From mohammedlawal08 at yahoo.com  Wed Dec 12 09:57:44 2018
From: mohammedlawal08 at yahoo.com (Lawal Mohammed)
Date: Wed, 12 Dec 2018 08:57:44 +0000 (UTC)
Subject: [xcrysden] Problem creating xsf file
References: <971702377.2726561.1544605064791.ref@mail.yahoo.com>
Message-ID: <971702377.2726561.1544605064791@mail.yahoo.com>

Dear Developers and User,
I got a problem using isosurface control window, with?xcrysden-1.5.60.?In the isosurface property-plane control, the minimum grid and maximum grid values are fixed (not?editable). I use isovalue based on the minimum grid value, but I am getting:?Error: specified isolevel 0.00001 is out of range.?
How to resolve this issue?
Thanks a lot for your time.?
With kind regards.?
Lawal


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From quanyundi at gmail.com  Wed Dec 12 10:31:03 2018
From: quanyundi at gmail.com (Yundi Quan)
Date: Wed, 12 Dec 2018 01:31:03 -0800
Subject: [xcrysden] Problem creating xsf file
In-Reply-To: <971702377.2726561.1544605064791@mail.yahoo.com>
References: <971702377.2726561.1544605064791.ref@mail.yahoo.com>
	<971702377.2726561.1544605064791@mail.yahoo.com>
Message-ID: <CALsd9ris0ih=BR7BtbxTKH7D0LP=CQqSqgtPsR1zYDEp3ZU2uw@mail.gmail.com>

Hi, Lawal,

What is the minimum isosurface value? Is it smaller than 0.00001? The value
for isosurface has to be in between the minimum and the maximum. And there
is box "+/- values". Did you uncheck that?




On Wed, Dec 12, 2018 at 12:58 AM Lawal Mohammed <mohammedlawal08 at yahoo.com>
wrote:

> Dear Developers and User,
>
> I got a problem using isosurface control window, with xcrysden-1.5.60. In
> the isosurface property-plane control, the minimum grid and maximum grid
> values are fixed (not editable). I use isovalue based on the minimum grid
> value, but I am getting: Error: specified isolevel 0.00001 is out of
> range.
>
> How to resolve this issue?
>
> Thanks a lot for your time.
>
> With kind regards.
>
> Lawal
>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
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From mohammedlawal08 at yahoo.com  Wed Dec 12 11:42:52 2018
From: mohammedlawal08 at yahoo.com (Lawal Mohammed)
Date: Wed, 12 Dec 2018 10:42:52 +0000 (UTC)
Subject: [xcrysden] Problem creating xsf file
In-Reply-To: <CALsd9ris0ih=BR7BtbxTKH7D0LP=CQqSqgtPsR1zYDEp3ZU2uw@mail.gmail.com>
References: <971702377.2726561.1544605064791.ref@mail.yahoo.com>
	<971702377.2726561.1544605064791@mail.yahoo.com>
	<CALsd9ris0ih=BR7BtbxTKH7D0LP=CQqSqgtPsR1zYDEp3ZU2uw@mail.gmail.com>
Message-ID: <1013689105.2747877.1544611372059@mail.yahoo.com>

Dear Yundi,
Thank you so much.
The minimum isosurface value was 0.000002, I used smaller value as well, like 0.000001. No, but I unchecked it now, but still got the error.
Minimum grid value: 0.000002Maximum grid value: 13.303840

With kind regards.

Lawal 

 

    On Wednesday, December 12, 2018, 5:31:16 PM GMT+8, Yundi Quan <quanyundi at gmail.com> wrote:  
 
 Hi, Lawal,
What is the minimum isosurface value? Is it smaller than 0.00001? The value for isosurface has to be in between the minimum and the maximum. And there is box "+/- values". Did you uncheck that?



On Wed, Dec 12, 2018 at 12:58 AM Lawal Mohammed <mohammedlawal08 at yahoo.com> wrote:

Dear Developers and User,
I got a problem using isosurface control window, with?xcrysden-1.5.60.?In the isosurface property-plane control, the minimum grid and maximum grid values are fixed (not?editable). I use isovalue based on the minimum grid value, but I am getting:?Error: specified isolevel 0.00001 is out of range.?
How to resolve this issue?
Thanks a lot for your time.?
With kind regards.?
Lawal


_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden

  
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From quanyundi at gmail.com  Wed Dec 12 12:08:40 2018
From: quanyundi at gmail.com (Yundi Quan)
Date: Wed, 12 Dec 2018 03:08:40 -0800
Subject: [xcrysden] Problem creating xsf file
In-Reply-To: <1013689105.2747877.1544611372059@mail.yahoo.com>
References: <971702377.2726561.1544605064791.ref@mail.yahoo.com>
	<971702377.2726561.1544605064791@mail.yahoo.com>
	<CALsd9ris0ih=BR7BtbxTKH7D0LP=CQqSqgtPsR1zYDEp3ZU2uw@mail.gmail.com>
	<1013689105.2747877.1544611372059@mail.yahoo.com>
Message-ID: <CALsd9rjZ=1LebmwHiPtXntRhYAPAY-0r1zg+ztsFeAs7QB8jvQ@mail.gmail.com>

Can you try a larger value, say 1 or 2? If you don't mind, you can send the
xsf through private email and I can take a look at it on my own laptop.


Yundi



On Wed, Dec 12, 2018 at 2:42 AM Lawal Mohammed <mohammedlawal08 at yahoo.com>
wrote:

> Dear Yundi,
>
> Thank you so much.
> The minimum isosurface value was 0.000002, I used smaller value as well,
> like 0.000001. No, but I unchecked it now, but still got the error.
> Minimum grid value: 0.000002
> Maximum grid value: 13.303840
>
> With kind regards.
>
>
> *Lawal *
>
>
> On Wednesday, December 12, 2018, 5:31:16 PM GMT+8, Yundi Quan <
> quanyundi at gmail.com> wrote:
>
>
> Hi, Lawal,
>
> What is the minimum isosurface value? Is it smaller than 0.00001? The
> value for isosurface has to be in between the minimum and the maximum. And
> there is box "+/- values". Did you uncheck that?
>
>
>
>
> On Wed, Dec 12, 2018 at 12:58 AM Lawal Mohammed <mohammedlawal08 at yahoo.com>
> wrote:
>
> Dear Developers and User,
>
> I got a problem using isosurface control window, with xcrysden-1.5.60. In
> the isosurface property-plane control, the minimum grid and maximum grid
> values are fixed (not editable). I use isovalue based on the minimum grid
> value, but I am getting: Error: specified isolevel 0.00001 is out of
> range.
>
> How to resolve this issue?
>
> Thanks a lot for your time.
>
> With kind regards.
>
> Lawal
>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>
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From drosso at Princeton.EDU  Mon Dec 17 21:00:27 2018
From: drosso at Princeton.EDU (Douglas Rosso)
Date: Mon, 17 Dec 2018 20:00:27 +0000
Subject: [xcrysden] MacOS Mojave
Message-ID: <2001BBA9-6E49-4C8F-BF81-6C3672E2B597@contoso.com>

I have xcrysden installed on a Ubuntu machine and am trying to run xcrysden in Xquartz (2.7.11) on a Mac (10.14.2).

I keep getting the same errors:
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

xcrysden works fine in xterm on a Linux computer and also works fine in MobaXterm on Windows.
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From quanyundi at gmail.com  Mon Dec 17 21:32:17 2018
From: quanyundi at gmail.com (Yundi Quan)
Date: Mon, 17 Dec 2018 12:32:17 -0800
Subject: [xcrysden] MacOS Mojave
In-Reply-To: <2001BBA9-6E49-4C8F-BF81-6C3672E2B597@contoso.com>
References: <2001BBA9-6E49-4C8F-BF81-6C3672E2B597@contoso.com>
Message-ID: <CALsd9rg2m_D8SX3wCGxRt-r92TBUb2d0V5DMRNpsChE2exTiNQ@mail.gmail.com>

Did you install xcrysden using Fink? I installed xcrysden using Fink on Mac
OS 10.12.3 with XQuartz 2.7.11. And it works.




On Mon, Dec 17, 2018 at 12:06 PM Douglas Rosso <drosso at princeton.edu> wrote:

> I have xcrysden installed on a Ubuntu machine and am trying to run
> xcrysden in Xquartz (2.7.11) on a Mac (10.14.2).
>
>
>
> I keep getting the same errors:
>
> libGL error: No matching fbConfigs or visuals found
>
> libGL error: failed to load driver: swrast
>
>
>
> xcrysden works fine in xterm on a Linux computer and also works fine in
> MobaXterm on Windows.
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
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From eyert at physik.uni-augsburg.de  Mon Dec 17 22:42:32 2018
From: eyert at physik.uni-augsburg.de (Volker Eyert)
Date: Mon, 17 Dec 2018 22:42:32 +0100
Subject: [xcrysden] MacOS Mojave
In-Reply-To: <CALsd9rg2m_D8SX3wCGxRt-r92TBUb2d0V5DMRNpsChE2exTiNQ@mail.gmail.com>
References: <2001BBA9-6E49-4C8F-BF81-6C3672E2B597@contoso.com>
	<CALsd9rg2m_D8SX3wCGxRt-r92TBUb2d0V5DMRNpsChE2exTiNQ@mail.gmail.com>
Message-ID: <8570c542-f9be-f754-2409-0405db0ceac3@physik.uni-augsburg.de>

I suggest installing xcrysden via mac ports. Worked perfectly fine for me!


On 17.12.18 21:32, Yundi Quan wrote:
> Did you install xcrysden using Fink? I installed xcrysden using Fink on 
> Mac OS 10.12.3 with XQuartz 2.7.11. And it works.
> 
> 
> 
> 
> On Mon, Dec 17, 2018 at 12:06 PM Douglas Rosso <drosso at princeton.edu 
> <mailto:drosso at princeton.edu>> wrote:
> 
>     I have xcrysden installed on a Ubuntu machine and am trying to run
>     xcrysden in Xquartz (2.7.11) on a Mac (10.14.2). ____
> 
>     __ __
> 
>     I keep getting the same errors:____
> 
>     libGL error: No matching fbConfigs or visuals found____
> 
>     libGL error: failed to load driver: swrast____
> 
>     __ __
> 
>     xcrysden works fine in xterm on a Linux computer and also works fine
>     in MobaXterm on Windows.____
> 
>     _______________________________________________
>     XCrySDen mailing list
>     XCrySDen at democritos.it <mailto:XCrySDen at democritos.it>
>     http://www.democritos.it/mailman/listinfo/xcrysden
> 
> 
> 
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
> 

From pascal.boulet at univ-amu.fr  Sat Dec 29 00:11:39 2018
From: pascal.boulet at univ-amu.fr (pboulet)
Date: Sat, 29 Dec 2018 00:11:39 +0100
Subject: [xcrysden] Yet another problem with display on MAC
Message-ID: <C0158BFF-EC39-4658-9F4C-CCF51D6FDD43@univ-amu.fr>

Dear all,

I am facing a problem for a while with the display on my MAC.  I have installed XQuartz and XCrysDen with homebrew. I have updated my MAC with HighSierra version 10.13.6. Now xcrysden is no longer working. The problem is the display, as it says:
application-specific initialization failed: couldn't connect to display "/private/tmp/com.apple.launchd.uGojk87b2L/:0"
Error in startup script: can't read "xcrys(platform)": no such variable

In the /private/? directory I have:
org.macosforge.xquartz:0=

The display is set to:
/private/tmp/com.apple.launchd.uGojk87b2L/:0

Can you please help me to solve this problem, as I could not find the answer on the web?

Thank you
Best,
Pascal


Pascal Boulet
?
Professor in computational chemistry - DEPARTMENT OF CHEMISTRY
Director of the Madirel laboratory
Aix-Marseille University - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE
T?l: +33(0)4 13 55 18 10 et +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50
Email : pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>



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From gsabo at crimson.ua.edu  Sat Dec 29 02:31:11 2018
From: gsabo at crimson.ua.edu (Gavin Abo)
Date: Fri, 28 Dec 2018 18:31:11 -0700
Subject: [xcrysden] Yet another problem with display on MAC
In-Reply-To: <C0158BFF-EC39-4658-9F4C-CCF51D6FDD43@univ-amu.fr>
References: <C0158BFF-EC39-4658-9F4C-CCF51D6FDD43@univ-amu.fr>
Message-ID: <fd718f26-1577-b60d-decf-77d9513c62a4@crimson.ua.edu>

Unfortunately, I don't have Mac.

Have you read the following webpages?? If not, maybe they can help:

https://discussions.apple.com/thread/6765192

https://stackoverflow.com/questions/37826094/xt-error-cant-open-display-if-using-default-display 
<- This says a restart might be important.

On 12/28/2018 4:11 PM, pboulet wrote:
> Dear all,
>
> I am facing a problem for a while with the display on my MAC. ?I have 
> installed XQuartz and XCrysDen with homebrew. I have updated my MAC 
> with HighSierra version 10.13.6. Now xcrysden is no longer working. 
> The problem is the display, as it says:
> application-specific initialization failed: couldn't connect to 
> display "/private/tmp/com.apple.launchd.uGojk87b2L/:0"
> Error in startup script: can't read "xcrys(platform)": no such variable
>
> In the /private/? directory I have:
> org.macosforge.xquartz:0=
>
> The display is set to:
> /private/tmp/com.apple.launchd.uGojk87b2L/:0
>
> Can you please help me to solve this problem, as I could not find the 
> answer on the web?
>
> Thank you
> Best,
> Pascal
>
>
> Pascal Boulet
> ?
> /Professor in computational chemistry - DEPARTMENT OF CHEMISTRY/
> Director of the Madirel laboratory
> Aix-Marseille University - Avenue Escadrille Normandie Niemen - 
> F-13013 Marseille - FRANCE
> T?l: +33(0)4 13 55 18 10 et +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 
> 18 50
> Email?: pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>
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From pascal.boulet at univ-amu.fr  Sat Dec 29 22:57:38 2018
From: pascal.boulet at univ-amu.fr (pboulet)
Date: Sat, 29 Dec 2018 22:57:38 +0100
Subject: [xcrysden] XCrySDen Digest, Vol 118, Issue 3
In-Reply-To: <mailman.1.1546065322.27955.xcrysden@democritos.it>
References: <mailman.1.1546065322.27955.xcrysden@democritos.it>
Message-ID: <DD922416-DFD1-4306-BBDC-7A55E410BBD9@univ-amu.fr>

Thanks Gavin! I found the solution from these links. We just have to set manually the DISPLAY to ':0'.

All the best,
Pascal


Pascal Boulet
?
Professor in computational chemistry - DEPARTMENT OF CHEMISTRY
Director of the Madirel laboratory
Aix-Marseille University - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE
T?l: +33(0)4 13 55 18 10 et +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50
Email : pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>



> Le 29 d?c. 2018 ? 07:35, xcrysden-request at democritos.it a ?crit :
> 
> Send XCrySDen mailing list submissions to
> 	xcrysden at democritos.it
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.democritos.it/mailman/listinfo/xcrysden
> or, via email, send a message with subject or body 'help' to
> 	xcrysden-request at democritos.it
> 
> You can reach the person managing the list at
> 	xcrysden-owner at democritos.it
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of XCrySDen digest..."
> 
> 
> Today's Topics:
> 
>   1. Yet another problem with display on MAC (pboulet)
>   2. Re: Yet another problem with display on MAC (Gavin Abo)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sat, 29 Dec 2018 00:11:39 +0100
> From: pboulet <pascal.boulet at univ-amu.fr>
> Subject: [xcrysden] Yet another problem with display on MAC
> To: xcrysden at democritos.it
> Message-ID: <C0158BFF-EC39-4658-9F4C-CCF51D6FDD43 at univ-amu.fr>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear all,
> 
> I am facing a problem for a while with the display on my MAC.  I have installed XQuartz and XCrysDen with homebrew. I have updated my MAC with HighSierra version 10.13.6. Now xcrysden is no longer working. The problem is the display, as it says:
> application-specific initialization failed: couldn't connect to display "/private/tmp/com.apple.launchd.uGojk87b2L/:0"
> Error in startup script: can't read "xcrys(platform)": no such variable
> 
> In the /private/? directory I have:
> org.macosforge.xquartz:0=
> 
> The display is set to:
> /private/tmp/com.apple.launchd.uGojk87b2L/:0
> 
> Can you please help me to solve this problem, as I could not find the answer on the web?
> 
> Thank you
> Best,
> Pascal
> 
> 
> Pascal Boulet
> ?
> Professor in computational chemistry - DEPARTMENT OF CHEMISTRY
> Director of the Madirel laboratory
> Aix-Marseille University - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE
> T?l: +33(0)4 13 55 18 10 et +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50
> Email : pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>
> 
> 
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 28 Dec 2018 18:31:11 -0700
> From: Gavin Abo <gsabo at crimson.ua.edu>
> Subject: Re: [xcrysden] Yet another problem with display on MAC
> To: xcrysden at democritos.it
> Message-ID: <fd718f26-1577-b60d-decf-77d9513c62a4 at crimson.ua.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> Unfortunately, I don't have Mac.
> 
> Have you read the following webpages?? If not, maybe they can help:
> 
> https://discussions.apple.com/thread/6765192
> 
> https://stackoverflow.com/questions/37826094/xt-error-cant-open-display-if-using-default-display 
> <- This says a restart might be important.
> 
> On 12/28/2018 4:11 PM, pboulet wrote:
>> Dear all,
>> 
>> I am facing a problem for a while with the display on my MAC. ?I have 
>> installed XQuartz and XCrysDen with homebrew. I have updated my MAC 
>> with HighSierra version 10.13.6. Now xcrysden is no longer working. 
>> The problem is the display, as it says:
>> application-specific initialization failed: couldn't connect to 
>> display "/private/tmp/com.apple.launchd.uGojk87b2L/:0"
>> Error in startup script: can't read "xcrys(platform)": no such variable
>> 
>> In the /private/? directory I have:
>> org.macosforge.xquartz:0=
>> 
>> The display is set to:
>> /private/tmp/com.apple.launchd.uGojk87b2L/:0
>> 
>> Can you please help me to solve this problem, as I could not find the 
>> answer on the web?
>> 
>> Thank you
>> Best,
>> Pascal
>> 
>> 
>> Pascal Boulet
>> ?
>> /Professor in computational chemistry - DEPARTMENT OF CHEMISTRY/
>> Director of the Madirel laboratory
>> Aix-Marseille University - Avenue Escadrille Normandie Niemen - 
>> F-13013 Marseille - FRANCE
>> T?l: +33(0)4 13 55 18 10 et +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 
>> 18 50
>> Email?: pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>
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> 
> ------------------------------
> 
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
> 
> 
> End of XCrySDen Digest, Vol 118, Issue 3
> ****************************************

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