47 PM Jarrett Johnson < jar...@sc...> wrote: > Hi Lei, > > I may need more details on how you're producing your movies. I would note > that the File menu will only produce a movie based on the movie that's in > the timeline *not* the one from PyMOL 2. So if you're using the old movie > API to export out a movie in PyMOL 3, your results won't be as expected > unless you use the legacy export menu. The `load_traj` command, I believe, > was unchanged moving to PyMOL3, if you can provide more details on what has > changed for you, that'd be great. While the interface is improved in > PyMOL3, I've also made sure to accommodate for most use cases of the > Timeline to be configured via scripting. The Python API for it is located > here: https://pymolwiki.org/index.php/Timeline_Python_API. > > Jarrett J > > On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote: > >> Hi Istvan, >> >> I have related but not the same problems with pymol3 when making the >> movies. Using the pymol script that works for pymol 2.5, pymol3 could only >> produce a movie for the first 240(?) frames and I could not find the >> setting to fix this issue. In addition, I believe they also changed the >> default options of load_traj in pymol3. Overall, it appears pymol3 counts >> on you using the interface but this is not always ideal for heavy duty >> work, e.g., requiring running "pymol -c" (text mode) on a linux server to >> finish the job. >> >> Lei >> >> >> >> On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...> >> wrote: >> >>> Hi, >>> >>> I have had these issues with the new timeline. It works fine with scenes >>> and short multi-state objects (like those showcased in the Pymol 3 online >>> visualization course) but when it comes to real life MD trajectories I >>> found two "dealbreaker" issues. >>> >>> 1) With complex movies based on MD trajectories and not scenes, the Draw >>> mode is not working. If I select Draw to generate a movie file quickly for >>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie >>> is complete garbage, showing only random parts of the system. >>> >>> 2) The Ray Tracing mode works fine, but processing time is prohibitively >>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5 >>> automatically uses all the available cores for ray tracing. The way Pymol 3 >>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is >>> only 100 seconds. >>> >>> Has anyone encountered similar issues? >>> >>> Thanks, >>> >>> Istvan >>> _______________________________________________ >>> PyMOL-users mailing list >>> Archives: http://www.mail-archive.com/pym...@li... >>> Unsubscribe: >>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > |
From: Jarrett J. <jar...@sc...> - 2024-07-21 02:50:57
|
Hi Lei, I may need more details on how you're producing your movies. I would note that the File menu will only produce a movie based on the movie that's in the timeline *not* the one from PyMOL 2. So if you're using the old movie API to export out a movie in PyMOL 3, your results won't be as expected unless you use the legacy export menu. The `load_traj` command, I believe, was unchanged moving to PyMOL3, if you can provide more details on what has changed for you, that'd be great. While the interface is improved in PyMOL3, I've also made sure to accommodate for most use cases of the Timeline to be configured via scripting. The Python API for it is located here: https://pymolwiki.org/index.php/Timeline_Python_API. Jarrett J On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote: > Hi Istvan, > > I have related but not the same problems with pymol3 when making the > movies. Using the pymol script that works for pymol 2.5, pymol3 could only > produce a movie for the first 240(?) frames and I could not find the > setting to fix this issue. In addition, I believe they also changed the > default options of load_traj in pymol3. Overall, it appears pymol3 counts > on you using the interface but this is not always ideal for heavy duty > work, e.g., requiring running "pymol -c" (text mode) on a linux server to > finish the job. > > Lei > > > > On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...> > wrote: > >> Hi, >> >> I have had these issues with the new timeline. It works fine with scenes >> and short multi-state objects (like those showcased in the Pymol 3 online >> visualization course) but when it comes to real life MD trajectories I >> found two "dealbreaker" issues. >> >> 1) With complex movies based on MD trajectories and not scenes, the Draw >> mode is not working. If I select Draw to generate a movie file quickly for >> testing then (a) it takes almost as long as Ray Tracing and (b) the movie >> is complete garbage, showing only random parts of the system. >> >> 2) The Ray Tracing mode works fine, but processing time is prohibitively >> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5 >> automatically uses all the available cores for ray tracing. The way Pymol 3 >> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is >> only 100 seconds. >> >> Has anyone encountered similar issues? >> >> Thanks, >> >> Istvan >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Lei S. <le...@gm...> - 2024-07-20 16:25:27
|
Hi Istvan, I have related but not the same problems with pymol3 when making the movies. Using the pymol script that works for pymol 2.5, pymol3 could only produce a movie for the first 240(?) frames and I could not find the setting to fix this issue. In addition, I believe they also changed the default options of load_traj in pymol3. Overall, it appears pymol3 counts on you using the interface but this is not always ideal for heavy duty work, e.g., requiring running "pymol -c" (text mode) on a linux server to finish the job. Lei On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...> wrote: > Hi, > > I have had these issues with the new timeline. It works fine with scenes > and short multi-state objects (like those showcased in the Pymol 3 online > visualization course) but when it comes to real life MD trajectories I > found two "dealbreaker" issues. > > 1) With complex movies based on MD trajectories and not scenes, the Draw > mode is not working. If I select Draw to generate a movie file quickly for > testing then (a) it takes almost as long as Ray Tracing and (b) the movie > is complete garbage, showing only random parts of the system. > > 2) The Ray Tracing mode works fine, but processing time is prohibitively > slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5 > automatically uses all the available cores for ray tracing. The way Pymol 3 > is right now, it takes 24-48 hours to produce a 3000 frame movie, which is > only 100 seconds. > > Has anyone encountered similar issues? > > Thanks, > > Istvan > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Jarrett J. <jar...@sc...> - 2024-07-19 22:48:51
|
Hi Istvan, With regards to CPU ray tracing only running on a single core, that sounds like a major regression; we haven't changed anything in regards to that so I'll investigate. As for your first issue, do you have any examples that I can inspect myself to see what the issue is? Jarrett J. On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary <iko...@gm...> wrote: > Hi, > > I have had these issues with the new timeline. It works fine with scenes > and short multi-state objects (like those showcased in the Pymol 3 online > visualization course) but when it comes to real life MD trajectories I > found two "dealbreaker" issues. > > 1) With complex movies based on MD trajectories and not scenes, the Draw > mode is not working. If I select Draw to generate a movie file quickly for > testing then (a) it takes almost as long as Ray Tracing and (b) the movie > is complete garbage, showing only random parts of the system. > > 2) The Ray Tracing mode works fine, but processing time is prohibitively > slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5 > automatically uses all the available cores for ray tracing. The way Pymol 3 > is right now, it takes 24-48 hours to produce a 3000 frame movie, which is > only 100 seconds. > > Has anyone encountered similar issues? > > Thanks, > > Istvan > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Istvan K. <iko...@gm...> - 2024-07-19 22:45:11
|
Hi, It seems that the Create command can only copy either a single state or all states but no ranges. The range option would be very useful in stitching together a trajectory from parts of other trajectories. This functionality is readily available in the Timeline, but AFAIK not available in Create. Right now the only solution seems to use a hugely inefficient loop copying a whole range state by state. Does anyone know a better solution? Thanks, Istvan |
From: Istvan K. <iko...@gm...> - 2024-07-19 22:35:01
|
Hi Jarrett, Thanks for the quick reply. I am using version 3.03 on Linux and Mac. No conda package is yet available, so these are the Schrödinger provided binaries. Ray Tracing definitely uses only a single CPU. Regarding the Draw problem, I have the example that I used in my coursework. Can you point me to a place where I can upload it to? I have the Pymol session and the Draw/Ray videos. The total size is ~440 MB. BTW, I thought that saving a session with an active Timeline would save the Timeline as well, but that doesn't seem to be the case as you can see when you open the session file. Many thanks, Istvan On Fri, Jul 19, 2024 at 6:19 PM Jarrett Johnson < jar...@sc...> wrote: > Hi Istvan, > > With regards to CPU ray tracing only running on a single core, that sounds > like a major regression; we haven't changed anything in regards to that so > I'll investigate. As for your first issue, do you have any examples that I > can inspect myself to see what the issue is? > > Jarrett J. > > On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary <iko...@gm...> > wrote: > >> Hi, >> >> I have had these issues with the new timeline. It works fine with scenes >> and short multi-state objects (like those showcased in the Pymol 3 online >> visualization course) but when it comes to real life MD trajectories I >> found two "dealbreaker" issues. >> >> 1) With complex movies based on MD trajectories and not scenes, the Draw >> mode is not working. If I select Draw to generate a movie file quickly for >> testing then (a) it takes almost as long as Ray Tracing and (b) the movie >> is complete garbage, showing only random parts of the system. >> >> 2) The Ray Tracing mode works fine, but processing time is prohibitively >> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5 >> automatically uses all the available cores for ray tracing. The way Pymol 3 >> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is >> only 100 seconds. >> >> Has anyone encountered similar issues? >> >> Thanks, >> >> Istvan >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > |
From: Istvan K. <iko...@gm...> - 2024-07-19 22:10:01
|
Hi, I have had these issues with the new timeline. It works fine with scenes and short multi-state objects (like those showcased in the Pymol 3 online visualization course) but when it comes to real life MD trajectories I found two "dealbreaker" issues. 1) With complex movies based on MD trajectories and not scenes, the Draw mode is not working. If I select Draw to generate a movie file quickly for testing then (a) it takes almost as long as Ray Tracing and (b) the movie is complete garbage, showing only random parts of the system. 2) The Ray Tracing mode works fine, but processing time is prohibitively slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5 automatically uses all the available cores for ray tracing. The way Pymol 3 is right now, it takes 24-48 hours to produce a 3000 frame movie, which is only 100 seconds. Has anyone encountered similar issues? Thanks, Istvan |
From: Jarrett J. <jar...@sc...> - 2024-07-17 17:54:16
|
Hi Robert, BinaryCIF is already available in PyMOL open-source master <https://github.com/schrodinger/pymol-open-source/pull/353>. This is expected to be shipped with a patched PyMOL 2.6 LTS next week and PyMOL 3.1 when that version is shipped. Best, Jarrett J. On Wed, Jul 17, 2024 at 1:23 PM Robert Hanson via PyMOL-users < pym...@li...> wrote: > 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 > in...@rc.... > > > > --- > 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/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Robert H. <ha...@st...> - 2024-07-17 17:22:39
|
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 in...@rc.... --- 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.* |
From: Joel S. <mjs...@al...> - 2024-07-16 13:09:19
|
Hello Pymol Community, I hope you're well:). Towards the above-topic, my trajectory files .inp File´s water coordinates need to be flipped to the other side of the ligand C5´s interaction-site to preclude inappropriate interactions with the adjacent C-atom and to moreover bring the final .xyz trajectory file distance to less than 5.0 A (see screenshots attached labeled .inp and .xyz, first and last coordinates of the trajectory file, dashed lines exhibit water H-bonds to C5). How would I flip these Cartesian Coordinates to the other side of C5? Thanks if you know:), Joel 🚀 |
From: Jorge M. <jor...@gm...> - 2024-07-15 23:17:59
|
I am wondering if anyone has an example of embedding the main pymol window inside a wxPython application as a widget. Since in the wx toolkit, both the C++ layer (wxWidgets) and the python layer (wxPython) support having a custom widget rendered by OpenGL, this should be possible ( https://wiki.wxwidgets.org/WxGLCanvas and https://docs.wxpython.org/wx.glcanvas.GLCanvas.html either at the C++ level or the python level. My goal is to create an open source project containing such a widget if it doesn't already exist. I am not familiar with pymol but I am a regular contributor to wxPython and I have in particular contributed to the embedding of matplotlib figures inside wxPython (See https://github.com/matplotlib/matplotlib/pull/26710) Any help getting started on this would be greatly appreciated. Thank you, Jorge |
From: <724...@qq...> - 2024-07-08 03:49:00
|
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? |