From gb1995 at zju.edu.cn Wed Dec 2 00:58:08 2020 From: gb1995 at zju.edu.cn (gb1995 at zju.edu.cn) Date: Wed, 2 Dec 2020 16:58:08 +0800 (GMT+08:00) Subject: [Chimera-users] pythonw.exe always run new windows Message-ID: <6ed5daee.12878.17622ac5650.Coremail.gb1995@zju.edu.cn> After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6135c7da-bb44-44ed-be9b-6e1d14afa98d.png Type: image/png Size: 1498822 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: fe8b296c-b964-4d1d-b0ff-0577d1be443c.png Type: image/png Size: 62235 bytes Desc: not available URL: From goddard at sonic.net Wed Dec 2 09:54:13 2020 From: goddard at sonic.net (Tom Goddard) Date: Wed, 2 Dec 2020 09:54:13 -0800 Subject: [Chimera-users] pythonw.exe always run new windows In-Reply-To: <6ed5daee.12878.17622ac5650.Coremail.gb1995@zju.edu.cn> References: <6ed5daee.12878.17622ac5650.Coremail.gb1995@zju.edu.cn> Message-ID: That looks like some malware triggering all the Chimera menu entries. It is possible to tell Chimera to start specific windows when it starts using its menu Favorites / Preferences / Tools the Auto Start checkbuttons. But your screen shot shows Fetch by Id (from File menu) and that cannot be auto-started so I don't think autostart is doing it. The fact that your web browser starts showing pages is probably because Chimera Help menu entries show web pages in your default browser for Chimera documentation. Possibly Chimera could be getting a whole stream of menu shortcut keys that invoke the menu entries, but again their is no shortcut for Fetch by Id so that seems unlikely, So I have no good idea about the crazy behavior you see other than malware on your computer being able to trigger all the Chimera menu entries. Tom > On Dec 2, 2020, at 12:58 AM, gb1995 at zju.edu.cn wrote: > > After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally. > <6135c7da-bb44-44ed-be9b-6e1d14afa98d.png> > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From Ruchika at ucsf.edu Wed Dec 2 12:48:34 2020 From: Ruchika at ucsf.edu (Ruchika) Date: Wed, 2 Dec 2020 20:48:34 +0000 Subject: [Chimera-users] label position Message-ID: Hi Elaine I selected alpha carbon of some specific residues and labeled them using label option (one letter specifier + number) in actions menu. After labeling these residues and setting these fonts, some of the labels are overlapping onto one another. I used following command (setattr m residueLabelPos 2) to place them on the alpha carbon. However, they are still overlapping. I am just wondering if there is any other way to separate the label and not overlap on each other. Please let me know. Thanks !! Regards Ruchika -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Dec 2 12:59:06 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Dec 2020 12:59:06 -0800 Subject: [Chimera-users] label position In-Reply-To: References: Message-ID: <58E6431F-BF0A-4319-80DB-D4589B54BDB2@cgl.ucsf.edu> Hi Ruchika, You can use the mouse to drag the labels. Open the Preferences from the Favorites menu, go to Category: Mouse, and then choose which mouse button to assign to moving the labels. See: After you are done dragging the labels, you should probably reassign that mouse button back to its previous function. However, to make nice labels for figures, 2D Labels are often better than the regular "3D" labels that move with the structure. You are using those 3D labels, which are mostly for your own interactive use as you move the structure around. The 2D Labels tool is in the menu under Tools... Depiction. See: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 2, 2020, at 12:48 PM, Ruchika wrote: > > Hi Elaine > I selected alpha carbon of some specific residues and labeled them using label option (one letter specifier + number) in actions menu. After labeling these residues and setting these fonts, some of the labels are overlapping onto one another. > I used following command (setattr m residueLabelPos 2) to place them on the alpha carbon. However, they are still overlapping. I am just wondering if there is any other way to separate the label and not overlap on each other. Please let me know. > Thanks !! > Regards > Ruchika From gb1995 at zju.edu.cn Wed Dec 2 22:31:45 2020 From: gb1995 at zju.edu.cn (gb1995 at zju.edu.cn) Date: Thu, 3 Dec 2020 14:31:45 +0800 (GMT+08:00) Subject: [Chimera-users] pythonw.exe always run new windows is the same computer In-Reply-To: References: <6ed5daee.12878.17622ac5650.Coremail.gb1995@zju.edu.cn> Message-ID: <2329cee1.16b87.176274caf3a.Coremail.gb1995@zju.edu.cn> Dear Tom: Thank you for your reply, I want to supply some important informations. last day? I use another users' picture to introduce my problem. He aslo meet the same thing with me . The link :https://answers.microsoft.com/zh-hans/windows/forum/all/%E5%AE%89%E8%A3%85%E5%B9%B6%E6%89%93%E5%BC%80ucsf/19c5e5d3-064a-47b7-8514-7b87059530aa And I'm sure , we use the same computer Huawei rongyao magic book 2019. The link:https://www.giztop.com/huawei-honor-magicbook-2019.html So i use his picture and translate his chinses words into english to send your team. My problem is little different from him ,I can install on D data,but D data 's startion is alwasys "pythonw.exe always run new windows " .But when i install on C data in default way ,it can start normally that the computer is on just. When the computer is on 1 hour maybe ,it daam wrong. However, the one hour when i use, only the chrome and wechat start, I have done the experiment. But The chimera X is OK on D Data,and never happen it. And on the another usr's problem wbsite ,i saw ohther people meet the same question. I think maybe the Chimera have wrong in rongyao computer? if the inter program have conflict? here are my picture? > -----????----- > ???: "Tom Goddard" > ????: 2020-12-03 01:54:13 (???) > ???: gb1995 at zju.edu.cn > ??: "chimera-users at cgl.ucsf.edu BB" > ??: Re: [Chimera-users] pythonw.exe always run new windows > > That looks like some malware triggering all the Chimera menu entries. It is possible to tell Chimera to start specific windows when it starts using its menu Favorites / Preferences / Tools the Auto Start checkbuttons. But your screen shot shows Fetch by Id (from File menu) and that cannot be auto-started so I don't think autostart is doing it. The fact that your web browser starts showing pages is probably because Chimera Help menu entries show web pages in your default browser for Chimera documentation. Possibly Chimera could be getting a whole stream of menu shortcut keys that invoke the menu entries, but again their is no shortcut for Fetch by Id so that seems unlikely, > > So I have no good idea about the crazy behavior you see other than malware on your computer being able to trigger all the Chimera menu entries. > > Tom > > > > On Dec 2, 2020, at 12:58 AM, gb1995 at zju.edu.cn wrote: > > > > After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally. > > <6135c7da-bb44-44ed-be9b-6e1d14afa98d.png> > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- A non-text attachment was scrubbed... Name: 1606975436(1).png Type: image/png Size: 549728 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ??.PNG Type: image/png Size: 49594 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ?? 1.PNG Type: image/png Size: 68350 bytes Desc: not available URL: From goddard at sonic.net Thu Dec 3 09:07:25 2020 From: goddard at sonic.net (Tom Goddard) Date: Thu, 3 Dec 2020 09:07:25 -0800 Subject: [Chimera-users] pythonw.exe always run new windows is the same computer In-Reply-To: <2329cee1.16b87.176274caf3a.Coremail.gb1995@zju.edu.cn> References: <6ed5daee.12878.17622ac5650.Coremail.gb1995@zju.edu.cn> <2329cee1.16b87.176274caf3a.Coremail.gb1995@zju.edu.cn> Message-ID: This problem has also been reported in past years and we never figured it out. It looks like random Chimera menu entries are being pressed. I see that your laptop has a touch screen. I wonder if somehow the touch screen is sending events to Chimera. Is it possible to turn off the touch screen and see if Chimera works then? Chimera uses the Tk window toolkit and possibly that is not behaving correctly with the touch screen. I made a bug report for your problem. http://plato.cgl.ucsf.edu/trac/chimera/ticket/17910 You will get email about that bug report. Reply to that email to discuss the problem further. Probably few people on the general mailing list are interested to hear about it. Tom > On Dec 2, 2020, at 10:31 PM, gb1995 at zju.edu.cn wrote: > > Dear Tom: > Thank you for your reply, I want to supply some important informations. last day? I use another users' picture to introduce my problem. He aslo meet the same thing with me . The link :https://answers.microsoft.com/zh-hans/windows/forum/all/%E5%AE%89%E8%A3%85%E5%B9%B6%E6%89%93%E5%BC%80ucsf/19c5e5d3-064a-47b7-8514-7b87059530aa > And I'm sure , we use the same computer Huawei rongyao magic book 2019. The link:https://www.giztop.com/huawei-honor-magicbook-2019.html > So i use his picture and translate his chinses words into english to send your team. My problem is little different from him ,I can install on D data,but D data 's startion is alwasys "pythonw.exe always run new windows " .But when i install on C data in default way ,it can start normally that the computer is on just. When the computer is on 1 hour maybe ,it daam wrong. However, the one hour when i use, only the chrome and wechat start, I have done the experiment. But The chimera X is OK on D Data,and never happen it. > And on the another usr's problem wbsite ,i saw ohther people meet the same question. I think maybe the Chimera have wrong in rongyao computer? if the inter program have conflict? > here are my picture? > >> -----????----- >> ???: "Tom Goddard" >> ????: 2020-12-03 01:54:13 (???) >> ???: gb1995 at zju.edu.cn >> ??: "chimera-users at cgl.ucsf.edu BB" >> ??: Re: [Chimera-users] pythonw.exe always run new windows >> >> That looks like some malware triggering all the Chimera menu entries. It is possible to tell Chimera to start specific windows when it starts using its menu Favorites / Preferences / Tools the Auto Start checkbuttons. But your screen shot shows Fetch by Id (from File menu) and that cannot be auto-started so I don't think autostart is doing it. The fact that your web browser starts showing pages is probably because Chimera Help menu entries show web pages in your default browser for Chimera documentation. Possibly Chimera could be getting a whole stream of menu shortcut keys that invoke the menu entries, but again their is no shortcut for Fetch by Id so that seems unlikely, >> >> So I have no good idea about the crazy behavior you see other than malware on your computer being able to trigger all the Chimera menu entries. >> >> Tom >> >> >>> On Dec 2, 2020, at 12:58 AM, gb1995 at zju.edu.cn wrote: >>> >>> After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally. >>> <6135c7da-bb44-44ed-be9b-6e1d14afa98d.png> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > <1606975436(1).png>_______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Dec 3 13:02:33 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 3 Dec 2020 13:02:33 -0800 Subject: [Chimera-users] downtime on Monday, December 7, 2020 Message-ID: <74EBC24E-E2A9-481A-8EC4-B669BDFB3A97@cgl.ucsf.edu> Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco From e.choi0309 at gmail.com Thu Dec 3 22:23:21 2020 From: e.choi0309 at gmail.com (Eric Choi) Date: Fri, 4 Dec 2020 01:23:21 -0500 Subject: [Chimera-users] Failure Running ANTECHAMER Message-ID: To whom it may concern, My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? Thank you very much for your time and help. Sincerely, Eric Choi -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ANTECHAMBER Error Message.png Type: image/png Size: 62469 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Reply Log.png Type: image/png Size: 193054 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Dec 4 12:34:15 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 4 Dec 2020 12:34:15 -0800 Subject: [Chimera-users] Failure Running ANTECHAMER In-Reply-To: References: Message-ID: <8F7AF23F-5FC4-4A51-A700-0233BC97DE07@cgl.ucsf.edu> Hi Eric, There are occasionally specific compounds that the Antechamber method and/or AM1-BCC just can't handle, e.g. with conjugated bond patterns that are hard to discern the correct hybridization or bond order, elements not often found in organic compounds, or high charge density like polyphosphates. On those specific compounds (you would have to figure out which ones exactly are failing) you may need to fall back to the simpler Gasteiger charge method, or if that also fails, find some other way to parametrize them. Normally you would tell by residue name, but I'm guessing all of your residues have the same name, ZIN. In that case, no idea other than something really tedious like counting the number of times Antechamber was called in the Log. Maybe an alternative (also ugly) is to make your script do the ligands one by one, writing separate mol2 files for each, and then you could see how many you got before the error. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 3, 2020, at 10:23 PM, Eric Choi wrote: > > To whom it may concern, > > My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. > > In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? > > Thank you very much for your time and help. > > Sincerely, > Eric Choi > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Fri Dec 4 12:45:23 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 4 Dec 2020 12:45:23 -0800 Subject: [Chimera-users] Failure Running ANTECHAMER In-Reply-To: <8F7AF23F-5FC4-4A51-A700-0233BC97DE07@cgl.ucsf.edu> References: <8F7AF23F-5FC4-4A51-A700-0233BC97DE07@cgl.ucsf.edu> Message-ID: <989B9B4D-893B-43E9-9654-E011F73D9308@cgl.ucsf.edu> To supplement Elaine's answer, Chimera itself will sometimes protonate an unusual structure incorrectly or make an incorrect estimate of the formal charge. That's what happened here, which results in Antechamber's complaint about an odd number of electrons. You would need to correct the protonation or charge estimate "by hand". However, actually finding which compound is the problematic one is still an issue. I don't have any better suggestions for that than what Elaine provided. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 4, 2020, at 12:34 PM, Elaine Meng wrote: > > Hi Eric, > There are occasionally specific compounds that the Antechamber method and/or AM1-BCC just can't handle, e.g. with conjugated bond patterns that are hard to discern the correct hybridization or bond order, elements not often found in organic compounds, or high charge density like polyphosphates. On those specific compounds (you would have to figure out which ones exactly are failing) you may need to fall back to the simpler Gasteiger charge method, or if that also fails, find some other way to parametrize them. > > Normally you would tell by residue name, but I'm guessing all of your residues have the same name, ZIN. In that case, no idea other than something really tedious like counting the number of times Antechamber was called in the Log. > > Maybe an alternative (also ugly) is to make your script do the ligands one by one, writing separate mol2 files for each, and then you could see how many you got before the error. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Dec 3, 2020, at 10:23 PM, Eric Choi wrote: >> >> To whom it may concern, >> >> My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. >> >> In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? >> >> Thank you very much for your time and help. >> >> Sincerely, >> Eric Choi >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From nagy at fpharm.uniba.sk Mon Dec 7 23:31:38 2020 From: nagy at fpharm.uniba.sk (Nagy Milan) Date: Tue, 8 Dec 2020 07:31:38 +0000 Subject: [Chimera-users] Chimera and All-in-One system tune up tools Message-ID: Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Dec 8 16:26:46 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 8 Dec 2020 16:26:46 -0800 Subject: [Chimera-users] Chimera and All-in-One system tune up tools In-Reply-To: References: Message-ID: <21901063-39E2-44B2-9F25-20EDAD6A9DBF@cgl.ucsf.edu> Hi Milan, According to the Wise Care 365 web page, it will "stop any processes that try to secretly change Windows registry". Chimera adds keys to the registry. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 7, 2020, at 11:31 PM, Nagy Milan wrote: > > Hello, > how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. > > Greetings > Milan > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmsstarlight at gmail.com Wed Dec 9 07:01:45 2020 From: jmsstarlight at gmail.com (Jeff Saxon) Date: Wed, 9 Dec 2020 16:01:45 +0100 Subject: [Chimera-users] Using UCSF Chimera inside python environment Message-ID: Dear Chimera Users, I would like to use chimera to do some calculations on PDB filles (mainly I am interesting to cluster conformations in multi-model PDB using Ensemble cluster) Could you explain to me how I could install chimera (I am using python3 with conda) in order that I could use some of Chimera's functions directly inside of my python scripts? I have already tried install package pychimers but did not succeed conda install -c insilichem pychimera nsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] - pychimera -> python[version='3.4.*|3.5.*'] Your python: python=3.8 May I use chimera with my python using alternative ways of installations? Thank you in advance! J. From nagy at fpharm.uniba.sk Tue Dec 8 21:50:02 2020 From: nagy at fpharm.uniba.sk (Nagy Milan) Date: Wed, 9 Dec 2020 05:50:02 +0000 Subject: [Chimera-users] Chimera and All-in-One system tune up tools In-Reply-To: <21901063-39E2-44B2-9F25-20EDAD6A9DBF@cgl.ucsf.edu> References: , <21901063-39E2-44B2-9F25-20EDAD6A9DBF@cgl.ucsf.edu> Message-ID: Hi Eric, thank you for the answer. It means creating a registry check exception in Wise Care 365 could solve above mentioned problem ...? Milan ________________________________ Od: Eric Pettersen Odoslan?: streda 9. decembra 2020 1:26 Komu: Nagy Milan K?pia: chimera-users at cgl.ucsf.edu Predmet: Re: [Chimera-users] Chimera and All-in-One system tune up tools Hi Milan, According to the Wise Care 365 web page, it will "stop any processes that try to secretly change Windows registry". Chimera adds keys to the registry. --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 7, 2020, at 11:31 PM, Nagy Milan > wrote: Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Dec 9 09:22:57 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 9 Dec 2020 09:22:57 -0800 Subject: [Chimera-users] Chimera and All-in-One system tune up tools In-Reply-To: References: <21901063-39E2-44B2-9F25-20EDAD6A9DBF@cgl.ucsf.edu> Message-ID: <1C5B6E9D-4C78-4BB6-803C-F391AE4291C0@cgl.ucsf.edu> Hi Milan, It could. I don't know what other operations the tune-up tools you used prevent -- I only took a cursory glance at the Wise Care 365 web page. Nonetheless, it is possible that making that exception would be enough. --Eric > On Dec 8, 2020, at 9:50 PM, Nagy Milan wrote: > > Hi Eric, > thank you for the answer. It means creating a registry check exception in Wise Care 365 could solve above mentioned problem ...? > Milan > > Od: Eric Pettersen > > Odoslan?: streda 9. decembra 2020 1:26 > Komu: Nagy Milan > > K?pia: chimera-users at cgl.ucsf.edu > > Predmet: Re: [Chimera-users] Chimera and All-in-One system tune up tools > > Hi Milan, > According to the Wise Care 365 web page, it will "stop any processes that try to secretly change Windows registry". Chimera adds keys to the registry. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Dec 7, 2020, at 11:31 PM, Nagy Milan > wrote: >> >> Hello, >> how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. >> >> Greetings >> Milan >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Dec 9 14:08:50 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 9 Dec 2020 14:08:50 -0800 Subject: [Chimera-users] Using UCSF Chimera inside python environment In-Reply-To: References: Message-ID: <2426AE0C-6294-4E01-8DDD-72B710DBFD3E@cgl.ucsf.edu> Unfortunately this is nigh impossible. First, the entire code base of Chimera is Python 2 and will not import into a Python 3 interpreter, so you can't use it directly. Second, the Ensemble Cluster code was written entirely with a graphical user interface in mind, and the computation code can't easily be called directly, even from a Python 2 script. I don't have any good suggestions for you here that don't involve a Herculean amount of effort. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 9, 2020, at 7:01 AM, Jeff Saxon wrote: > > Dear Chimera Users, > > I would like to use chimera to do some calculations on PDB filles > (mainly I am interesting to cluster conformations in multi-model PDB > using Ensemble cluster) > > Could you explain to me how I could install chimera (I am using > python3 with conda) in order that I could use some of Chimera's > functions directly inside of my python scripts? > > > I have already tried install package pychimers but did not succeed > > conda install -c insilichem pychimera > > nsatisfiableError: The following specifications were found > > to be incompatible with the existing python installation in your environment: > > Specifications: > > - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] > > - pychimera -> python[version='3.4.*|3.5.*'] > > Your python: python=3.8 > > May I use chimera with my python using alternative ways of installations? > > Thank you in advance! > J. > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From bbasanta at scripps.edu Wed Dec 9 14:29:36 2020 From: bbasanta at scripps.edu (Benjamin Basanta) Date: Wed, 9 Dec 2020 22:29:36 +0000 Subject: [Chimera-users] Using UCSF Chimera inside python environment In-Reply-To: References: Message-ID: Hi Jeff, I wrote a short explanation on how to put together a conda environment with pychemera in this git repo: https://github.com/GrotjahnLab/guided_tomo_align You don't need all the files there, just pychimera.yml I don't know enough about the cluster conformations function help you, sadly. Best, Benja ________________________________ From: Chimera-users on behalf of Jeff Saxon Sent: Wednesday, December 9, 2020 7:01 AM To: chimera-users at cgl.ucsf.edu BB Subject: [Chimera-users] Using UCSF Chimera inside python environment Dear Chimera Users, I would like to use chimera to do some calculations on PDB filles (mainly I am interesting to cluster conformations in multi-model PDB using Ensemble cluster) Could you explain to me how I could install chimera (I am using python3 with conda) in order that I could use some of Chimera's functions directly inside of my python scripts? I have already tried install package pychimers but did not succeed conda install -c insilichem pychimera nsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] - pychimera -> python[version='3.4.*|3.5.*'] Your python: python=3.8 May I use chimera with my python using alternative ways of installations? Thank you in advance! J. _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmsstarlight at gmail.com Thu Dec 10 01:19:02 2020 From: jmsstarlight at gmail.com (Jeff Saxon) Date: Thu, 10 Dec 2020 10:19:02 +0100 Subject: [Chimera-users] Using UCSF Chimera inside python environment In-Reply-To: References: Message-ID: Hello everyone, Many thanks for your kind responses! Anyway, I will try to integrate pychimera in my python environment to test it for other purposes. May someone suggest another python library suitable to do cluster analysis of pdbs ?? In fact I am dealing with a trivial problem, having a multi-model of PDB (ligand poses predicted by protein-ligand docking), that I need to cluster based on the RMSD between these models and then plot a bar plot representing the clusters and their populations.. Many thanks in advance! Cheers, J ??, 9 ???. 2020 ?. ? 23:29, Benjamin Basanta : > > Hi Jeff, > > I wrote a short explanation on how to put together a conda environment with pychemera in this git repo: https://github.com/GrotjahnLab/guided_tomo_align > > You don't need all the files there, just pychimera.yml > > I don't know enough about the cluster conformations function help you, sadly. > > Best, > Benja > ________________________________ > From: Chimera-users on behalf of Jeff Saxon > Sent: Wednesday, December 9, 2020 7:01 AM > To: chimera-users at cgl.ucsf.edu BB > Subject: [Chimera-users] Using UCSF Chimera inside python environment > > Dear Chimera Users, > > I would like to use chimera to do some calculations on PDB filles > (mainly I am interesting to cluster conformations in multi-model PDB > using Ensemble cluster) > > Could you explain to me how I could install chimera (I am using > python3 with conda) in order that I could use some of Chimera's > functions directly inside of my python scripts? > > > I have already tried install package pychimers but did not succeed > > conda install -c insilichem pychimera > > nsatisfiableError: The following specifications were found > > to be incompatible with the existing python installation in your environment: > > Specifications: > > - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] > > - pychimera -> python[version='3.4.*|3.5.*'] > > Your python: python=3.8 > > May I use chimera with my python using alternative ways of installations? > > Thank you in advance! > J. > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From nagy at fpharm.uniba.sk Wed Dec 9 22:20:38 2020 From: nagy at fpharm.uniba.sk (Nagy Milan) Date: Thu, 10 Dec 2020 06:20:38 +0000 Subject: [Chimera-users] Chimera and All-in-One system tune up tools In-Reply-To: <1C5B6E9D-4C78-4BB6-803C-F391AE4291C0@cgl.ucsf.edu> References: <21901063-39E2-44B2-9F25-20EDAD6A9DBF@cgl.ucsf.edu> , <1C5B6E9D-4C78-4BB6-803C-F391AE4291C0@cgl.ucsf.edu> Message-ID: ? ________________________________ Od: Eric Pettersen Odoslan?: streda 9. decembra 2020 18:22 Komu: Nagy Milan K?pia: Chimera Predmet: Re: [Chimera-users] Chimera and All-in-One system tune up tools Hi Milan, It could. I don't know what other operations the tune-up tools you used prevent -- I only took a cursory glance at the Wise Care 365 web page. Nonetheless, it is possible that making that exception would be enough. --Eric On Dec 8, 2020, at 9:50 PM, Nagy Milan > wrote: Hi Eric, thank you for the answer. It means creating a registry check exception in Wise Care 365 could solve above mentioned problem ...? Milan ________________________________ Od: Eric Pettersen > Odoslan?: streda 9. decembra 2020 1:26 Komu: Nagy Milan > K?pia: chimera-users at cgl.ucsf.edu > Predmet: Re: [Chimera-users] Chimera and All-in-One system tune up tools Hi Milan, According to the Wise Care 365 web page, it will "stop any processes that try to secretly change Windows registry". Chimera adds keys to the registry. --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 7, 2020, at 11:31 PM, Nagy Milan > wrote: Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From wswran001 at myuct.ac.za Sat Dec 12 01:25:04 2020 From: wswran001 at myuct.ac.za (Rani Wiswedel) Date: Sat, 12 Dec 2020 11:25:04 +0200 Subject: [Chimera-users] scaling models Message-ID: Good day, Is there any way to ensure that the scale you are looking at is kept constant when taking images of different models? I would like to include photos of pores from my structure, but each pore is saved in a different file, so I have to re-open Chimera and adjust the view each time. I have the scale bar open and the projection set to orthographic, but I am struggling to manually adjust the view so that the scale bar looks the same length in each picture (attached below is my manual attempt (pic1)). Is there any way to set the scale each time chimera is opened so that I don't end up with pictures that have scale bars that appear to be different sizes?(example of what I would like to achieve is in the second image(pic2)) Thank you! Regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: scale bar same size.png Type: image/png Size: 396368 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pic1-scale bar diff size.png Type: image/png Size: 153559 bytes Desc: not available URL: From luiza at strubi.ox.ac.uk Sat Dec 12 03:33:08 2020 From: luiza at strubi.ox.ac.uk (=?UTF-8?Q?Luiza_Mendon=C3=A7a?=) Date: Sat, 12 Dec 2020 11:33:08 +0000 Subject: [Chimera-users] Can't open IMOD .mod file Message-ID: Good morning, Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help. Best, Luiza Mendonca Zhang Lab University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Dec 12 07:30:17 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 12 Dec 2020 07:30:17 -0800 Subject: [Chimera-users] scaling models In-Reply-To: References: Message-ID: Hi Rani, There was an experimental command "setzoom" available as a separate zip file from 2006. Although the "window" command has been included in the standard Chimera, the "setzoom" command is not. You could try installing that zip file but I don't know if it works with current Chimera. For the zip file and link to details of the command and installation, search for "Set Magnification and Window Size" in this page: Another possibility is to use ChimeraX instead of Chimera. ChimeraX has a command option to scale pixel size in length units: ?zoom" command ?pixelSize? option I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 12, 2020, at 1:25 AM, Rani Wiswedel wrote: > > Good day, > Is there any way to ensure that the scale you are looking at is kept constant when taking images of different models? I would like to include photos of pores from my structure, but each pore is saved in a different file, so I have to re-open Chimera and adjust the view each time. I have the scale bar open and the projection set to orthographic, but I am struggling to manually adjust the view so that the scale bar looks the same length in each picture (attached below is my manual attempt (pic1)). Is there any way to set the scale each time chimera is opened so that I don't end up with pictures that have scale bars that appear to be different sizes?(example of what I would like to achieve is in the second image(pic2)) > Thank you! > Regards, > Rani From meng at cgl.ucsf.edu Sat Dec 12 07:35:25 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 12 Dec 2020 07:35:25 -0800 Subject: [Chimera-users] Can't open IMOD .mod file In-Reply-To: References: Message-ID: <1625CB0D-0EDB-475F-81B9-B5269FD5A1BB@cgl.ucsf.edu> Hi Luiza, This page lists the file types Chimera can read: Searching for "IMOD" in the above, I see IMOD map format (.rec) and IMOD segmentation meshes (.imod, .mod) and link to more detailed information about the latter in another page: That second link says only mesh data are read from the IMOD segmentation, not the contour data. However, it also explains how to make a small change to the code to also read the contours. I hope this helps Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 12, 2020, at 3:33 AM, Luiza Mendon?a wrote: > > Good morning, > > Is it possible to open IMOD .mod file in chimera? > I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. > My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? > I appreciate any help. > > Best, > Luiza Mendonca > Zhang Lab > University of Oxford From goddard at sonic.net Sat Dec 12 11:11:22 2020 From: goddard at sonic.net (Tom Goddard) Date: Sat, 12 Dec 2020 11:11:22 -0800 Subject: [Chimera-users] Can't open IMOD .mod file In-Reply-To: References: Message-ID: <6FC17EA0-E8A1-4E6E-9CD4-A98BEA61BBD7@sonic.net> Hi Luiza, Our newer program ChimeraX can read points from imod files. You have to open it with the "contours true" option, for example, open ~/Desktop/particles.imod contours true Documentation https://www.rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html I just tested it and it gave an error. I fixed the code so tonight's ChimeraX build will be able to read IMOD points and contour lines. The daily builds are below the releases on the download page https://www.rbvi.ucsf.edu/chimerax/download.html#daily Tom > On Dec 12, 2020, at 3:33 AM, Luiza Mendon?a wrote: > > Good morning, > > Is it possible to open IMOD .mod file in chimera? > I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. > My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? > I appreciate any help. > > Best, > Luiza Mendonca > Zhang Lab > University of Oxford > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From luiza at strubi.ox.ac.uk Sat Dec 12 11:58:37 2020 From: luiza at strubi.ox.ac.uk (=?UTF-8?Q?Luiza_Mendon=C3=A7a?=) Date: Sat, 12 Dec 2020 19:58:37 +0000 Subject: [Chimera-users] Can't open IMOD .mod file In-Reply-To: <6FC17EA0-E8A1-4E6E-9CD4-A98BEA61BBD7@sonic.net> References: <6FC17EA0-E8A1-4E6E-9CD4-A98BEA61BBD7@sonic.net> Message-ID: Thank you Elaine and Tom, Elaine, even after changing the .py and restarting chimera, the model points won't open... But thank you for the help anyway. Tom, I will wait for tomorrow to download ChimeraX, thanks! Best, Luiza On Sat, 12 Dec 2020 at 19:11, Tom Goddard wrote: > Hi Luiza, > > Our newer program ChimeraX can read points from imod files. You have to > open it with the "contours true" option, for example, > > open ~/Desktop/particles.imod contours true > > Documentation > > https://www.rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html > > I just tested it and it gave an error. I fixed the code so tonight's > ChimeraX build will be able to read IMOD points and contour lines. The > daily builds are below the releases on the download page > > https://www.rbvi.ucsf.edu/chimerax/download.html#daily > > Tom > > > > On Dec 12, 2020, at 3:33 AM, Luiza Mendon?a > wrote: > > > > Good morning, > > > > Is it possible to open IMOD .mod file in chimera? > > I am trying to do so, and I select the IMOD .mod file in the pop-up > window asking about the file type, but nothing is showing up (blue initial > chimera window unchanged), even though the log states 'finished opening > file'. > > My .mod file is just XYZ scattered points. Do I need to do any > conversion before being able to open it? > > I appreciate any help. > > > > Best, > > Luiza Mendonca > > Zhang Lab > > University of Oxford > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: > https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdickson6 at gmail.com Mon Dec 14 07:58:28 2020 From: jdickson6 at gmail.com (Juleen Dickson) Date: Mon, 14 Dec 2020 09:58:28 -0600 Subject: [Chimera-users] Volume information from segmentation data Message-ID: Good Morning Everyone, I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help. Cheers, Juleen "Never interrupt someone doing what you said couldn't be done." *--Amelia Earhart, American aviator* "Friends... they cherish one another's hopes. They are kind to one another's dreams." *-- Henry David Thoreau* *?Life isn?t about waiting for the storm to pass. It?s about learning how to dance in the rain?? -Vivian Greene* -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Dec 14 10:55:43 2020 From: goddard at sonic.net (Tom Goddard) Date: Mon, 14 Dec 2020 10:55:43 -0800 Subject: [Chimera-users] Volume information from segmentation data In-Reply-To: References: Message-ID: <3BD1BD0D-022E-48C4-835C-3074BC8B6D7E@sonic.net> Hi Juleen, In our newer program ChimeraX there is the "mark connected" command that places a marker on each connected piece of a surface. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html I just added a "stats" option to output measurements for each blob including the surface area, enclosed volume, and number of holes. This will be tonight's ChimeraX builds. https://www.rbvi.ucsf.edu/chimerax/download.html#daily The mark connected command originally from this ChimeraX example code https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html Tom > open 22000 from emdb > volume #1 level 0.6903 > surface dust #1 size 10 > marker connected #1 stats true Found 21 connected surface pieces Surface #1.1 has 21 visible blobs # id, center xyz, surface area, enclosed volume, holes 1 154.58 152.55 149.36 108.7 43.23 0 2 173.32 149.15 156.33 212.8 86.06 0 3 156.96 165.48 158.25 320.1 148.3 0 4 160.32 175.48 154.98 98.6 38.59 0 5 143.37 151.62 162.12 77.07 25.17 0 ... > On Dec 14, 2020, at 7:58 AM, Juleen Dickson wrote: > > Good Morning Everyone, > > I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help. > > > Cheers, > Juleen > > "Never interrupt someone doing what you said couldn't be done." > --Amelia Earhart, > American aviator > > "Friends... they cherish one another's hopes. They are kind to one another's dreams." > > -- Henry David Thoreau > ?Life isn?t about waiting for the storm to pass. It?s about learning how to dance in the rain?? -Vivian Greene > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From yasser.almeida at gmail.com Tue Dec 15 02:02:18 2020 From: yasser.almeida at gmail.com (Yasser Almeida) Date: Tue, 15 Dec 2020 11:02:18 +0100 Subject: [Chimera-users] Create an atom object Message-ID: Hello, How can I create an atom object, with a given xyz coordinates, via command or python? Thanks in advance, Yasser -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Dec 15 08:16:22 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 15 Dec 2020 08:16:22 -0800 Subject: [Chimera-users] Create an atom object In-Reply-To: References: Message-ID: <5F719056-41DE-44E3-BCA9-CCF52CB92FFC@cgl.ucsf.edu> Hi Yasser, Chimera does not have a command to do this. In Chimera you could do it with menu Tools... Structure Editing... Build Structure, the "Start Structure" atom option. I don't know python, so I can't give details on that. Other possibilities in Chimera are to manually create (with a text editor) a PDB file or marker file and then open it. If you use ChimeraX instead, there is a "build start atom" command to do it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 15, 2020, at 2:02 AM, Yasser Almeida wrote: > > Hello, > > How can I create an atom object, with a given xyz coordinates, via command or python? > > Thanks in advance, > > Yasser From pett at cgl.ucsf.edu Tue Dec 15 09:17:29 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 15 Dec 2020 09:17:29 -0800 Subject: [Chimera-users] Create an atom object In-Reply-To: <5F719056-41DE-44E3-BCA9-CCF52CB92FFC@cgl.ucsf.edu> References: <5F719056-41DE-44E3-BCA9-CCF52CB92FFC@cgl.ucsf.edu> Message-ID: The Python to place a helium atom named He1 at position x,y,z is: from BuildStructure import placeHelium from chimera import Point atom = placeHelium(residue_name, position=Point(x,y,z)) --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 15, 2020, at 8:16 AM, Elaine Meng wrote: > > Hi Yasser, > Chimera does not have a command to do this. In Chimera you could do it with menu Tools... Structure Editing... Build Structure, the "Start Structure" atom option. I don't know python, so I can't give details on that. > > > Other possibilities in Chimera are to manually create (with a text editor) a PDB file or marker file and then open it. > > If you use ChimeraX instead, there is a "build start atom" command to do it. > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Dec 15, 2020, at 2:02 AM, Yasser Almeida wrote: >> >> Hello, >> >> How can I create an atom object, with a given xyz coordinates, via command or python? >> >> Thanks in advance, >> >> Yasser > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Dec 18 11:56:03 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Dec 2020 11:56:03 -0800 Subject: [Chimera-users] Holiday greetings from the ChimeraX team! References: Message-ID: <4BB77C60-4AEF-40CD-9E7B-80B947C482AF@cgl.ucsf.edu> The Chimera(X) team at the UCSF RBVI wishes you a safe and happy holiday season! Our holiday card is virtual this year: =-=-=-=-=-= Atoms of Apoferritin At a miraculous 1.22 ? resolution, the electron microscopy map of mouse apoferritin (right, EMDB 11638) can be mistaken for an atomic model (left, PDB 7a4m), with each atom standing out. The map from Nakane et al. (2020 Nature 587:152-156) shows glimpses of the lightest atoms, hydrogen, directly revealing the hydrogen-bonding network. Ferritin stores iron, as many as 4500 ions (Fe3+), as crystallites within its shell of 24 proteins. Apoferritin, ferritin without its iron cargo, has rock-like stability, making it ideal for divining the limits of electron microscope resolution. The images were made with UCSF ChimeraX, using ambient-occlusion lighting, coloring to delineate trimeric subunits within the dodecahedral shell, and curved helix tubes. Best wishes for a happy and healthy 2021! Conrad, Greg, Elaine, Tristan, Tom, Scooter, Eric and Tom =-=-=-=-=-= Full-resolution image: > Gallery of previous cards back to 1985: > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RBVI-holiday-2020.png Type: image/png Size: 740297 bytes Desc: not available URL: From underoath006 at gmail.com Fri Dec 18 22:09:42 2020 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Fri, 18 Dec 2020 22:09:42 -0800 Subject: [Chimera-users] Density map tranformation Message-ID: Hello, When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? Best regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephane.duquerroy at pasteur.fr Mon Dec 21 07:15:42 2020 From: stephane.duquerroy at pasteur.fr (=?iso-8859-1?Q?St=E9phane__DUQUERROY?=) Date: Mon, 21 Dec 2020 15:15:42 +0000 Subject: [Chimera-users] Movies and Symetries Message-ID: <2f41e6dcfa0547ee9d86f048082013dd@pasteur.fr> Hi, I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags) I can read it and play it with MD movie menu The PDB File has also BIOMT matrices set for displaying the biological assembly My question is how can I play the movie with multiscale model? How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!) S Duquerroy -- -------------------------------------------- Duquerroy St?phane, PhD, Assistant Professor, Univ Paris Saclay Structural Virology Unit, Institut Pasteur 28 rue du Dr Roux, 75015 Paris - France 33 - (0) 140 613 575 -------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Dec 21 09:13:33 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 21 Dec 2020 09:13:33 -0800 Subject: [Chimera-users] Density map tranformation In-Reply-To: References: Message-ID: <1AF87485-8CDF-42C7-87FF-722EB76B3563@cgl.ucsf.edu> Hi Ahmad, You can report in the Reply Log the transformation of a model relative to another model with "measure rotation" Also, you can save the current overall transformation of models (including any rotations/translations of the whole scene) to a text file with command "matrixget" I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2020, at 10:09 PM, Ahmad Khalifa wrote: > > Hello, > > When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? > > Best regards. From pett at cgl.ucsf.edu Mon Dec 21 11:40:43 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 21 Dec 2020 11:40:43 -0800 Subject: [Chimera-users] Movies and Symetries In-Reply-To: <2f41e6dcfa0547ee9d86f048082013dd@pasteur.fr> References: <2f41e6dcfa0547ee9d86f048082013dd@pasteur.fr> Message-ID: <3ED95647-90B5-4E5B-8FAC-85737DF1D9D4@cgl.ucsf.edu> Hello, As far as I know you will have to run a script every frame to create the assembly and color it the way you want. It is pretty easy to run a script every frame of a trajectory. Use MD Movie's Per-Frame?Define script... menu item to bring up a dialog to run commands every frame. In the dialog make sure you change the "Interpret script as" value to "Chimera commands". The command to expand the BIOMT records is: sym This will create full atomic coordinate copies. You could use the "surfaces true" argument to only make surface copies instead. I'm a little hazy on exactly what you are saying about how you want to do the coloring, but whatever it is you just need to determine what the equivalent commands are and add them to the script. Each symmetry copy has its own model number (look at the Model Panel), so to color them you should be able to do something like "color red #1.1". Clicking OK in the dialog will accept the commands you've entered and you should be able to just play through your trajectory normally. The playback will likely be slow due to the overhead of running 'sym' every frame. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 21, 2020, at 7:15 AM, St?phane DUQUERROY wrote: > > Hi, > I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags) > I can read it and play it with MD movie menu > The PDB File has also BIOMT matrices set for displaying the biological assembly > My question is how can I play the movie with multiscale model? > How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? > (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!) > > S Duquerroy > -- > > > -------------------------------------------- > Duquerroy St?phane, PhD, > Assistant Professor, Univ Paris Saclay > Structural Virology Unit, Institut Pasteur > 28 rue du Dr Roux, 75015 Paris - France > 33 - (0) 140 613 575 > -------------------------------------------- > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Tue Dec 22 12:31:45 2020 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Tue, 22 Dec 2020 12:31:45 -0800 Subject: [Chimera-users] Density map tranformation In-Reply-To: <1AF87485-8CDF-42C7-87FF-722EB76B3563@cgl.ucsf.edu> References: <1AF87485-8CDF-42C7-87FF-722EB76B3563@cgl.ucsf.edu> Message-ID: Thanks a lot. I had experimented with fitting pdb structures and calculating their transformation with the match move false showMatrix true command, which slightly differ than measure rotation, I wonder why. On Mon, Dec 21, 2020, 9:13 AM Elaine Meng wrote: > Hi Ahmad, > You can report in the Reply Log the transformation of a model relative to > another model with "measure rotation" > < > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation > > > > Also, you can save the current overall transformation of models (including > any rotations/translations of the whole scene) to a text file with command > "matrixget" > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Dec 18, 2020, at 10:09 PM, Ahmad Khalifa > wrote: > > > > Hello, > > > > When I fit two maps into each other, I get the transformation matrix in > the reply log, but what if the moving map doesn't converge by fitmap and > require some initial manual alignment, how can I calculate the > transformation matrix for that? > > > > Best regards. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Dec 22 12:58:56 2020 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 22 Dec 2020 12:58:56 -0800 Subject: [Chimera-users] Density map tranformation In-Reply-To: References: <1AF87485-8CDF-42C7-87FF-722EB76B3563@cgl.ucsf.edu> Message-ID: <3B4BA375-E090-488B-97BF-F522B80C594C@cgl.ucsf.edu> The match command reports the transformation of one model compared to itself before running that command, whereas measure rotation would report any current transformation of one model relative to another model. If you expect those to be the same, but the difference is small, it might just be rounding differences. Elaine > On Dec 22, 2020, at 12:31 PM, Ahmad Khalifa wrote: > > Thanks a lot. I had experimented with fitting pdb structures and calculating their transformation with the match move false showMatrix true command, which slightly differ than measure rotation, I wonder why. > > On Mon, Dec 21, 2020, 9:13 AM Elaine Meng wrote: > Hi Ahmad, > You can report in the Reply Log the transformation of a model relative to another model with "measure rotation" > > > Also, you can save the current overall transformation of models (including any rotations/translations of the whole scene) to a text file with command "matrixget" > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Dec 18, 2020, at 10:09 PM, Ahmad Khalifa wrote: > > > > Hello, > > > > When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? > > > > Best regards. > From Lorena.Roldan at uab.cat Wed Dec 23 08:20:36 2020 From: Lorena.Roldan at uab.cat (=?UTF-8?Q?Lorena_Rold=c3=a1n?=) Date: Wed, 23 Dec 2020 17:20:36 +0100 Subject: [Chimera-users] Clustering saving PDB Message-ID: <2c34deb9-329c-6fb4-5c47-63d943e5615c@uab.cat> Good afternoon, I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: ??? lines=f.readlines() ??? cluster_number = 1 ??? for i in range(len(lines)): ??? ??? frame = i ??? ??? if mdInfo["frame number"] == frame: ??? ??? ??? name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) ??? ??? ??? runCommand('write format pdb 0 $name) which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. However, this script is not working, and I would greatly thank any help you could provide me with. Lorena. -- Lorena Rold?n Mart?n *PhD Student in Bioinformatics* Departament de Qu?mica Unitat de Qu?mica F?sica Campus de la UAB ? 08193 Bellaterra (Cerdanyola del Vall?s) ? Barcelona ? Spain +34 690799431 www.uab.cat -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Dec 23 10:31:28 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 23 Dec 2020 10:31:28 -0800 Subject: [Chimera-users] Clustering saving PDB In-Reply-To: <2c34deb9-329c-6fb4-5c47-63d943e5615c@uab.cat> References: <2c34deb9-329c-6fb4-5c47-63d943e5615c@uab.cat> Message-ID: Hi Lorena, I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']): from chimera import runCommand with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: cluster_number = 1 for line in f: if line.startswith('#'): #comment line continue runCommand("coordset #0 " + line.strip().split()[0]) name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand("write format pdb 0 " + name) cluster_number += 1 --Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 23, 2020, at 8:20 AM, Lorena Rold?n wrote: > > Good afternoon, > > I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: > > > > with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: > lines=f.readlines() > cluster_number = 1 > for i in range(len(lines)): > frame = i > if mdInfo["frame number"] == frame: > name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) > runCommand('write format pdb 0 $name) > > > > which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. > > > > However, this script is not working, and I would greatly thank any help you could provide me with. > > > > Lorena. > > -- > Lorena Rold?n Mart?n > PhD Student in Bioinformatics > > Departament de Qu?mica > Unitat de Qu?mica F?sica > > Campus de la UAB ? 08193 Bellaterra > (Cerdanyola del Vall?s) ? Barcelona ? Spain > > +34 690799431 > www.uab.cat > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorena.roldan at uab.cat Thu Dec 24 02:10:12 2020 From: lorena.roldan at uab.cat (=?utf-8?Q?Lorena_Rold=C3=A1n_Mart=C3=ADn?=) Date: Thu, 24 Dec 2020 11:10:12 +0100 Subject: [Chimera-users] Clustering saving PDB In-Reply-To: References: <2c34deb9-329c-6fb4-5c47-63d943e5615c@uab.cat> Message-ID: <37998BE1-2B38-4F9D-8375-B926E079DFA4@uab.cat> Hi Eric, Thank you so much for your quick response. I have tried the script you sent me and the only problem with this is that all the PDBs saved correspond to the same frame, although I have tested that the frames are correctly parsed to the coordset command. I have also loaded the full trajectory to the MD movie and visualized every single frame. Do you know why this might happen? Thank you, Lorena > El 23 dic 2020, a las 19:31, Eric Pettersen escribi?: > > Hi Lorena, > I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']): > > from chimera import runCommand > with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: > cluster_number = 1 > for line in f: > if line.startswith('#'): #comment line > continue > runCommand("coordset #0 " + line.strip().split()[0]) > name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) > runCommand("write format pdb 0 " + name) > cluster_number += 1 > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Dec 23, 2020, at 8:20 AM, Lorena Rold?n > wrote: >> >> Good afternoon, >> >> I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: >> >> >> >> with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: >> lines=f.readlines() >> cluster_number = 1 >> for i in range(len(lines)): >> frame = i >> if mdInfo["frame number"] == frame: >> name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) >> runCommand('write format pdb 0 $name) >> >> >> >> which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. >> >> >> >> However, this script is not working, and I would greatly thank any help you could provide me with. >> >> >> >> Lorena. >> >> -- >> Lorena Rold?n Mart?n >> PhD Student in Bioinformatics >> >> Departament de Qu?mica >> Unitat de Qu?mica F?sica >> >> Campus de la UAB ? 08193 Bellaterra >> (Cerdanyola del Vall?s) ? Barcelona ? Spain >> >> +34 690799431 >> www.uab.cat >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorena.roldan at uab.cat Thu Dec 24 03:02:26 2020 From: lorena.roldan at uab.cat (=?utf-8?Q?Lorena_Rold=C3=A1n_Mart=C3=ADn?=) Date: Thu, 24 Dec 2020 12:02:26 +0100 Subject: [Chimera-users] Clustering saving PDB In-Reply-To: References: <2c34deb9-329c-6fb4-5c47-63d943e5615c@uab.cat> Message-ID: <0C0E4E82-C5BA-4342-8F02-5784AF083DC3@uab.cat> Finally solved! runCommand("coordset #0 " + line.strip().split()[0] + ?; wait 1?) did the trick. Thank you so much, Merry Christmas and Happy New Year Lorena > El 23 dic 2020, a las 19:31, Eric Pettersen escribi?: > > Hi Lorena, > I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']): > > from chimera import runCommand > with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: > cluster_number = 1 > for line in f: > if line.startswith('#'): #comment line > continue > runCommand("coordset #0 " + line.strip().split()[0]) > name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) > runCommand("write format pdb 0 " + name) > cluster_number += 1 > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Dec 23, 2020, at 8:20 AM, Lorena Rold?n > wrote: >> >> Good afternoon, >> >> I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: >> >> >> >> with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: >> lines=f.readlines() >> cluster_number = 1 >> for i in range(len(lines)): >> frame = i >> if mdInfo["frame number"] == frame: >> name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) >> runCommand('write format pdb 0 $name) >> >> >> >> which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. >> >> >> >> However, this script is not working, and I would greatly thank any help you could provide me with. >> >> >> >> Lorena. >> >> -- >> Lorena Rold?n Mart?n >> PhD Student in Bioinformatics >> >> Departament de Qu?mica >> Unitat de Qu?mica F?sica >> >> Campus de la UAB ? 08193 Bellaterra >> (Cerdanyola del Vall?s) ? Barcelona ? Spain >> >> +34 690799431 >> www.uab.cat >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Dec 28 11:40:15 2020 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 28 Dec 2020 11:40:15 -0800 Subject: [Chimera-users] Clustering saving PDB In-Reply-To: <0C0E4E82-C5BA-4342-8F02-5784AF083DC3@uab.cat> References: <2c34deb9-329c-6fb4-5c47-63d943e5615c@uab.cat> <0C0E4E82-C5BA-4342-8F02-5784AF083DC3@uab.cat> Message-ID: <39517EC4-4502-46AD-A5F4-5E5FBFEA3E3F@cgl.ucsf.edu> Glad you were able to figure it out! I'm surprised that coordset requires a 'wait' to work, but not totally shocked I guess. :-) --Eric > On Dec 24, 2020, at 3:02 AM, Lorena Rold?n Mart?n wrote: > > Finally solved! > runCommand("coordset #0 " + line.strip().split()[0] + ?; wait 1?) did the trick. > > > Thank you so much, Merry Christmas and Happy New Year > Lorena > > >> El 23 dic 2020, a las 19:31, Eric Pettersen > escribi?: >> >> Hi Lorena, >> I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']): >> >> from chimera import runCommand >> with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: >> cluster_number = 1 >> for line in f: >> if line.startswith('#'): #comment line >> continue >> runCommand("coordset #0 " + line.strip().split()[0]) >> name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) >> runCommand("write format pdb 0 " + name) >> cluster_number += 1 >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >>> On Dec 23, 2020, at 8:20 AM, Lorena Rold?n > wrote: >>> >>> Good afternoon, >>> >>> I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: >>> >>> >>> >>> with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: >>> lines=f.readlines() >>> cluster_number = 1 >>> for i in range(len(lines)): >>> frame = i >>> if mdInfo["frame number"] == frame: >>> name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) >>> runCommand('write format pdb 0 $name) >>> >>> >>> >>> which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. >>> >>> >>> >>> However, this script is not working, and I would greatly thank any help you could provide me with. >>> >>> >>> >>> Lorena. >>> >>> -- >>> Lorena Rold?n Mart?n >>> PhD Student in Bioinformatics >>> >>> Departament de Qu?mica >>> Unitat de Qu?mica F?sica >>> >>> Campus de la UAB ? 08193 Bellaterra >>> (Cerdanyola del Vall?s) ? Barcelona ? Spain >>> >>> +34 690799431 >>> www.uab.cat >>> >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ynh97.yn at gmail.com Thu Dec 31 17:05:24 2020 From: ynh97.yn at gmail.com (Yasmeen Nasr) Date: Fri, 1 Jan 2021 03:05:24 +0200 Subject: [Chimera-users] Accession number Message-ID: <6B91B896-F5FC-4854-ADF1-2CD1030D42B8@gmail.com> Hello there, This doesn?t seem very much chimera related but I hope someone could help me out. I?m trying to use phD-SNP server and SNP&GO server and they require a Swiss prot code and a uni-prot accession number respectively. Does anyone know where I retrieve such numbers for SNPs? Thank you in advance. Yasmeen Abdulhadi Sent from my iPhone