From R.Darkins at warwick.ac.uk Sat Apr 2 00:27:01 2011 From: R.Darkins at warwick.ac.uk (Darkins, Robert) Date: Fri, 1 Apr 2011 22:27:01 +0000 Subject: [xcrysden] Problem on OpenSUSE In-Reply-To: <1300293813.8349.14.camel@catalyst.ijs.si> References: , <1300292761.8349.10.camel@catalyst.ijs.si> , <1300293813.8349.14.camel@catalyst.ijs.si> Message-ID: I have resolved this issue: just needed to add myself to the X server access control list, using the xhost command. Wallah! ________________________________________ From: xcrysden-bounces at democritos.it [xcrysden-bounces at democritos.it] on behalf of Tone Kokalj [tone.kokalj at ijs.si] Sent: 16 March 2011 16:43 To: XCrySDen mailing list Subject: Re: [xcrysden] Problem on OpenSUSE On Wed, 2011-03-16 at 16:37 +0000, Darkins, Robert wrote: > Thanks for the response, Tone. Unfortunately, it doesn't appear to be that simple, since I AM running it locally. Now, I remember that some years ago one user had a similar problem and it used to be related to some paranoid "selinux" settings. (I'will try to contact him if he remembers what was the solution) Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From germaneau at gucas.ac.cn Sat Apr 2 16:48:26 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 02 Apr 2011 10:48:26 -0400 Subject: [xcrysden] output with transparent background Message-ID: <4D97373A.4010207@gucas.ac.cn> Dear all, Is it possible to generate a postscript with transparent background with XCrySDen? Thanks, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110402/f0276577/attachment.htm From tone.kokalj at ijs.si Wed Apr 6 16:30:19 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 06 Apr 2011 16:30:19 +0200 Subject: [xcrysden] output with transparent background In-Reply-To: <4D97373A.4010207@gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> Message-ID: <1302100219.3296.14.camel@catalyst.ijs.si> On Sat, 2011-04-02 at 10:48 -0400, Eric Germaneau wrote: > Dear all, > > Is it possible to generate a postscript with transparent background > with XCrySDen? If you save an EPS image as bitmap, then you may transform the background color to transparent by any image manipulation programs such as Gimp or ImageMagick. In this case I would first save as PNG, transform background to trasnparent, and then convert to EPS. On the other hand, if you save a vectorial EPS, it should be transparent by default. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From germaneau at gucas.ac.cn Thu Apr 7 04:45:01 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 06 Apr 2011 22:45:01 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502099903.29466@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> Message-ID: <4D9D252D.5070002@gucas.ac.cn> Thank you, I'll try this but you know gimp cannot handle with alpha channel when saving postscript file. I'll let you know. Yours, Eric. On 04/06/2011 10:30 AM, Tone Kokalj wrote: > On Sat, 2011-04-02 at 10:48 -0400, Eric Germaneau wrote: >> Dear all, >> >> Is it possible to generate a postscript with transparent background >> with XCrySDen? > > If you save an EPS image as bitmap, then you may transform the > background color to transparent by any image manipulation programs such > as Gimp or ImageMagick. In this case I would first save as PNG, > transform background to trasnparent, and then convert to EPS. > > On the other hand, if you save a vectorial EPS, it should be transparent > by default. > > Regards, Tone -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110406/b7a10fed/attachment.htm From tone.kokalj at ijs.si Wed Apr 6 16:48:31 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 06 Apr 2011 16:48:31 +0200 Subject: [xcrysden] output with transparent background In-Reply-To: <4D9D252D.5070002@gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> Message-ID: <1302101311.3296.20.camel@catalyst.ijs.si> On Wed, 2011-04-06 at 22:45 -0400, Eric Germaneau wrote: > Thank you, > > I'll try this but you know gimp cannot handle with alpha channel when > saving postscript file. Why don't you use/save-in other format then? -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From germaneau at gucas.ac.cn Thu Apr 7 05:02:25 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 06 Apr 2011 23:02:25 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502100979.29467@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> Message-ID: <4D9D2941.50109@gucas.ac.cn> because I image Latex only accept transparency from postscript and PDF. Am I right? On 04/06/2011 10:48 AM, Tone Kokalj wrote: > On Wed, 2011-04-06 at 22:45 -0400, Eric Germaneau wrote: >> Thank you, >> >> I'll try this but you know gimp cannot handle with alpha channel when >> saving postscript file. > Why don't you use/save-in other format then? > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110406/cf3e9ab3/attachment.htm From tone.kokalj at ijs.si Wed Apr 6 17:09:51 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 06 Apr 2011 17:09:51 +0200 Subject: [xcrysden] output with transparent background In-Reply-To: <4D9D2941.50109@gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> <4D9D2941.50109@gucas.ac.cn> Message-ID: <1302102591.3296.25.camel@catalyst.ijs.si> On Wed, 2011-04-06 at 23:02 -0400, Eric Germaneau wrote: > because I image Latex only accept transparency from postscript and > PDF. > Am I right? With pdflatex you may also use PNG format. This combination I usually use for manuscripts. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From germaneau at gucas.ac.cn Thu Apr 7 12:19:39 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 07 Apr 2011 06:19:39 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502102259.10479@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> <4D9D2941.50109@gucas.ac.cn> <502102259.10479@test1.gucas.ac.cn> Message-ID: <4D9D8FBB.9000607@gucas.ac.cn> Thanks, I'm going to try right now then. On 04/06/2011 11:09 AM, Tone Kokalj wrote: > On Wed, 2011-04-06 at 23:02 -0400, Eric Germaneau wrote: >> because I image Latex only accept transparency from postscript and >> PDF. >> Am I right? > With pdflatex you may also use PNG format. This combination I usually > use for manuscripts. > > Regards, Tone -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110407/fcb0207e/attachment.htm From germaneau at gucas.ac.cn Thu Apr 7 13:49:06 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 07 Apr 2011 07:49:06 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502128040.27380@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> <4D9D2941.50109@gucas.ac.cn> <502102259.10479@test1.gucas.ac.cn> <502128040.27380@test1.gucas.ac.cn> Message-ID: <4D9DA4B2.10908@gucas.ac.cn> Well, transparent PNG appear with a white background in my beamer presentation unfortunately. On 04/07/2011 06:19 AM, Eric Germaneau wrote: > Thanks, I'm going to try right now then. > > On 04/06/2011 11:09 AM, Tone Kokalj wrote: >> On Wed, 2011-04-06 at 23:02 -0400, Eric Germaneau wrote: >>> because I image Latex only accept transparency from postscript and >>> PDF. >>> Am I right? >> With pdflatex you may also use PNG format. This combination I usually >> use for manuscripts. >> >> Regards, Tone > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110407/8714c90b/attachment-0001.htm From germaneau at gucas.ac.cn Thu Apr 7 13:52:48 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 07 Apr 2011 07:52:48 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502099903.29466@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> Message-ID: <4D9DA590.3000402@gucas.ac.cn> I've just tried the vectorial EPS and it takes forever to pdflatex to generate presentation. I had to kill the process. I'll figure, Thanks, Eric. On 04/06/2011 10:30 AM, Tone Kokalj wrote: > On Sat, 2011-04-02 at 10:48 -0400, Eric Germaneau wrote: >> Dear all, >> >> Is it possible to generate a postscript with transparent background >> with XCrySDen? > > If you save an EPS image as bitmap, then you may transform the > background color to transparent by any image manipulation programs such > as Gimp or ImageMagick. In this case I would first save as PNG, > transform background to trasnparent, and then convert to EPS. > > On the other hand, if you save a vectorial EPS, it should be transparent > by default. > > Regards, Tone -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110407/3c46c5d9/attachment.htm From germaneau at gucas.ac.cn Thu Apr 7 15:27:35 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 07 Apr 2011 09:27:35 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502102259.10479@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> <4D9D2941.50109@gucas.ac.cn> <502102259.10479@test1.gucas.ac.cn> Message-ID: <4D9DBBC7.9040206@gucas.ac.cn> Hey Tone, I think I got it. It seems that latex can handle transparency with vector image only. I found the solution to my issue in the last release of inskcape (0.48). It can read/write postscrip files (even eps, pdf, ....) with transparent background compatible with pdflatex. It's juts awesome. Thanks for your help. Best, Eric. On 04/06/2011 11:09 AM, Tone Kokalj wrote: > On Wed, 2011-04-06 at 23:02 -0400, Eric Germaneau wrote: >> because I image Latex only accept transparency from postscript and >> PDF. >> Am I right? > With pdflatex you may also use PNG format. This combination I usually > use for manuscripts. > > Regards, Tone -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110407/f9f4dea5/attachment.htm From sebastijan.peljhan at ijs.si Thu Apr 7 09:30:33 2011 From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan) Date: Thu, 07 Apr 2011 09:30:33 +0200 Subject: [xcrysden] output with transparent background In-Reply-To: <4D9DA4B2.10908@gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> <4D9D2941.50109@gucas.ac.cn> <502102259.10479@test1.gucas.ac.cn> <502128040.27380@test1.gucas.ac.cn> <4D9DA4B2.10908@gucas.ac.cn> Message-ID: <1302161433.5152.9.camel@surf> On Thu, 2011-04-07 at 07:49 -0400, Eric Germaneau wrote: > Well, transparent PNG appear with a white background in my beamer > presentation unfortunately. It works just fine in my case (see the examples in the attachment). The PNG picture of the molecule is generated with Xcrysden, then the background is removed with Gimp and finally posted into a beamer slide (I used just a simple tex \rule posted below the picture to show the transparency of the image). Regards, Sebastijan -------------- next part -------------- A non-text attachment was scrubbed... Name: btah1.png Type: image/png Size: 8868 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20110407/6edff873/attachment-0001.png -------------- next part -------------- A non-text attachment was scrubbed... Name: transp_beamer.tex Type: text/x-tex Size: 396 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20110407/6edff873/attachment-0001.tex -------------- next part -------------- A non-text attachment was scrubbed... Name: transp_beamer.pdf Type: application/pdf Size: 16391 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20110407/6edff873/attachment-0001.pdf From reza.sarhaddi at yahoo.com Thu Apr 7 14:14:27 2011 From: reza.sarhaddi at yahoo.com (reza sarhaddi) Date: Thu, 7 Apr 2011 05:14:27 -0700 (PDT) Subject: [xcrysden] Installation fail Message-ID: <843978.39772.qm@web120611.mail.ne1.yahoo.com> Dear all, I am using XCrySDen for the first time in CentOS 5 OS. I have configures everything using ./xcConfigure and registered the XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH and everything went alright. I want now to start using XCrysden. When I try to execute (or just type the command xcrysden), I get: ./xcrysden: line 129: /Xcrysden/XCrysDen-1.4bin-static/scripts/xclib.sh: No such file or directory Can anyone tell me what have I missed. Thank you. Regards, Reza -- ********************************************************************************************************************************************* ****** "If A is success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut." - Albert Einstein ********************************************************************************************************************************************* ****** Reza Sarhaddi Department of Physics, University of Birjand, Birjand, Iran. Tell: +98561250230-2?? ext:595 Fax: +985612502041 ? P.O.BOX: 97175/615???? ? Reza.Sarhaddi at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110407/bffb9f1c/attachment.htm From sebastijan.peljhan at ijs.si Thu Apr 7 16:42:06 2011 From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan) Date: Thu, 07 Apr 2011 16:42:06 +0200 Subject: [xcrysden] Installation fail In-Reply-To: <843978.39772.qm@web120611.mail.ne1.yahoo.com> References: <843978.39772.qm@web120611.mail.ne1.yahoo.com> Message-ID: <1302187326.5152.26.camel@surf> > I am using XCrySDen for the first time in CentOS 5 OS. I have > configures everything using ./xcConfigure and registered the > XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH and everything went alright. > I want now to start using XCrysden. When I try to execute (or just > type the command xcrysden), I get: > ./xcrysden: line > 129: /Xcrysden/XCrysDen-1.4bin-static/scripts/xclib.sh: No such file > or directory That means that XCrysDen is not installed in you at your_machine:/Xcrysden/... directory and you probably miss-configured your XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH (probably "/home/you" is missing before "/Xcrsden"). So you have to reconfigure the XCRYSDEN_TOPDIR or, even better, download the newest version of XCrysDen which doesn't need any configuration and works just out of the box. You can download it from: http://www.xcrysden.org/download/xc-1.5.23-linux_x86_64-semishared.tar.gz Don't forget to unset XCRYSDEN_TOPDIR that you configured previously before you run the newest xcrysden. Regards, Sebastijan -- Sebastijan Peljhan Department of Physical and Organic Chemistry "Jozef Stefan" Institute Jamova 39 1000 Ljubljana Slovenia tel.:+386 1 4773 523 fax.:+386 1 4773 822 email: sebastijan.peljhan at IJS.SI From germaneau at gucas.ac.cn Sat Apr 9 20:23:31 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 09 Apr 2011 14:23:31 -0400 Subject: [xcrysden] output with transparent background In-Reply-To: <502161089.07698@test1.gucas.ac.cn> References: <4D97373A.4010207@gucas.ac.cn> <502099903.29466@test1.gucas.ac.cn> <4D9D252D.5070002@gucas.ac.cn> <502100979.29467@test1.gucas.ac.cn> <4D9D2941.50109@gucas.ac.cn> <502102259.10479@test1.gucas.ac.cn> <502128040.27380@test1.gucas.ac.cn> <4D9DA4B2.10908@gucas.ac.cn> <502161089.07698@test1.gucas.ac.cn> Message-ID: <4DA0A423.30708@gucas.ac.cn> It works good, thank you. Best, Eric. On 04/07/2011 03:30 AM, Sebastijan Peljhan wrote: > On Thu, 2011-04-07 at 07:49 -0400, Eric Germaneau wrote: >> Well, transparent PNG appear with a white background in my beamer >> presentation unfortunately. > It works just fine in my case (see the examples in the attachment). The > PNG picture of the molecule is generated with Xcrysden, then the > background is removed with Gimp and finally posted into a beamer slide > (I used just a simple tex \rule posted below the picture to show the > transparency of the image). > > Regards, > Sebastijan > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110409/d861baa6/attachment.htm