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<div dir="auto">Hi,
<div dir="auto">Is it possible to read a .pqr file from pdb2pqr to the script for calculating dipole moment (from the chimera repository) rather than running addcharge?</div>
<div dir="auto">Thanks,</div>
<div dir="auto">Boaz<br>
<br>
<div dir="auto">Boaz Shaanan, Ph.D.<br>
Department of Life Sciences<br>
Ben Gurion University of the Negev<br>
Beer Sheva<br>
Israel</div>
</div>
</div>
<div class="x_gmail_extra"><br>
<div class="x_gmail_quote">On Apr 4, 2019 04:10, chimera-users-request@cgl.ucsf.edu wrote:<br type="attribution">
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Today's Topics:<br>
<br>
1. Re: PDB file of D-amino acids (Elaine Meng)<br>
2. Re: PDB file of D-amino acids (Mohsen Asadbegi)<br>
3. Re: PDB file of D-amino acids (Elaine Meng)<br>
4. Re: Visualisation in Headless Chimera (Greg Couch)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 3 Apr 2019 10:42:32 -0700<br>
From: Elaine Meng <meng@cgl.ucsf.edu><br>
To: Mohsen Asadbegi <mohsenasad.7091@gmail.com><br>
Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu><br>
Subject: Re: [Chimera-users] PDB file of D-amino acids<br>
Message-ID: <CE388B02-3F3C-4B14-9823-D18C66ACDE06@cgl.ucsf.edu><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Hi Mohsen,<br>
For entirely D-amino acids, I like Mark?s suggestion of inverting the coordinates. However, I think it would work to just invert the sign of X, Y, or Z coordinates (rather than all 3) since any of those would reflect the molecule across a plane. There is
some python code to flip the sign of all X-coordinates in this previous post:<br>
<<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html</a>><br>
<br>
For mixtures of D- and L-amino acids,<br>
<br>
(1) there is a Chimera ?invert? command to swap two substituents of an atom, which could be used to change chirality.<br>
<<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html</a>><br>
<br>
(2) for a variety of nonstandard or nonnatural amino acid sidechains, there is a Chimera plugin available from the SwissSidechain folks for adding the sidechains to make D-amino acids, see:<br>
<<a href="https://www.swisssidechain.ch/visualization/chimera.php">https://www.swisssidechain.ch/visualization/chimera.php</a>><br>
You could build the residues you want to make into D-amino acids as Gly in Chimera and then use this plugin to mutate them.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Apr 3, 2019, at 3:05 AM, Mark J van Raaij <mjvanraaij@cnb.csic.es> wrote:<br>
> <br>
> may not the smartest way, but you could generate a peptide of L-amino acids and then make the mirror image by inverting the sign of all the x, y, z coordinates.<br>
> Either by hand in a text editor or with a program (I know of PDBSET from CCP4, but there are probably other options). The program may complain that you are doing something that is "not allowed" in protein structure, but you can probably override that.<br>
> In protein crystallography this is sometimes needed when heavy atom positions have been determined, sometimes we don't know if the given coordinates are correct or if the mirror image is it.<br>
> <br>
> Mark J van Raaij<br>
> Dpto de Estructura de Macromoleculas<br>
> Centro Nacional de Biotecnologia - CSIC<br>
> calle Darwin 3<br>
> E-28049 Madrid, Spain<br>
> tel. (+34) 91 585 4616<br>
> <a href="http://wwwuser.cnb.csic.es/~mjvanraaij">http://wwwuser.cnb.csic.es/~mjvanraaij</a><br>
> Section Editor of Acta Crystallographica F, Structural Biology Communications<br>
> <a href="http://journals.iucr.org/f/">http://journals.iucr.org/f/</a><br>
> <br>
> <br>
>> On 3 Apr 2019, at 12:47, Mohsen Asadbegi <mohsenasad.7091@gmail.com> wrote:<br>
>> <br>
>> Hello every one!<br>
>> I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file.<br>
>> How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact way
of building PDB files.<br>
>> <br>
>> <br>
>> Regards,<br>
>> Mohsen Asadbegi<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 3 Apr 2019 23:35:10 +0430<br>
From: Mohsen Asadbegi <mohsenasad.7091@gmail.com><br>
To: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu><br>
Subject: Re: [Chimera-users] PDB file of D-amino acids<br>
Message-ID:<br>
<CANbAvf3C=RJSsCQ2XC0=09xO6OdKeVA0Uwn7hg8kicTDfWKRWw@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Dr. Elaine<br>
<br>
Thanks for your comprehensive answer,<br>
<br>
Regarding construction of d-peptide, I have found another answer, that is<br>
provided below:<br>
<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010366.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010366.html</a><br>
<br>
In above web page, it is suggested to invert only alpha-carbon of each<br>
residue to convert a L-amino acid to D-amino acid.<br>
Do you confirm this method? Which atoms of a L-amino acid should be<br>
inverted by invert command in CHIMERA?<br>
<br>
Reagrds,<br>
Mohsen Asadbegi.<br>
<br>
<br>
On Wed, 3 Apr 2019 at 22:12, Elaine Meng <meng@cgl.ucsf.edu> wrote:<br>
<br>
> Hi Mohsen,<br>
> For entirely D-amino acids, I like Mark?s suggestion of inverting the<br>
> coordinates. However, I think it would work to just invert the sign of X,<br>
> Y, or Z coordinates (rather than all 3) since any of those would reflect<br>
> the molecule across a plane. There is some python code to flip the sign of<br>
> all X-coordinates in this previous post:<br>
> <<br>
> <a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html">
http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html</a><br>
> ><br>
><br>
> For mixtures of D- and L-amino acids,<br>
><br>
> (1) there is a Chimera ?invert? command to swap two substituents of an<br>
> atom, which could be used to change chirality.<br>
> <<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html</a>><br>
><br>
> (2) for a variety of nonstandard or nonnatural amino acid sidechains,<br>
> there is a Chimera plugin available from the SwissSidechain folks for<br>
> adding the sidechains to make D-amino acids, see:<br>
> <<a href="https://www.swisssidechain.ch/visualization/chimera.php">https://www.swisssidechain.ch/visualization/chimera.php</a>><br>
> You could build the residues you want to make into D-amino acids as Gly in<br>
> Chimera and then use this plugin to mutate them.<br>
><br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
> > On Apr 3, 2019, at 3:05 AM, Mark J van Raaij <mjvanraaij@cnb.csic.es><br>
> wrote:<br>
> ><br>
> > may not the smartest way, but you could generate a peptide of L-amino<br>
> acids and then make the mirror image by inverting the sign of all the x, y,<br>
> z coordinates.<br>
> > Either by hand in a text editor or with a program (I know of PDBSET from<br>
> CCP4, but there are probably other options). The program may complain that<br>
> you are doing something that is "not allowed" in protein structure, but you<br>
> can probably override that.<br>
> > In protein crystallography this is sometimes needed when heavy atom<br>
> positions have been determined, sometimes we don't know if the given<br>
> coordinates are correct or if the mirror image is it.<br>
> ><br>
> > Mark J van Raaij<br>
> > Dpto de Estructura de Macromoleculas<br>
> > Centro Nacional de Biotecnologia - CSIC<br>
> > calle Darwin 3<br>
> > E-28049 Madrid, Spain<br>
> > tel. (+34) 91 585 4616<br>
> > <a href="http://wwwuser.cnb.csic.es/~mjvanraaij">http://wwwuser.cnb.csic.es/~mjvanraaij</a><br>
> > Section Editor of Acta Crystallographica F, Structural Biology<br>
> Communications<br>
> > <a href="http://journals.iucr.org/f/">http://journals.iucr.org/f/</a><br>
> ><br>
> ><br>
> >> On 3 Apr 2019, at 12:47, Mohsen Asadbegi <mohsenasad.7091@gmail.com><br>
> wrote:<br>
> >><br>
> >> Hello every one!<br>
> >> I want to convert a sequence of d-amino acids or a sequence of d-amino<br>
> acids and L-amino acids to a PDB file.<br>
> >> How can I construct such PDB file? I know that this is possible to<br>
> enter the sequence of L-amino acids in CHIMERA (uppercase characters of the<br>
> amino acids for example: LFVVA), But regarding d-peptides and retro-inverso<br>
> peptides I don't know the exact way of building PDB files.<br>
> >><br>
> >><br>
> >> Regards,<br>
> >> Mohsen Asadbegi<br>
><br>
><br>
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Message: 3<br>
Date: Wed, 3 Apr 2019 11:19:56 -0700<br>
From: Elaine Meng <meng@cgl.ucsf.edu><br>
To: Mohsen Asadbegi <mohsenasad.7091@gmail.com><br>
Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu><br>
Subject: Re: [Chimera-users] PDB file of D-amino acids<br>
Message-ID: <E1DFBF25-B85D-4E9D-8F70-0A1894F02BAB@cgl.ucsf.edu><br>
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<br>
Yes, D- and L- refer to the configuration at the alpha-carbon of an amino acid. For further explanation see any biochemistry textbook, or:<br>
<<a href="https://en.wikipedia.org/wiki/Amino_acid#Isomerism">https://en.wikipedia.org/wiki/Amino_acid#Isomerism</a>><br>
<br>
I wrote that previous answer and I still agree with it (and using this ?invert? command was same as suggestion #1 in my reply today). However, the example commands should contain ?@? instead of ? at ? which is shown in the page because it was automatically
substituted in by the mail system.<br>
<br>
Elaine<br>
<br>
<br>
> On Apr 3, 2019, at 12:05 PM, Mohsen Asadbegi <mohsenasad.7091@gmail.com> wrote:<br>
> <br>
> Dear Dr. Elaine<br>
> <br>
> Thanks for your comprehensive answer,<br>
> <br>
> Regarding construction of d-peptide, I have found another answer, that is provided below:<br>
> <a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010366.html">
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010366.html</a> <br>
> <br>
> In above web page, it is suggested to invert only alpha-carbon of each residue to convert a L-amino acid to D-amino acid.<br>
> Do you confirm this method? Which atoms of a L-amino acid should be inverted by invert command in CHIMERA?<br>
> <br>
> Reagrds,<br>
> Mohsen Asadbegi. <br>
> <br>
> <br>
> On Wed, 3 Apr 2019 at 22:12, Elaine Meng <meng@cgl.ucsf.edu> wrote:<br>
> Hi Mohsen,<br>
> For entirely D-amino acids, I like Mark?s suggestion of inverting the coordinates. However, I think it would work to just invert the sign of X, Y, or Z coordinates (rather than all 3) since any of those would reflect the molecule across a plane. There is
some python code to flip the sign of all X-coordinates in this previous post:<br>
> <<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html</a>><br>
> <br>
> For mixtures of D- and L-amino acids,<br>
> <br>
> (1) there is a Chimera ?invert? command to swap two substituents of an atom, which could be used to change chirality.<br>
> <<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html</a>><br>
> <br>
> (2) for a variety of nonstandard or nonnatural amino acid sidechains, there is a Chimera plugin available from the SwissSidechain folks for adding the sidechains to make D-amino acids, see:<br>
> <<a href="https://www.swisssidechain.ch/visualization/chimera.php">https://www.swisssidechain.ch/visualization/chimera.php</a>><br>
> You could build the residues you want to make into D-amino acids as Gly in Chimera and then use this plugin to mutate them.<br>
> <br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> > On Apr 3, 2019, at 3:05 AM, Mark J van Raaij <mjvanraaij@cnb.csic.es> wrote:<br>
> > <br>
> > may not the smartest way, but you could generate a peptide of L-amino acids and then make the mirror image by inverting the sign of all the x, y, z coordinates.<br>
> > Either by hand in a text editor or with a program (I know of PDBSET from CCP4, but there are probably other options). The program may complain that you are doing something that is "not allowed" in protein structure, but you can probably override that.<br>
> > In protein crystallography this is sometimes needed when heavy atom positions have been determined, sometimes we don't know if the given coordinates are correct or if the mirror image is it.<br>
> > <br>
> > Mark J van Raaij<br>
> > Dpto de Estructura de Macromoleculas<br>
> > Centro Nacional de Biotecnologia - CSIC<br>
> > calle Darwin 3<br>
> > E-28049 Madrid, Spain<br>
> > tel. (+34) 91 585 4616<br>
> > <a href="http://wwwuser.cnb.csic.es/~mjvanraaij">http://wwwuser.cnb.csic.es/~mjvanraaij</a><br>
> > Section Editor of Acta Crystallographica F, Structural Biology Communications<br>
> > <a href="http://journals.iucr.org/f/">http://journals.iucr.org/f/</a><br>
> > <br>
> > <br>
> >> On 3 Apr 2019, at 12:47, Mohsen Asadbegi <mohsenasad.7091@gmail.com> wrote:<br>
> >> <br>
> >> Hello every one!<br>
> >> I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file.<br>
> >> How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact
way of building PDB files.<br>
> >> <br>
> >> <br>
> >> Regards,<br>
> >> Mohsen Asadbegi<br>
> <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>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 3 Apr 2019 18:07:11 -0700<br>
From: Greg Couch <gregc@cgl.ucsf.edu><br>
To: James Starlight <jmsstarlight@gmail.com><br>
Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu><br>
Subject: Re: [Chimera-users] Visualisation in Headless Chimera<br>
Message-ID: <2b117422-4643-fc7b-983c-a66b3f42b0e6@cgl.ucsf.edu><br>
Content-Type: text/plain; charset=utf-8; format=flowed<br>
<br>
You have Chimera 1.13.1, not ChimeraX.? ChimeraX is our eventual <br>
replacement for Chimera and "early releases" are available from <br>
<a href="https://www.cgl.ucsf.edu/chimerax/.?">https://www.cgl.ucsf.edu/chimerax/.?</a> ChimeraX's scripting is similar to
<br>
Chimera, and the graphics are much better.<br>
<br>
??? -- Greg<br>
<br>
On 4/3/2019 12:51 AM, James Starlight wrote:<br>
> Thanks Greg!<br>
> So I need to update libOSMesa.so in the /lib of my chimera-headles, needn't it?<br>
> Actually I have found only libOSMesa.so in the lib of chimera-headless<br>
> but not in the ChimeraX - I have version 1.13.1 installed in parallel<br>
> on my ubuntu machine...<br>
><br>
> ??, 2 ???. 2019 ?. ? 18:20, Greg Couch <gregc@cgl.ucsf.edu>:<br>
>> The crash due to "set silhouette" is probably due to the ancient version<br>
>> of libOSMesa.so that is bundled with Chimera. See my earlier response<br>
>> to you, that I mistakenly only sent to the mailing list:<br>
>> <a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-March/015584.html">
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-March/015584.html</a>.<br>
>><br>
>> And if you're going to use povray for the final image, then "set<br>
>> silhouette" doesn't help you, as that setting is not exported, so you<br>
>> could remove it and not crash :-).<br>
>><br>
>> Bonne chance,<br>
>><br>
>> Greg<br>
>><br>
>> On 4/2/2019 12:39 AM, James Starlight wrote:<br>
>>> Thank you very much, Elaine!<br>
>>> The only thing is to understand why "set silhouette" produces crush at<br>
>>> the stage of the image rendering both with chimera-headless or pow-ray<br>
>>> rendering ;o<br>
>>><br>
>>> ??, 1 ???. 2019 ?. ? 20:10, Elaine Meng <meng@cgl.ucsf.edu>:<br>
>>>> Hi James,<br>
>>>> In my experience, i get much better images just using Chimera rendering, not POVray. If you want shadows you can turn them on directly in Chimera (e.g. command: set shadows), and some Chimera settings are not relevant to POVray (silhouette edges, etc.).<br>
>>>> <<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips</a>><br>
>>>><br>
>>>> However, if you really want to use it, you can set POV-Ray Options in the Preferences, save the preferences, and then copy that preferences file to the headless machine. Still this is only a small subset of the things one could possibly change in povray,
so if you?re a POVray expert you could fiddle with the POVray conf file (see Chimera Log for where this would be), and possibly re-run povray directly using the Chimera-generated .ini and .pov files (from the ?copy? command with ?raytrace?).<br>
>>>> <<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html</a>><br>
>>>><br>
>>>> I hope this helps,<br>
>>>> Elaine<br>
>>>> -----<br>
>>>> Elaine C. Meng, Ph.D.<br>
>>>> UCSF Chimera(X) team<br>
>>>> Department of Pharmaceutical Chemistry<br>
>>>> University of California, San Francisco<br>
>>>><br>
>>>>> On Apr 1, 2019, at 2:58 AM, James Starlight <jmsstarlight@gmail.com> wrote:<br>
>>>>><br>
>>>>> P.S. could you also suggest me how it would be possible to change<br>
>>>>> pov-ray options working in Headless Chimera?<br>
>>>>><br>
>>>>> I am using it with a simple script:<br>
>>>>><br>
>>>>> # make visualisation of b-factors<br>
>>>>> rangecolor bfactor 2 dark red 20 firebrick 40 orange red 60 orange 100 yellow<br>
>>>>><br>
>>>>> # make a png immage<br>
>>>>> copy file ${output}/structure/${pdb_name}.png png width 800 height 600<br>
>>>>> supersample 4 raytrace rtwait" > "${temp}/chimera.${pdb_name}.com"<br>
>>>>><br>
>>>>> As the result I have an image with the alpha channel (although I<br>
>>>>> indicated not to use it in my session via<br>
>>>>> chimera-headless ${pdb} script.com --nobgopacity<br>
>>>>><br>
>>>>> finally I would like to change some rendeting options using the same<br>
>>>>> scripting work-flow like "Quality", "Antialias depth" etc<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>
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