Hi,

I've attached a screen shot of the problem she's having. She's unable to open that mutation file. She mentioned she got it from your website. I tried to find it so that she can maybe download it in the proper format. She explained that it was a file that came with the installation. Is there any way you guys can be of assistance I'd highly appreciate it.

Jerquan Goins (Contractor) Desktop Support Technician Team GRSi National Cancer Institute Center for Biomedical Informatics and Information Technology Building 10, 10 Center Drive Bethesda Maryland, 20892 Email: Jerquan.Goins@nih.gov Phone: 2407606706

On 9/25/20, 6:47 PM, "Elaine Meng" meng@cgl.ucsf.edu wrote:

Hi Tanuja, The address for asking Chimera questions is chimera-users@cgl.ucsf.edu, CC'd here.

Probably you were using some tools that call web services: PDB2PQR, APBS, and/or Autodock Vina. These web services were provided by another group (not our lab) and they have been discontinued, sorry.

There are suggestions of what you could do instead in the help pages for these tools in Chimera: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html

Probably for APBS and PDB2PQR the simplest approach is to skip Chimera and use the web service at http://server.poissonboltzmann.org/

If you were trying to do docking, besides the Vina help link above, there are several posts to the chimera-users list with suggestions of alternatives, for example: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017079.html http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

> On Sep 25, 2020, at 2:13 PM, Cain, Cheryl A Cheryl.Cain@ucsf.edu wrote: > > Hi Tanuja, > > I've added chimera-users@cgl.ucsf.edu to this email as they should be able to help you there. > > Thanks, > Cheryl > > > Cheryl Cain > cheryl.cain@ucsf.edu > Operations Coordinator, Department of Pharmaceutical Chemistry > Accreditation Project Coordinator, School of Pharmacy > UCSF > > From: Saswat, Tanuja (NIH/NCI) [F] tanuja.saswat@nih.gov > Sent: Friday, September 25, 2020 9:56 AM > To: chimera@cgl.ucsf.edu chimera@cgl.ucsf.edu > Cc: Goins, Jerquan (NIH/NCI) [C] jerquan.goins@nih.gov > Subject: Troubleshooting request for help > > Hi, > > I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. > > I’ve CC’s my IT support in case there was something above my cresds level. > > Regards > -- > Tanuja Saswat, Ph.D. > Postdoctoral Research Fellow > Laboratory of Dr. Laurie T. Krug > HIV and AIDS Malignancy Branch (HAMB) > Center for Cancer Research > National Cancer Institute > tanuja.saswat@nih.gov > Building 10, Room 4A08 > Ph:240-858-3201 > NCI Website > > > _______________________________________________ > Chimera-users mailing list: Chimera-users@cgl.ucsf.edu > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Elaine,

I used the Chimera long back but after while could not open some of the modified file and found error, whenever I tried to open (attached).

Meanwhile, I tried to make scene based molecular movie by help of the options 'Tools-Utility-Animation...' but again I did not find the movies and it always showing error after completion.

Thanks Tanuja

On 9/28/20, 11:26 AM, "Elaine Meng" meng@cgl.ucsf.edu wrote:

It would have helped if the question had actually stated the problem! If they are .py and .pyc files they might be "Chimera session files" which somebody could have created with Chimera, but they could also be some other python files that are not Chimera sessions.

(1) I do not see a problem in this screenshot, only a bunch of files and some information dialogs. Is there an error message of some kind if you try to open any of them with Chimera?

(2) As far as I know, files with these names are not included in any downloaded software and do not appear anywhere on our website. How did you find any of these files, and what information are you expecting them to contain? Since I don't believe we provide any of those files, Tanuja would have to ask the third party (whoever made them) if they are Chimera sessions. If they are Chimera sessions, she might need to use a different version of Chimera, i.e. at least as new as the version that was used to make them.

Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

> On Sep 28, 2020, at 6:54 AM, Goins, Jerquan (NIH/NCI) [C] jerquan.goins@nih.gov wrote: > > Hi, > > I've attached a screen shot of the problem she's having. She's unable to open that mutation file. She mentioned she got it from your website. I tried to find it so that she can maybe download it in the proper format. She explained that it was a file that came with the installation. Is there any way you guys can be of assistance I'd highly appreciate it. > > Jerquan Goins (Contractor) > Desktop Support Technician > Team GRSi > National Cancer Institute > Center for Biomedical Informatics and Information Technology > Building 10, 10 Center Drive Bethesda Maryland, 20892 > Email: Jerquan.Goins@nih.gov > Phone: 2407606706 > > > > On 9/25/20, 6:47 PM, "Elaine Meng" meng@cgl.ucsf.edu wrote: > > Hi Tanuja, > The address for asking Chimera questions is chimera-users@cgl.ucsf.edu, CC'd here. > > Probably you were using some tools that call web services: PDB2PQR, APBS, and/or Autodock Vina. These web services were provided by another group (not our lab) and they have been discontinued, sorry. > > There are suggestions of what you could do instead in the help pages for these tools in Chimera: > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html > > Probably for APBS and PDB2PQR the simplest approach is to skip Chimera and use the web service at > http://server.poissonboltzmann.org/ > > If you were trying to do docking, besides the Vina help link above, there are several posts to the chimera-users list with suggestions of alternatives, for example: > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017079.html > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017126.html > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 25, 2020, at 2:13 PM, Cain, Cheryl A Cheryl.Cain@ucsf.edu wrote: >> >> Hi Tanuja, >> >> I've added chimera-users@cgl.ucsf.edu to this email as they should be able to help you there. >> >> Thanks, >> Cheryl >> >> >> Cheryl Cain >> cheryl.cain@ucsf.edu >> Operations Coordinator, Department of Pharmaceutical Chemistry >> Accreditation Project Coordinator, School of Pharmacy >> UCSF >> >> From: Saswat, Tanuja (NIH/NCI) [F] tanuja.saswat@nih.gov >> Sent: Friday, September 25, 2020 9:56 AM >> To: chimera@cgl.ucsf.edu chimera@cgl.ucsf.edu >> Cc: Goins, Jerquan (NIH/NCI) [C] jerquan.goins@nih.gov >> Subject: Troubleshooting request for help >> >> Hi, >> >> I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. >> >> I’ve CC’s my IT support in case there was something above my cresds level. >> >> Regards >> -- >> Tanuja Saswat, Ph.D. >> Postdoctoral Research Fellow >> Laboratory of Dr. Laurie T. Krug >> HIV and AIDS Malignancy Branch (HAMB) >> Center for Cancer Research >> National Cancer Institute >> tanuja.saswat@nih.gov >> Building 10, Room 4A08 >> Ph:240-858-3201 >> NCI Website >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > <Screen Shot 2020-09-25 at 1.26.38 PM.png>

Hi Elaine,

Now, Chimera is working fine. I can retrieve my old file.

Thanks Tanuja

On 9/28/20, 5:28 PM, "Elaine Meng" meng@cgl.ucsf.edu wrote:

Hi Tanuja, I see, you mean that you made these files yourself by previously saving them from Chimera. The problem is that the files do not have sensible names, in that the filenames do not end with an extension that tells Chimera what kind of files they are. I changed the subject line of this e-mail to describe this topic.

Apparently "10. All variants in one" is a py file and the filename should end in ".py" and "10. Total mutant 06232020c" is a pyc file and the filename should end in ".pyc". If I just rename these files to "10. All variants in one.py" and "10. Total mutant 06232020c.pyc" then they open fine in Chimera.

I have no idea what the problem is when you try to save a movie. If you get an error message and you really can't understand the error message (e.g. maybe you just tried to write a file in a folder where you don't have permission to write it), instead of sending e-mail here, you should use the "Report Bug" button or Chimera menu: Help... Report a Bug and enter into the dialog a description of what you did and what happened. Include your e-mail address in that report if you want an answer back.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

> On Sep 28, 2020, at 2:10 PM, Saswat, Tanuja (NIH/NCI) [F] tanuja.saswat@nih.gov wrote: > > Hi Elaine, > I used the Chimera long back but after while could not open some of the modified file and found error, whenever I tried to open (attached). > > Meanwhile, I tried to make scene based molecular movie by help of the options 'Tools-Utility-Animation...' but again I did not find the movies and it always showing error after completion. > Thanks > Tanuja > > On 9/28/20, 11:26 AM, "Elaine Meng" meng@cgl.ucsf.edu wrote: > > It would have helped if the question had actually stated the problem! If they are .py and .pyc files they might be "Chimera session files" which somebody could have created with Chimera, but they could also be some other python files that are not Chimera sessions. > > (1) I do not see a problem in this screenshot, only a bunch of files and some information dialogs. Is there an error message of some kind if you try to open any of them with Chimera? > > (2) As far as I know, files with these names are not included in any downloaded software and do not appear anywhere on our website. How did you find any of these files, and what information are you expecting them to contain? Since I don't believe we provide any of those files, Tanuja would have to ask the third party (whoever made them) if they are Chimera sessions. If they are Chimera sessions, she might need to use a different version of Chimera, i.e. at least as new as the version that was used to make them. > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <10. All variants in one><Chimer error_Screen Shot 2020-09-28 at 4.52.58 PM.png><10. Total mutant 06232020c>