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Comments for Molecular Art http://molecularart.dk An amateurish molecular visualization blog Sun, 15 Apr 2018 17:34:57 +0000 hourly 1 Comment on Cryo-EM: How to generate an initial reference map from pdb by TheEMgeek http://molecularart.dk/2015/10/cryo-em-how-to-generate-an-initial-reference-map-from-pdb/#comment-94162 Sun, 15 Apr 2018 17:34:57 +0000 http://molecularart.dk/?p=394#comment-94162 Hi,
Why do u want a spherical object for your reference ?

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Comment on Cryo-EM: How to change box size and pixel size by ruki http://molecularart.dk/2015/11/cryo-em-how-to-change-box-size-and-pixel-size/#comment-94152 Fri, 23 Mar 2018 21:41:53 +0000 http://molecularart.dk/?p=411#comment-94152 Yes indeed, as already stated in comments and the post.

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Comment on Cryo-EM: How to change box size and pixel size by anonymous http://molecularart.dk/2015/11/cryo-em-how-to-change-box-size-and-pixel-size/#comment-94151 Fri, 23 Mar 2018 19:47:37 +0000 http://molecularart.dk/?p=411#comment-94151 should be –rescale_angpix, not –new_angpix

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Comment on About by ruki http://molecularart.dk/about/#comment-93952 Wed, 17 Jan 2018 06:47:35 +0000 http://molecularart.dk/?page_id=85#comment-93952 Sure send me a mail at rtk at mbg . Au . Dk

/Ruki

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Comment on About by Troy Gilliam http://molecularart.dk/about/#comment-93951 Tue, 16 Jan 2018 21:02:25 +0000 http://molecularart.dk/?page_id=85#comment-93951 We are looking to make an in-depth complement system poster and would be interested in using some of the images you have generated. Would it be possible to contact you to discuss? Thank you.

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Comment on Cryo-EM: How to change box size and pixel size by Gaya P Yadav http://molecularart.dk/2015/11/cryo-em-how-to-change-box-size-and-pixel-size/#comment-93935 Fri, 12 Jan 2018 14:49:37 +0000 http://molecularart.dk/?p=411#comment-93935 Hello,
I have question about changing box size and pixel size. I generated a map from the pdb file in chimrea and it looks good. Itried to change the pixel size using relion_image_handler but volume just become a ball like structure. here are th ecommands i used:
relion_image_handler –i old.mrc –rescale_angpix 1.009 –o newp.mrc
and
relion_image_handler –i newp.mrc –new_box 196 –o newp_newB.mrc

Any help was appreciated?

thanks

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Comment on Cryo-EM: How to change box size and pixel size by Gaya http://molecularart.dk/2015/11/cryo-em-how-to-change-box-size-and-pixel-size/#comment-93740 Tue, 24 Oct 2017 16:49:15 +0000 http://molecularart.dk/?p=411#comment-93740 Hello,
When we change pixel size from 2 to 1, volume of the map reduces by half. How to compensate that?

thanks

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Comment on Cryo-EM: How to generate an initial reference map from pdb by ruki http://molecularart.dk/2015/10/cryo-em-how-to-generate-an-initial-reference-map-from-pdb/#comment-93732 Thu, 19 Oct 2017 03:54:09 +0000 http://molecularart.dk/?p=394#comment-93732 Hi Shaik,

I do not have any experience with that myself, but I seem to remember that you can use spider for that.

https://spider.wadsworth.org/spider_doc/spider/docs/man/mo3.html
You can also use IMAGIC for that I believe but we do not have access to that at my department.
Sorry I can not help you any further right now, but you can always write the CCPEM mailing list or the 3DEM list for help.

/ Ruki

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Comment on Cryo-EM: How to generate an initial reference map from pdb by shaik http://molecularart.dk/2015/10/cryo-em-how-to-generate-an-initial-reference-map-from-pdb/#comment-93731 Thu, 19 Oct 2017 02:17:50 +0000 http://molecularart.dk/?p=394#comment-93731 Hi,
This page is very helpful. I am not sure is anyone still responding or not. My question is I want make to shapes, like cylinder or sphere with specific box size, pixel value and radius for using 3D classification in Relion.

I read in some mailing list to discuss about it but couldn’t find it anymore. please help.

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Comment on About by Mark Alto http://molecularart.dk/about/#comment-93531 Sun, 28 May 2017 11:47:26 +0000 http://molecularart.dk/?page_id=85#comment-93531 Hello!

We looking for big size 3d printer for printing frames.

Our looking for size is 1250 x 2500 x 40
printing details height – 40mm

Frame profile section is maximum 30x40mm height – 40mm

Can you make kit for it ?
What is price idea for it?

Best regards
Mark Alto
Annerman Oy
Finland

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