<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">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.</div><div class="">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.</div><div class="">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.</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px;">Mark J van Raaij<br class="">Dpto de Estructura de Macromoleculas<br class="">Centro Nacional de Biotecnologia - CSIC<br class="">calle Darwin 3<br class="">E-28049 Madrid, Spain<br class="">tel. (+34) 91 585 4616<br class=""><a href="http://wwwuser.cnb.csic.es/~mjvanraaij" class="">http://wwwuser.cnb.csic.es/~mjvanraaij</a><br class="">Section Editor of Acta Crystallographica F, Structural Biology Communications<br class="">http://journals.iucr.org/f/<br class=""><br class=""></div></div></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On 3 Apr 2019, at 12:47, Mohsen Asadbegi <<a href="mailto:mohsenasad.7091@gmail.com" class="">mohsenasad.7091@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px 0px 15px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3">Hello every one!</div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px 0px 15px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3"></div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3">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.</div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3"> 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.</div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3"><br class=""></div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3"><br class=""></div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3">Regards,</div><div class="gmail-nova-e-text--family-sans-serif gmail-nova-e-text--color-inherit gmail-redraft-text gmail-nova-e-text--size-m gmail-nova-e-text gmail-nova-e-text--spacing-s" style="border:0px;margin:0px;padding:0px;color:rgb(17,17,17);font-family:Roboto,Arial,sans-serif;font-size:14px;line-height:1.3">Mohsen Asadbegi</div></div>
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