<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-8-i">
<meta name="Generator" content="Microsoft Exchange Server">
<!-- converted from text --><style><!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: #800000 2px solid; } --></style>
</head>
<body>
<div>
<div>Hi Eric,</div>
<div> I'm sure this is a revelation for you but oddly enough (or maybe not) the Consurf output has .chinerax type but is easily read into good old chimera. I was puzzled the first time I noticed this but it works. Perhaps I'm off the point in this discussion.</div>
<div>Cheers,</div>
<div>Boaz</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div id="x_composer_signature">
<div style="font-size:85%; color:#575757">Boaz Shaanan, Ph.D.</div>
<div style="font-size:85%; color:#575757">Dept. of Life Sciences</div>
<div style="font-size:85%; color:#575757"><span style="font-size:85%">Ben Gurion University</span></div>
<div style="font-size:85%; color:#575757"><span style="font-size:85%">Beer Sheva, Israel</span></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>-------- Original message --------</div>
<div>From: chimera-users-request@cgl.ucsf.edu </div>
<div>Date: 4/10/18 18:04 (GMT+02:00) </div>
<div>To: chimera-users@cgl.ucsf.edu </div>
<div>Subject: Chimera-users Digest, Vol 180, Issue 8 </div>
<div><br>
</div>
</div>
<font size="2"><span style="font-size:10pt;">
<div class="PlainText">Send Chimera-users mailing list submissions to<br>
chimera-users@cgl.ucsf.edu<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
chimera-users-request@cgl.ucsf.edu<br>
<br>
You can reach the person managing the list at<br>
chimera-users-owner@cgl.ucsf.edu<br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Chimera-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: ConSurf script on ChimeraX (Eric Pettersen)<br>
2. Re: Dear team UCSF chimera, kindly help me I download and<br>
installed the UCSFf chimera but its showing short cut (Eric Pettersen)<br>
3. Re: ConSurf script on ChimeraX (Fabian Glaser)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 9 Apr 2018 15:59:20 -0700<br>
From: Eric Pettersen <pett@cgl.ucsf.edu><br>
To: Fabian Glaser <fabian.glaser@gmail.com><br>
Cc: Chimera BB <chimera-users@cgl.ucsf.edu>,<br>
fglase@techunix.technion.ac.il<br>
Subject: Re: [Chimera-users] ConSurf script on ChimeraX<br>
Message-ID: <A0F63E03-6D4C-471A-A922-62183FAFF88C@cgl.ucsf.edu><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Fabian,<br>
ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX ? such as what you tried to do below. We want to add a tool to Chimera that will write out a file that ChimeraX can read to restore the Chimera
session as best it can, but we haven?t gotten there yet.<br>
Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers. The features it lacks that ConSurf uses are:<br>
<br>
1) Read Clustal ALN alignments<br>
2) Show alignment headers<br>
2b) Make header values available as residue attributes<br>
3) Show Phylogeny trees<br>
4) Color alignment/structures from coloring file<br>
<br>
To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value. So I?d say ChimeraX is not ?ConSurf ready? yet. What I will do is open an ?enhancement request? ticket in our bug database with you on the
recipient list. As the above features get added I will update the ticket and at whatever point you feel it?s worthwhile you could work on getting ConSurf to deliver ChimeraX results. I would help with any questions or issues that popped up. Sorry I don?t
have better news.<br>
<br>
?Eric<br>
<br>
Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<br>
> On Apr 8, 2018, at 7:56 AM, Fabian Glaser <fabian.glaser@gmail.com> wrote:<br>
> <br>
> Hi, <br>
> <br>
> I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX<br>
> <br>
> ModuleNotFoundError: No module named 'cPickle'<br>
> <br>
> File "consurf_final_zn.py", line 1, in <br>
> <br>
> See log for complete Python traceback.<br>
> <br>
> If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu <<a href="mailto:chimerax-bugs@cgl.ucsf.edu">mailto:chimerax-bugs@cgl.ucsf.edu</a>> and describe what you were doing and include a copy of the contents of the log. Don't include any
data you wish to remain private since a publicly viewable bug report will be created.<br>
> <br>
> Is this something that can be fixed or updated?<br>
> <br>
> More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that?<br>
> <br>
> Here is the beginning of the original chimera script<br>
> <br>
> import cPickle, base64<br>
> try:<br>
> from SimpleSession.versions.v65 import beginRestore,\<br>
> registerAfterModelsCB, reportRestoreError, checkVersion<br>
> except ImportError:<br>
> from chimera import UserError<br>
> raise UserError('Cannot open session that was saved in a'<br>
> ' newer version of Chimera; update your version')<br>
> checkVersion([1, 12, 41623])<br>
> import chimera<br>
> from chimera import replyobj<br>
> replyobj.status('Restoring session...', \<br>
> blankAfter=0)<br>
> replyobj.status('Beginning session restore...', \<br>
> blankAfter=0, secondary=True)<br>
> beginRestore()<br>
> <br>
> def restoreCoreModels():<br>
> from SimpleSession.versions.v65 import init, restoreViewer, \<br>
> restoreMolecules, restoreColors, restoreSurfaces, \<br>
> restoreVRML, restorePseudoBondGroups, restoreModelAssociations<br>
> molInfo = <br>
> <br>
> Thanks a lot,<br>
> <br>
> Best,<br>
> <br>
> Fabian<br>
> <br>
> Fabian Glaser PhD<br>
> <br>
> Head of the Structural Bioinformatics section <br>
> Bioinformatics Knowledge Unit - BKU<br>
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering<br>
> Technion - Israel Institute of Technology, Haifa, Israel<br>
> Web <a href="http://bku.technion.ac.il/">http://bku.technion.ac.il/</a> <<a href="http://bku.technion.ac.il/">http://bku.technion.ac.il/</a>><br>
> Tel +972 (0) 4 8293701<br>
> _______________________________________________<br>
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180409/fe6615ad/attachment-0001.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180409/fe6615ad/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 9 Apr 2018 16:20:05 -0700<br>
From: Eric Pettersen <pett@cgl.ucsf.edu><br>
To: Maria Yousuf <drmariayousuf@hotmail.com><br>
Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu><br>
Subject: Re: [Chimera-users] Dear team UCSF chimera, kindly help me I<br>
download and installed the UCSFf chimera but its showing short cut<br>
Message-ID: <17A96307-8449-4458-8D83-C64D0B1491F5@cgl.ucsf.edu><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Dr. Maria,<br>
Could you use the ?Report a Bug?? entry in Chimera?s Help menu to submit a bug report about this? The bug report will automatically include a lot of useful information about your machine and operating system. Also, if you could attach the PDB that
won?t open to the bug report, that would help a lot in figuring out the problem. Finally, if in the bug report you could explain a little more about what ?a shortcut appeared in the file? means, that would also be helpful, since I don?t quite understand what
you mean with that phrase.<br>
Thanks!<br>
<br>
?Eric<br>
<br>
Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<br>
<br>
> On Apr 9, 2018, at 9:06 AM, Maria Yousuf <drmariayousuf@hotmail.com> wrote:<br>
> <br>
> <br>
> <br>
> Dear team UCSF chimera<br>
> Hi<br>
> <br>
> I download and installed the UCSFf chimera followed the linkon windows 7 <br>
> Microsoft Windows 64-bit chimera-1.12-win64.exe <<a href="https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/chimera-1.12-win64.exe">https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/chimera-1.12-win64.exe</a>><br>
> Size: 150984696 bytes<br>
> MD5: b662f97cdacb8be458662aa638dd6694 Oct 24, 2017 Instructions <<a href="https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/win64.html">https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/win64.html</a>>
<br>
> Documentation <<a href="https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/docs/">https://www.cgl.ucsf.edu/chimera/data/downloads/1.12/docs/</a>>
<br>
> Runs on Windows 7 or later.<br>
> <br>
> Initially It worked well, but after 2 days a shortcut appeared in the file and some of its features are not functional, I cant able to open a docked file in .pdb format<br>
> <br>
> Kindly share the functional link to download chimera on 64bit windows 7<br>
> <br>
> looking forward to hear from you soon<br>
> <br>
> regards<br>
> Dr.Maria<br>
> <<a href="http://aka.ms/weboutlook">http://aka.ms/weboutlook</a>><br>
> _______________________________________________<br>
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <<a href="mailto:Chimera-users@cgl.ucsf.edu">mailto:Chimera-users@cgl.ucsf.edu</a>><br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a> <<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180409/2d577040/attachment-0001.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180409/2d577040/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 10 Apr 2018 10:26:27 +0300<br>
From: Fabian Glaser <fabian.glaser@gmail.com><br>
To: Eric Pettersen <pett@cgl.ucsf.edu><br>
Cc: Nir Ben-Tal <bental@tauex.tau.ac.il>, Chimera BB<br>
<chimera-users@cgl.ucsf.edu>, fglase@techunix.technion.ac.il<br>
Subject: Re: [Chimera-users] ConSurf script on ChimeraX<br>
Message-ID: <38152421-F0F3-4971-9633-8D427131885D@gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Eric,<br>
<br>
Thanks for your detail answer, so maybe the only thing it will be really useful now is to be able to color the residues with consurf colors in ChimeraX, with that I will be able to make figures for a paper, which is what I am after at this point.
<br>
<br>
Of course we would be very happy to get a script for ChimeraX at some point that could be included in our output pages.<br>
<br>
Best,<br>
<br>
Fabian<br>
<br>
Fabian Glaser PhD<br>
<br>
Head of the Structural Bioinformatics section <br>
Bioinformatics Knowledge Unit - BKU<br>
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering<br>
Technion - Israel Institute of Technology, Haifa, Israel<br>
Web <a href="http://bku.technion.ac.il/">http://bku.technion.ac.il/</a><br>
Tel +972 (0) 4 8293701<br>
<br>
<br>
> On 10 Apr 2018, at 1:59, Eric Pettersen <pett@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Fabian,<br>
> ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX ? such as what you tried to do below. We want to add a tool to Chimera that will write out a file that ChimeraX can read to restore the Chimera
session as best it can, but we haven?t gotten there yet.<br>
> Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers. The features it lacks that ConSurf uses are:<br>
> <br>
> 1) Read Clustal ALN alignments<br>
> 2) Show alignment headers<br>
> 2b) Make header values available as residue attributes<br>
> 3) Show Phylogeny trees<br>
> 4) Color alignment/structures from coloring file<br>
> <br>
> To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value. So I?d say ChimeraX is not ?ConSurf ready? yet. What I will do is open an ?enhancement request? ticket in our bug database with you on the
recipient list. As the above features get added I will update the ticket and at whatever point you feel it?s worthwhile you could work on getting ConSurf to deliver ChimeraX results. I would help with any questions or issues that popped up. Sorry I don?t
have better news.<br>
> <br>
> ?Eric<br>
> <br>
> Eric Pettersen<br>
> UCSF Computer Graphics Lab<br>
> <br>
>> On Apr 8, 2018, at 7:56 AM, Fabian Glaser <fabian.glaser@gmail.com <<a href="mailto:fabian.glaser@gmail.com">mailto:fabian.glaser@gmail.com</a>>> wrote:<br>
>> <br>
>> Hi, <br>
>> <br>
>> I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX<br>
>> <br>
>> ModuleNotFoundError: No module named 'cPickle'<br>
>> <br>
>> File "consurf_final_zn.py", line 1, in <br>
>> <br>
>> See log for complete Python traceback.<br>
>> <br>
>> If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu <<a href="mailto:chimerax-bugs@cgl.ucsf.edu">mailto:chimerax-bugs@cgl.ucsf.edu</a>> and describe what you were doing and include a copy of the contents of the log. Don't include any
data you wish to remain private since a publicly viewable bug report will be created.<br>
>> <br>
>> Is this something that can be fixed or updated?<br>
>> <br>
>> More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that?<br>
>> <br>
>> Here is the beginning of the original chimera script<br>
>> <br>
>> import cPickle, base64<br>
>> try:<br>
>> from SimpleSession.versions.v65 import beginRestore,\<br>
>> registerAfterModelsCB, reportRestoreError, checkVersion<br>
>> except ImportError:<br>
>> from chimera import UserError<br>
>> raise UserError('Cannot open session that was saved in a'<br>
>> ' newer version of Chimera; update your version')<br>
>> checkVersion([1, 12, 41623])<br>
>> import chimera<br>
>> from chimera import replyobj<br>
>> replyobj.status('Restoring session...', \<br>
>> blankAfter=0)<br>
>> replyobj.status('Beginning session restore...', \<br>
>> blankAfter=0, secondary=True)<br>
>> beginRestore()<br>
>> <br>
>> def restoreCoreModels():<br>
>> from SimpleSession.versions.v65 import init, restoreViewer, \<br>
>> restoreMolecules, restoreColors, restoreSurfaces, \<br>
>> restoreVRML, restorePseudoBondGroups, restoreModelAssociations<br>
>> molInfo = <br>
>> <br>
>> Thanks a lot,<br>
>> <br>
>> Best,<br>
>> <br>
>> Fabian<br>
>> <br>
>> Fabian Glaser PhD<br>
>> <br>
>> Head of the Structural Bioinformatics section <br>
>> Bioinformatics Knowledge Unit - BKU<br>
>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering<br>
>> Technion - Israel Institute of Technology, Haifa, Israel<br>
>> Web <a href="http://bku.technion.ac.il/">http://bku.technion.ac.il/</a> <<a href="http://bku.technion.ac.il/">http://bku.technion.ac.il/</a>><br>
>> Tel +972 (0) 4 8293701<br>
>> _______________________________________________<br>
>> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <<a href="mailto:Chimera-users@cgl.ucsf.edu">mailto:Chimera-users@cgl.ucsf.edu</a>><br>
>> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a> <<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>><br>
> <br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180410/37bf0faa/attachment.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180410/37bf0faa/attachment.html</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
Chimera-users mailing list<br>
Chimera-users@cgl.ucsf.edu<br>
Manage subscription:<br>
<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
<br>
<br>
------------------------------<br>
<br>
End of Chimera-users Digest, Vol 180, Issue 8<br>
*********************************************<br>
</div>
</span></font>
</body>
</html>